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<article xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:oasis="http://docs.oasis-open.org/ns/oasis-exchange/table" xml:lang="en" dtd-version="3.0"><?xmltex \makeatother\@nolinetrue\makeatletter?>
  <front>
    <journal-meta><journal-id journal-id-type="publisher">AMT</journal-id><journal-title-group>
    <journal-title>Atmospheric Measurement Techniques</journal-title>
    <abbrev-journal-title abbrev-type="publisher">AMT</abbrev-journal-title><abbrev-journal-title abbrev-type="nlm-ta">Atmos. Meas. Tech.</abbrev-journal-title>
  </journal-title-group><issn pub-type="epub">1867-8548</issn><publisher>
    <publisher-name>Copernicus Publications</publisher-name>
    <publisher-loc>Göttingen, Germany</publisher-loc>
  </publisher></journal-meta>
    <article-meta>
      <article-id pub-id-type="doi">10.5194/amt-12-3963-2019</article-id><title-group><article-title>Comparison between the assimilation of IASI Level 2 ozone retrievals and Level 1 radiances in a chemical transport model</article-title><alt-title>A comparison between IASI L2 and L1 assimilation</alt-title>
      </title-group><?xmltex \runningtitle{A comparison between IASI L2 and L1 assimilation}?><?xmltex \runningauthor{E. Emili et al.}?>
      <contrib-group>
        <contrib contrib-type="author" corresp="yes" rid="aff1">
          <name><surname>Emili</surname><given-names>Emanuele</given-names></name>
          <email>emili@cerfacs.fr</email>
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2">
          <name><surname>Barret</surname><given-names>Brice</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2">
          <name><surname>Le Flochmoën</surname><given-names>Eric</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Cariolle</surname><given-names>Daniel</given-names></name>
          
        </contrib>
        <aff id="aff1"><label>1</label><institution>CECI, Université de Toulouse, Cerfacs, CNRS, Toulouse, France</institution>
        </aff>
        <aff id="aff2"><label>2</label><institution>Laboratoire d’Aérologie, Université de Toulouse, CNRS, UPS, Toulouse, France</institution>
        </aff>
      </contrib-group>
      <author-notes><corresp id="corr1">Emanuele Emili (emili@cerfacs.fr)</corresp></author-notes><pub-date><day>19</day><month>July</month><year>2019</year></pub-date>
      
      <volume>12</volume>
      <issue>7</issue>
      <fpage>3963</fpage><lpage>3984</lpage>
      <history>
        <date date-type="received"><day>5</day><month>December</month><year>2018</year></date>
           <date date-type="rev-request"><day>10</day><month>January</month><year>2019</year></date>
           <date date-type="rev-recd"><day>18</day><month>May</month><year>2019</year></date>
           <date date-type="accepted"><day>29</day><month>June</month><year>2019</year></date>
      </history>
      <permissions>
        <copyright-statement>Copyright: © 2019 Emanuele Emili et al.</copyright-statement>
        <copyright-year>2019</copyright-year>
      <license license-type="open-access"><license-p>This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this licence, visit <ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/licenses/by/4.0/">https://creativecommons.org/licenses/by/4.0/</ext-link></license-p></license></permissions><self-uri xlink:href="https://amt.copernicus.org/articles/12/3963/2019/amt-12-3963-2019.html">This article is available from https://amt.copernicus.org/articles/12/3963/2019/amt-12-3963-2019.html</self-uri><self-uri xlink:href="https://amt.copernicus.org/articles/12/3963/2019/amt-12-3963-2019.pdf">The full text article is available as a PDF file from https://amt.copernicus.org/articles/12/3963/2019/amt-12-3963-2019.pdf</self-uri>
      <abstract><title>Abstract</title>
    <p id="d1e113">The prior information used for Level 2 (L2) retrievals in the thermal infrared can influence the quality of the retrievals themselves and, therefore, their further assimilation in atmospheric composition models. In this study we evaluate the differences between assimilating L2 ozone profiles and Level 1 (L1) radiances from the Infrared Atmospheric Sounding Interferometer (IASI). We minimized potential differences between the two approaches by employing the same radiative transfer code (Radiative Transfer for TOVS, RTTOV) and a very similar setup for both the L2 retrievals (1D-Var) and the L1 assimilation (3D-Var). We computed hourly 3D-Var analyses assimilating L1 and L2 data in the chemical transport model MOCAGE and compared the resulting <inline-formula><mml:math id="M1" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> fields among each other and against ozonesondes. We also evaluated the joint assimilation of limb measurements from the Microwave Limb Sounder (MLS) in combination with IASI to assess the impact of stratospheric <inline-formula><mml:math id="M2" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> on tropospheric analyses. Results indicate that significant differences can arise between L2 and L1 assimilation, especially in regions where the L2 prior information is strongly biased (at low latitudes in this study). In these regions the L1 assimilation provides a better variability of the free-troposphere ozone column. L1 and L2 assimilation instead give very similar results at high latitudes, especially when MLS measurements are used to constrain the stratospheric <inline-formula><mml:math id="M3" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> column. A critical analysis of the potential benefits and drawbacks of L1 assimilation is given in the conclusions. We also list remaining issues that are common to both the L1 and L2 approaches and that deserve further research.</p>
  </abstract>
    </article-meta>
  </front>
<body>
      

<sec id="Ch1.S1" sec-type="intro">
  <label>1</label><title>Introduction</title>
      <p id="d1e158">The global monitoring of atmospheric composition relies on a large number of dedicated satellite missions and on the sustained improvement of numerical forecast models. Today, research and operational centres provide both satellite-based reanalyses and forecasts of atmospheric composition for a large number of applications, spanning from stratospheric ozone monitoring <xref ref-type="bibr" rid="bib1.bibx54" id="paren.1"/> to climate change <xref ref-type="bibr" rid="bib1.bibx19" id="paren.2"/> and air quality <xref ref-type="bibr" rid="bib1.bibx60 bib1.bibx34" id="paren.3"/>.</p>
      <p id="d1e170">Satellite sensors measure the spectral signature of gases and aerosols on the radiation field that traverse the atmosphere. Retrieving the concentration of a given gas from the radiation measured at the satellite position represents an inverse problem that is in most cases ill-posed and underdetermined; i.e. finding the solution requires some type of mathematical regularization or prior information <xref ref-type="bibr" rid="bib1.bibx49" id="paren.4"/>. The accuracy of the solution depends in general on the intensity of the spectral signature of the retrieved compound, the source of radiation (e.g. the Earth or the Sun), the observation geometry and the accuracy of the radiative transfer model (RTM). The last-mentioned factor also means correctly accounting for all the atmospheric constituents or surface properties that affect the radiation field but are not retrieved themselves (auxiliary RTM inputs).</p>
      <p id="d1e176">When the retrieval is done within a Bayesian framework, like the optimal estimation method <xref ref-type="bibr" rid="bib1.bibx49" id="paren.5"/>, the measurement errors, the RTM errors and the uncertainty in the prior information (also named background or a priori profile) are prescribed. The procedure then provides an estimation of the error covariance for the retrieved quantity and the averaging kernels (AKs), which quantify the sensitivity of<?pagebreak page3964?> the retrieval to the true state and are linked to the degrees of freedom (DOF) of the solution. The retrieval errors and the AKs (or the DOF) can be used first to diagnose the quality and the relevance of the atmospheric retrieval. They become even more important when retrievals are further assimilated in numerical forecast models because they weight the impact of the observations in the system.</p>
      <p id="d1e182">Chemical transport models (CTMs) solve the chemical and physical processes within the atmosphere but are based on meteorological fields from a numerical weather prediction (NWP) model to advect the chemical species. Coupled chemistry–meteorology models (CCMMs) that simulate both meteorology and chemistry online became available later but are quite common today in operational centres <xref ref-type="bibr" rid="bib1.bibx59 bib1.bibx18" id="paren.6"/>. There are currently growing efforts to introduce even stronger coupling of the atmosphere with both ocean and surface models, which has given rise to so-called Earth system models (ESMs; <xref ref-type="bibr" rid="bib1.bibx7 bib1.bibx27" id="altparen.7"/>). ESMs provide a comprehensive tool for climate predictions and reanalyses, but they are also considered for state-of-the-art air-quality modelling <xref ref-type="bibr" rid="bib1.bibx44" id="paren.8"/>.</p>
      <p id="d1e195">Closely following the historical advances in modelling, the assimilation of satellite data was first introduced in CTMs <xref ref-type="bibr" rid="bib1.bibx23 bib1.bibx31" id="paren.9"/>, and it is now also well integrated in operational CCMMs <xref ref-type="bibr" rid="bib1.bibx19" id="paren.10"/>.</p>
      <p id="d1e204">Today, numerous satellite retrievals of trace gases (e.g. <inline-formula><mml:math id="M4" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, CO, <inline-formula><mml:math id="M5" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">NO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math id="M6" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">CH</mml:mi><mml:mn mathvariant="normal">4</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, <inline-formula><mml:math id="M7" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">CO</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>) and aerosols (aerosol optical depth, AOD) are assimilated daily within operational CTMs and CCMMs <xref ref-type="bibr" rid="bib1.bibx28 bib1.bibx4" id="paren.11"/>.</p>
      <p id="d1e254">For a long time, meteorological variables such as temperature and water vapour profiles have been corrected by means of assimilating satellite radiances (Level 1 data) directly in NWP models. Therefore, the RTM became part of the observation operator of the assimilation system <xref ref-type="bibr" rid="bib1.bibx1" id="paren.12"/>. This avoided the introduction of biases in NWP that arose from poor prior information used in satellite retrievals at that time and neglect of the AKs <xref ref-type="bibr" rid="bib1.bibx17" id="paren.13"/>. On the other hand, chemical species and aerosols are mostly corrected by means of assimilating geophysical retrievals (Level 2 or L2 data) that are made available by satellite data providers. To remove the impact of the prior information when assimilating L2 retrievals, the AK of the retrieval must be multiplied by the modelled profiles before computing the innovation vectors <xref ref-type="bibr" rid="bib1.bibx49 bib1.bibx16 bib1.bibx39" id="paren.14"/>. However, within standard methods based on the linearization of the RTM, like optimal estimation, issues might still arise when the prior information used in the retrieval is far from the true atmospheric state: this might challenge the linearization of the observation operator and result in sub-optimal retrievals. Since the AKs themselves are also a result of the retrieval (and depend upon its prior information), we expect that a perfect removal of the prior information within data assimilation (DA) cannot always be ensured.</p>
      <p id="d1e266">The precise conditions that provide an equivalence between assimilating retrievals (using some kind of weighting function) and radiances have been formalized by <xref ref-type="bibr" rid="bib1.bibx39" id="text.15"/> and further tested by <xref ref-type="bibr" rid="bib1.bibx47" id="text.16"/> on synthetic satellite observations. These authors conclude that the equivalence holds under the hypothesis of an almost linear radiative transfer (RT) regime and with careful selection of the prior error covariances in order to maximize the measurement information in the retrieval step. Nonetheless, testing the two approaches within an operational system and with real observations remains crucial to verify whether these conditions are met in practice. Moreover, the perfect equivalence only holds when all the auxiliary inputs of the RTM are exactly the same in both the retrieval and the radiance assimilation. It is clear that a climatological option for some RTM inputs will always be a more practical choice when computing L2 retrievals. On the other hand, the evolution towards strongly integrated ESMs will allow in principle to dispose of the most accurate prior information for all RTM inputs and favours the radiance assimilation approach. In this context, it appears important to introduce and evaluate the assimilation of radiances for chemical applications as well.</p>
      <p id="d1e275">To the best of the authors' knowledge, the existent literature on this topic only concerns meteorological applications. <xref ref-type="bibr" rid="bib1.bibx24" id="text.17"/> explored the possibility of assimilating <inline-formula><mml:math id="M8" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> sensitive radiances within a NWP model but without comparing the two approaches. Similarly, <xref ref-type="bibr" rid="bib1.bibx57" id="text.18"/> examined the assimilation of satellite radiances for aerosols, but the focus was on the impact of using modelled aerosol microphysical properties as auxiliary input for the RTM, and no comparison was provided. No other studies could be found concerning the assimilation of chemical compounds.</p>
      <p id="d1e295">The objective of this study is to perform a first strict comparison between the assimilation of radiances and retrievals, with respect to <inline-formula><mml:math id="M9" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> estimation in the thermal infrared (TIR). To this end, systematic differences between the assimilation of retrieval and radiances have been minimized as much as possible, for example by means of employing the same RTM within the two approaches.</p>
      <?pagebreak page3965?><p id="d1e310">We consider the case of <inline-formula><mml:math id="M10" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> assimilation using the Infrared Atmospheric Sounding Interferometer (IASI) on board the European MetOp satellites <xref ref-type="bibr" rid="bib1.bibx8" id="paren.19"/>. Several IASI <inline-formula><mml:math id="M11" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> retrievals have already been well validated <xref ref-type="bibr" rid="bib1.bibx14" id="paren.20"/> and used directly to provide multi-annual time series of the global <inline-formula><mml:math id="M12" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> budget <xref ref-type="bibr" rid="bib1.bibx58" id="paren.21"/> or successfully assimilated within global <xref ref-type="bibr" rid="bib1.bibx46" id="paren.22"/> and regional CTMs <xref ref-type="bibr" rid="bib1.bibx9" id="paren.23"/>. However, an empirical correction of the retrievals has been found to be necessary to ensure globally unbiased reanalyses, and slightly degraded assimilation results are still found at mid-latitudes and high latitudes <xref ref-type="bibr" rid="bib1.bibx15" id="paren.24"/>. Since the tropospheric <inline-formula><mml:math id="M13" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> signature in the selected IASI spectral window decreases over colder surfaces, the impact of the retrieval's prior information might become more relevant at high latitudes. In addition, the majority of IASI <inline-formula><mml:math id="M14" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> retrievals use a single a priori profile globally <xref ref-type="bibr" rid="bib1.bibx3 bib1.bibx6" id="paren.25"/>, which might present very large local departures from the true <inline-formula><mml:math id="M15" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> profile. Hence, IASI <inline-formula><mml:math id="M16" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> assimilation represents a good benchmark to evaluate the differences between the assimilation of retrievals and radiances.</p>
      <p id="d1e413">The IASI SOFRID (Software for a Fast Retrieval of IASI Data) <inline-formula><mml:math id="M17" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> product <xref ref-type="bibr" rid="bib1.bibx3" id="paren.26"/> and MOCAGE CTM have been used here to benefit from the experience of previous studies <xref ref-type="bibr" rid="bib1.bibx15 bib1.bibx46" id="paren.27"/>. SOFRID and MOCAGE DA are based on a variational algorithm, and, since SOFRID employs RTTOV <xref ref-type="bibr" rid="bib1.bibx50" id="paren.28"/>, which is a community RTM developed originally for NWP applications, the same RTM has been implemented in the MOCAGE system. Global <inline-formula><mml:math id="M18" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> analyses are computed for July 2010, and the results are compared against all available radiosoundings to evaluate their accuracy. Since the sensitivity of IASI TIR measurements to <inline-formula><mml:math id="M19" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> is not uniform along the atmospheric column, we also investigate the impact of assimilating more accurate stratospheric profiles from the Microwave Limb Sounder (MLS) in combination with IASI radiances. This might reveal possible synergies when assimilating multiple instruments that sense different layers of the atmosphere.</p>
      <p id="d1e459">The paper is organized as follows. The satellite measurements, the Level 2 retrievals and the validation measurements used for this study are described in Sect. <xref ref-type="sec" rid="Ch1.S2"/>, as well as main steps concerning the preprocessing for some of the datasets. The chemical transport model, the radiative transfer model, the assimilation algorithm and the setup of the experiments are described in Sect. <xref ref-type="sec" rid="Ch1.S3"/>. The assimilation of IASI retrievals and radiances is compared in Sect. <xref ref-type="sec" rid="Ch1.S4.SS1"/>, and the impact of MLS assimilation in combination with IASI is discussed in Sect. <xref ref-type="sec" rid="Ch1.S4.SS3"/>. The conclusions are summarized in the last section, where some recommendations are also given.</p>
</sec>
<sec id="Ch1.S2">
  <label>2</label><title>Measurements</title>
<sec id="Ch1.S2.SS1">
  <label>2.1</label><title>IASI</title>
      <p id="d1e485">IASI flies on board the series of polar-orbiting satellites MetOp operated by the EUropean organization for the exploitation of METeorological SATellites (EUMETSAT). It provides hyper-spectral measurements of the Earth's thermal radiation in the 3.62–15.5 <inline-formula><mml:math id="M20" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">µ</mml:mi></mml:mrow></mml:math></inline-formula>m (2760–645 cm<inline-formula><mml:math id="M21" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>) window and serves meteorological and atmospheric chemistry applications <xref ref-type="bibr" rid="bib1.bibx8 bib1.bibx25" id="paren.29"/>. IASI is an operational mission meant to provide long-term (<inline-formula><mml:math id="M22" display="inline"><mml:mrow><mml:mo>&gt;</mml:mo><mml:mn mathvariant="normal">20</mml:mn></mml:mrow></mml:math></inline-formula> years) time series of accurate TIR spectra at high spatial resolution. A total of three IASI instruments will be flying simultaneously at the end of 2019, providing nearly global coverage six times per day (morning and evening overpasses). Hence, they represent a great opportunity for both NWP and climate–chemistry reanalyses. Only MetOp-A data, available from 2008 to present, have been employed for this study.</p>
<sec id="Ch1.S2.SS1.SSS1">
  <label>2.1.1</label><title>L1 radiances</title>
      <p id="d1e528">IASI L1c data contain calibrated and geolocalized spectra at 0.5 cm<inline-formula><mml:math id="M23" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> spectral resolution (after apodization), i.e. 8461 radiance values for each ground pixel, with a footprint of 12 km for nadir observations. For this study, historical L1c data granules have been downloaded from the EUMETSAT Earth Observation data portal (<uri>https://eoportal.eumetsat.int</uri>, last access: 16 July 2019) in NETCDF format. Data files also contain the observation geometry (Sun and satellite angles) for each ground pixel and the co-located land mask and cloud fraction values, obtained from the Advanced Very High Resolution Radiometer (AVHRR) measurements, also on board MetOp.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T1"><?xmltex \currentcnt{1}?><label>Table 1</label><caption><p id="d1e549">Number of validation profiles for July 2010.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="3">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="right"/>
     <oasis:colspec colnum="3" colname="col3" align="right"/>
     <oasis:thead>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">Latitudes</oasis:entry>
         <oasis:entry colname="col2">MLS</oasis:entry>
         <oasis:entry colname="col3">Radiosoundings</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>
         <oasis:entry colname="col1">Global</oasis:entry>
         <oasis:entry colname="col2">100 975</oasis:entry>
         <oasis:entry colname="col3">219</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">90–60<inline-formula><mml:math id="M24" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> S</oasis:entry>
         <oasis:entry colname="col2">16 967</oasis:entry>
         <oasis:entry colname="col3">19</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">60–30<inline-formula><mml:math id="M25" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> S</oasis:entry>
         <oasis:entry colname="col2">17 334</oasis:entry>
         <oasis:entry colname="col3">9</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">30–30<inline-formula><mml:math id="M26" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N</oasis:entry>
         <oasis:entry colname="col2">33 046</oasis:entry>
         <oasis:entry colname="col3">38</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">30–60<inline-formula><mml:math id="M27" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N</oasis:entry>
         <oasis:entry colname="col2">16 669</oasis:entry>
         <oasis:entry colname="col3">138</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">60–90<inline-formula><mml:math id="M28" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N</oasis:entry>
         <oasis:entry colname="col2">16 959</oasis:entry>
         <oasis:entry colname="col3">15</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

</sec>
<sec id="Ch1.S2.SS1.SSS2">
  <label>2.1.2</label><title>SOFRID L2 retrievals</title>
      <p id="d1e707">The Software for a Fast Retrieval of IASI Data (SOFRID) was developed at the Laboratoire d'Aérologie to retrieve <inline-formula><mml:math id="M29" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> <xref ref-type="bibr" rid="bib1.bibx3" id="paren.30"/> and CO <xref ref-type="bibr" rid="bib1.bibx13" id="paren.31"/> profiles from IASI. It is based on the Radiative Transfer for TOVS (RTTOV) RTM <xref ref-type="bibr" rid="bib1.bibx50" id="paren.32"/> and the 1D-VAR scheme developed within the Numerical Weather Prediction Satellite Application Facilities (NWP SAF) programme. SOFRID retrieves the <inline-formula><mml:math id="M30" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> profile in volume mixing ratio (vmr) units at 43 pressure levels between the surface and 0.1 hPa using 469 spectral channels within the main IASI <inline-formula><mml:math id="M31" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> window (980–1100 cm<inline-formula><mml:math id="M32" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>). The choices that are made in SOFRID and are relevant for this study are summarized in Table <xref ref-type="table" rid="Ch1.T2"/>. Note that a single a priori profile and error covariance matrix are used globally and that the surface skin temperature (SST) is estimated within the retrieval.</p>
      <p id="d1e767">The number of DOF of the SOFRID retrieval has been evaluated to be between 2 and 3 for the full atmospheric column, with about 1 DOF for the tropospheric column <xref ref-type="bibr" rid="bib1.bibx14" id="paren.33"/>. SOFRID's averaging kernels corresponding to the retrievals used within this study (see Sect. <xref ref-type="sec" rid="Ch1.S2.SS4"/>) are shown in Fig. <xref ref-type="fig" rid="Ch1.F1"/>. We remark that the largest sensitivities are found for the lower stratosphere (50–100 hPa) and upper troposphere (200–300 hPa) levels. The sensitivity in the free troposphere (400–600 hPa) is maximum at tropical latitudes<?pagebreak page3966?> and decreases towards the poles due to the decreasing thermal contrast. Very low sensitivities are in general found for levels below 700 hPa at all latitudes.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T2" specific-use="star"><?xmltex \currentcnt{2}?><label>Table 2</label><caption><p id="d1e780">Summary of the configuration of SOFRID L2 retrievals and MOCAGE L1 assimilation.</p></caption><oasis:table frame="topbot"><?xmltex \begin{scaleboxenv}{.90}[.90]?><oasis:tgroup cols="3">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:thead>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1"/>
         <oasis:entry colname="col2">L2 retrieval</oasis:entry>
         <oasis:entry colname="col3">L1 assimilation</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>
         <oasis:entry colname="col1">Radiative transfer model</oasis:entry>
         <oasis:entry colname="col2">RTTOV v11.1</oasis:entry>
         <oasis:entry colname="col3">RTTOV v11.3</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">Algorithm</oasis:entry>
         <oasis:entry colname="col2">1D-Var</oasis:entry>
         <oasis:entry colname="col3">3D-Var</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">Spectral window</oasis:entry>
         <oasis:entry colname="col2">980–1100 cm<inline-formula><mml:math id="M33" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>
         <oasis:entry colname="col3">980–1100 cm<inline-formula><mml:math id="M34" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula></oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">Measurement error</oasis:entry>
         <oasis:entry colname="col2">0.7 (mW m<inline-formula><mml:math id="M35" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> sr<inline-formula><mml:math id="M36" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> cm)</oasis:entry>
         <oasis:entry colname="col3">0.7 (mW m<inline-formula><mml:math id="M37" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> sr<inline-formula><mml:math id="M38" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> cm)</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">Control vector</oasis:entry>
         <oasis:entry colname="col2"><inline-formula><mml:math id="M39" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (1-D) <inline-formula><mml:math id="M40" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> surface skin temperature (SST)</oasis:entry>
         <oasis:entry colname="col3"><inline-formula><mml:math id="M41" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> (3-D) <inline-formula><mml:math id="M42" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> surface skin temperature (SST)</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">Vertical grid</oasis:entry>
         <oasis:entry colname="col2">43 pressure levels (1013–0.1 hPa)</oasis:entry>
         <oasis:entry colname="col3">60 hybrid sigma-pressure levels (surface–0.1 hPa)</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1"><inline-formula><mml:math id="M43" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> prior information</oasis:entry>
         <oasis:entry colname="col2">MLS <inline-formula><mml:math id="M44" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> ozonesonde global climatology</oasis:entry>
         <oasis:entry colname="col3">3-D-hourly model forecasts</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1"><inline-formula><mml:math id="M45" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> error covariance</oasis:entry>
         <oasis:entry colname="col2">MLS <inline-formula><mml:math id="M46" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> ozonesonde climatological covariance</oasis:entry>
         <oasis:entry colname="col3">3-D-hourly (standard deviation), parameterized</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1"/>
         <oasis:entry colname="col2"/>
         <oasis:entry colname="col3">(correlations)</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">SST prior information (<inline-formula><mml:math id="M47" display="inline"><mml:mrow><mml:mo>+</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:math></inline-formula> m <inline-formula><mml:math id="M48" display="inline"><mml:mi>U</mml:mi></mml:math></inline-formula>, <inline-formula><mml:math id="M49" display="inline"><mml:mi>V</mml:mi></mml:math></inline-formula>, <inline-formula><mml:math id="M50" display="inline"><mml:mi>P</mml:mi></mml:math></inline-formula>, <inline-formula><mml:math id="M51" display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula>)</oasis:entry>
         <oasis:entry colname="col2">ECMWF IFS analysis</oasis:entry>
         <oasis:entry colname="col3">ECMWF IFS forecast</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1"/>
         <oasis:entry colname="col2">6 h time step, <inline-formula><mml:math id="M52" display="inline"><mml:mrow><mml:mn mathvariant="normal">0.25</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup><mml:mo>×</mml:mo><mml:mn mathvariant="normal">0.25</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula></oasis:entry>
         <oasis:entry colname="col3">3 h time step, <inline-formula><mml:math id="M53" display="inline"><mml:mrow><mml:mn mathvariant="normal">0.125</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup><mml:mo>×</mml:mo><mml:mn mathvariant="normal">0.125</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula></oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">SST error covariance</oasis:entry>
         <oasis:entry colname="col2">4 <inline-formula><mml:math id="M54" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C</oasis:entry>
         <oasis:entry colname="col3">4 <inline-formula><mml:math id="M55" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1"><inline-formula><mml:math id="M56" display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula>, <inline-formula><mml:math id="M57" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">H</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub><mml:mi mathvariant="normal">O</mml:mi></mml:mrow></mml:math></inline-formula> profiles</oasis:entry>
         <oasis:entry colname="col2">ECMWF IFS analysis</oasis:entry>
         <oasis:entry colname="col3">ECMWF IFS forecast</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1"/>
         <oasis:entry colname="col2">6 h time step, <inline-formula><mml:math id="M58" display="inline"><mml:mrow><mml:mn mathvariant="normal">0.25</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup><mml:mo>×</mml:mo><mml:mn mathvariant="normal">0.25</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula>, 43 levels</oasis:entry>
         <oasis:entry colname="col3">3 h time step, <inline-formula><mml:math id="M59" display="inline"><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup><mml:mo>×</mml:mo><mml:mn mathvariant="normal">2</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula>, 60 levels</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">IR emissivity</oasis:entry>
         <oasis:entry colname="col2"><xref ref-type="bibr" rid="bib1.bibx5" id="paren.34"/></oasis:entry>
         <oasis:entry colname="col3"><xref ref-type="bibr" rid="bib1.bibx5" id="paren.35"/></oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup><?xmltex \end{scaleboxenv}?></oasis:table></table-wrap>

      <?xmltex \floatpos{t}?><fig id="Ch1.F1" specific-use="star"><?xmltex \currentcnt{1}?><label>Figure 1</label><caption><p id="d1e1285">SOFRID <inline-formula><mml:math id="M60" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> averaging kernels for the month of July 2010 averaged globally (first plot) and for five separate latitude bands (90–60<inline-formula><mml:math id="M61" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> S, 60–30<inline-formula><mml:math id="M62" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> S, 30<inline-formula><mml:math id="M63" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> S–30<inline-formula><mml:math id="M64" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N, 30–60<inline-formula><mml:math id="M65" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N, 60–90<inline-formula><mml:math id="M66" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N). Each coloured line corresponds to a retrieval's level, and the corresponding pressure is indicated in the colour bar. Only SOFRID levels with a pressure <inline-formula><mml:math id="M67" display="inline"><mml:mrow><mml:mo>&gt;</mml:mo><mml:mn mathvariant="normal">50</mml:mn></mml:mrow></mml:math></inline-formula> hPa are displayed for better clarity.</p></caption>
            <?xmltex \igopts{width=341.433071pt}?><graphic xlink:href="https://amt.copernicus.org/articles/12/3963/2019/amt-12-3963-2019-f01.png"/>

          </fig>

      <p id="d1e1370">The accuracy of the retrieved <inline-formula><mml:math id="M68" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> depends on the latitude and the vertical level but is generally within 10 %–20 % of the corresponding radiosounding values, once the averaging kernels are applied. However, biases are found in the troposphere with SOFRID (<inline-formula><mml:math id="M69" display="inline"><mml:mrow><mml:mo>+</mml:mo><mml:mn mathvariant="normal">10</mml:mn></mml:mrow></mml:math></inline-formula> %), and positive biases of about 15 % are found in the upper troposphere–lower stratosphere (UTLS) region with all current IASI <inline-formula><mml:math id="M70" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> products <xref ref-type="bibr" rid="bib1.bibx14" id="paren.36"/>. The reasons for such biases are not yet fully understood and can impact data assimilation <xref ref-type="bibr" rid="bib1.bibx15" id="paren.37"/> or trend analysis <xref ref-type="bibr" rid="bib1.bibx22" id="paren.38"/> negatively. This study will provide further insights about the impact of the constant a priori profile on IASI retrievals.</p>
      <p id="d1e1415">The SOFRID V1.5 retrievals described in <xref ref-type="bibr" rid="bib1.bibx3" id="text.39"/> are available for the full MetOp-A period at <uri>http://thredds.sedoo.fr/iasi-sofrid-o3-co</uri> (last access: 16 July 2019). The V3.0 version of SOFRID retrievals has been used for this study and was obtained from Brice Barret (personal communication, 2019). The main difference to version 1.5 concerns the temperature and water vapour profiles employed in the radiative transfer computations, which are taken from the ECMWF NWP model instead of EUMETSAT L2 retrievals. The SOFRID v3.0 preprocessor retrieves the operational analysis (type “an”) at 00:00, 06:00, 12:00, and 18:00 UTC from the ECMWF NWP model and assimilation system (Integrated Forecast System, IFS), regridded to a resolution of <inline-formula><mml:math id="M71" display="inline"><mml:mrow><mml:mn mathvariant="normal">0.25</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup><mml:mo>×</mml:mo><mml:mn mathvariant="normal">0.25</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula>. All the fields are then interpolated at the closest hour to the IASI pixel, and a nearest-neighbour interpolation is done to extract the corresponding profiles and surface properties. Since the CTM is also based on ECMWF NWP forcing fields (Sect. <xref ref-type="sec" rid="Ch1.S3.SS1"/>), this choice minimizes possible systematic differences between L2 retrievals and L1 assimilation. Also, SOFRID v3.0 is based on a more recent version of RTTOV and newer IASI coefficients (v11.1, coefficients on 101 levels) than the original L2 product (v9.0, coefficients on 43 levels). In addition to the <inline-formula><mml:math id="M72" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> retrieval and its error covariance, SOFRID files contain a number of auxiliary and diagnostic fields. The cloud fraction is based on a combination of the EUMETSAT L2 product (AVHRR) and a brightness temperature (BT) analysis at 11 and 12 <inline-formula><mml:math id="M73" display="inline"><mml:mrow class="unit"><mml:mi mathvariant="normal">µ</mml:mi></mml:mrow></mml:math></inline-formula>m to fill pixels with missing AVHRR data <xref ref-type="bibr" rid="bib1.bibx3" id="paren.40"/>. An index based on the V-shaped sand signature computed as <inline-formula><mml:math id="M74" display="inline"><mml:mrow><mml:mi mathvariant="normal">Δ</mml:mi><mml:mi mathvariant="normal">BT</mml:mi><mml:mo>=</mml:mo><mml:mo>(</mml:mo><mml:msub><mml:mi mathvariant="normal">BT</mml:mi><mml:mrow><mml:mn mathvariant="normal">829</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi mathvariant="normal">BT</mml:mi><mml:mrow><mml:mn mathvariant="normal">972.5</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:msub><mml:mo>)</mml:mo><mml:mo>+</mml:mo><mml:mo>(</mml:mo><mml:msub><mml:mi mathvariant="normal">BT</mml:mi><mml:mrow><mml:mn mathvariant="normal">1202.5</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:msub><mml:mo>-</mml:mo><mml:msub><mml:mi mathvariant="normal">BT</mml:mi><mml:mrow><mml:mn mathvariant="normal">1096</mml:mn><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">cm</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> is used to detect pixels affected by large aerosol load. Usage of these products will be detailed in Sect. <xref ref-type="sec" rid="Ch1.S2.SS4"/>, “Data preprocessing”.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F2" specific-use="star"><?xmltex \currentcnt{2}?><label>Figure 2</label><caption><p id="d1e1560">Total number of IASI observations per model grid box (<inline-formula><mml:math id="M75" display="inline"><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup><mml:mo>×</mml:mo><mml:mn mathvariant="normal">2</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula>) retained after the selection procedure described in Sect. <xref ref-type="sec" rid="Ch1.S2.SS4"/> and further assimilated in this study for the month of July 2010. The total number of assimilated observation for the entire globe (N) is given above the map.</p></caption>
            <?xmltex \igopts{width=341.433071pt}?><graphic xlink:href="https://amt.copernicus.org/articles/12/3963/2019/amt-12-3963-2019-f02.png"/>

          </fig>

</sec>
</sec>
<sec id="Ch1.S2.SS2">
  <label>2.2</label><title>MLS L2 retrievals</title>
      <p id="d1e1600">Since 2004 the Microwave Limb Sounder (MLS) has been flying on board the research mission AURA and measures thermal emission at the atmospheric limb <xref ref-type="bibr" rid="bib1.bibx55" id="paren.41"/>. It provides about 3500 stratospheric profiles of multiple atmospheric constituents each day, including <inline-formula><mml:math id="M76" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> <xref ref-type="bibr" rid="bib1.bibx20" id="paren.42"/>. Since version 3 of MLS products has been in operation, <inline-formula><mml:math id="M77" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> profiles have been retrieved on 55 pressure levels, with a recommended range for scientific usage between 0.02 and 261 hPa for version 4.2 <xref ref-type="bibr" rid="bib1.bibx33" id="paren.43"/>. The biases of MLS <inline-formula><mml:math id="M78" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> profiles are typically within 5 % with respect to ozonesondes and lidar measurements <xref ref-type="bibr" rid="bib1.bibx26" id="paren.44"/>, with slightly higher values below 200 hPa. Given its good accuracy, MLS <inline-formula><mml:math id="M79" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> has been widely used both for trend analysis <xref ref-type="bibr" rid="bib1.bibx21" id="paren.45"/> and assimilation experiments <xref ref-type="bibr" rid="bib1.bibx36 bib1.bibx42 bib1.bibx28" id="paren.46"/>. Similarly to previous studies <xref ref-type="bibr" rid="bib1.bibx15" id="paren.47"/>, we retain only the most accurate data using MLS, i.e. above 170 hPa. The MLS V4.2 product used in this study has been downloaded from the Goddard Earth Sciences Data and Information Services Center (GES DISC) web portal (<uri>https://disc.gsfc.nasa.gov</uri>, last access: 16 July 2019).</p>
</sec>
<sec id="Ch1.S2.SS3">
  <label>2.3</label><title>Radiosoundings</title>
      <p id="d1e1681">Ozonesondes are launched on a weekly basis by meteorological services and provide accurate profiles of <inline-formula><mml:math id="M80" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> up to 10 hPa with a vertical resolution of 150–200 m. Electrochemical concentration cell (ECC) sondes, which represent the largest percentage of the global network, have a precision of about 5 % <xref ref-type="bibr" rid="bib1.bibx53" id="paren.48"/>.  Radiosoundings are relatively sparse, and their geographical distribution is much more representative of the northern mid-latitudes. However, for several decades they have provided the most precise information on vertical ozone distribution in the troposphere. Therefore, they have been used to derive widely used tropospheric <inline-formula><mml:math id="M81" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> climatologies <xref ref-type="bibr" rid="bib1.bibx38" id="paren.49"/> and validate both satellite products <xref ref-type="bibr" rid="bib1.bibx14" id="paren.50"/> or models <xref ref-type="bibr" rid="bib1.bibx23" id="paren.51"/>. They will be used in this study to validate all model simulations. Data are collected and distributed by the World Ozone and Ultraviolet Radiation Data Center (WOUDC; <uri>http://www.woudc.org</uri>, last access: 16 July 2019).</p>
</sec>
<sec id="Ch1.S2.SS4">
  <label>2.4</label><title>Data preprocessing</title>
      <p id="d1e1730">Some further preprocessing has been applied to the original L1c and SOFRID datasets to ease the interpretation of the assimilation experiments presented later in Sect. <xref ref-type="sec" rid="Ch1.S4"/>. The objective was to ensure that exactly the same spectra are used for both L1 and L2 assimilation.</p>
      <p id="d1e1735">Only the spectral channels that are used in SOFRID are extracted from IASI L1c granules, i.e. channel no. 1350 (980 cm<inline-formula><mml:math id="M82" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>) to 1818 (1100 cm<inline-formula><mml:math id="M83" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>). Some further screening is applied to remove channels that are affected by strong <inline-formula><mml:math id="M84" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">H</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msub><mml:mi mathvariant="normal">O</mml:mi></mml:mrow></mml:math></inline-formula> absorption, as also done in SOFRID.</p>
      <p id="d1e1775">The spatial resolution of the CTM (<inline-formula><mml:math id="M85" display="inline"><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup><mml:mo>×</mml:mo><mml:mn mathvariant="normal">2</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula>; Sect. <xref ref-type="sec" rid="Ch1.S3.SS1"/>) is much coarser than IASI pixel size. Since it is preferable to avoid all kind of spatial averaging of the observations, a significant reduction of ground pixels is needed. In return, we<?pagebreak page3967?> employ strict selection criteria to avoid contamination from clouds and bright surfaces as much as possible, which reduces the RT accuracy and increases retrieval or assimilation errors. The data selection is performed as follows.</p>
      <p id="d1e1800">First, only L1 pixels with both IASI and AVHRR highest-quality flags are kept.</p>
      <p id="d1e1804">Then, ground pixels from IASI L1 and SOFRID products are filtered using their respective cloud masks (Sect. <xref ref-type="sec" rid="Ch1.S2.SS1.SSS1"/> and <xref ref-type="sec" rid="Ch1.S2.SS1.SSS2"/>) and only keeping pixels with a cloud fraction less than or equal to 1 %.</p>
      <p id="d1e1811">SOFRID pixels with a sand signature greater than 0.5 and with a number of retrieved levels lower than 35 (mountains) are also filtered out.</p>
      <p id="d1e1814">Resulting datasets are then matched; i.e. only common ground pixels that remained available after the previous L1 and SOFRID independent selections are kept. Finally, data thinning is performed using a regular grid of <inline-formula><mml:math id="M86" display="inline"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup><mml:mo>×</mml:mo><mml:mn mathvariant="normal">1</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula> resolution and only keeping the first pixel that falls in every two grid boxes. This ensures a minimum distance of 1<inline-formula><mml:math id="M87" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> among assimilated observations. After the completion of the data selection procedure the final number of retained ground pixels for L1 and SOFRID is about 5000 per day, compared to about 10<inline-formula><mml:math id="M88" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">5</mml:mn></mml:msup></mml:math></inline-formula> when only the cloud screening is applied. The total number of L1 and L2 observations resulting from the above selection and further assimilated in this study is displayed in Fig. <xref ref-type="fig" rid="Ch1.F2"/>.</p>
</sec>
</sec>
<sec id="Ch1.S3">
  <label>3</label><title>Method</title>
      <p id="d1e1866">This section summarizes the main characteristics of the CTM (Sect. <xref ref-type="sec" rid="Ch1.S3.SS1"/>), the RTM (Sect. <xref ref-type="sec" rid="Ch1.S3.SS2"/>) and the assimilation algorithm (Sect. <xref ref-type="sec" rid="Ch1.S3.SS3"/>) used in this study. Further details on the particular selection of the main parameters of the assimilation experiments (e.g. the error covariances) are given in Sect. <xref ref-type="sec" rid="Ch1.S3.SS4"/>.</p>
<sec id="Ch1.S3.SS1">
  <label>3.1</label><title>Chemical transport model</title>
      <p id="d1e1884">The chemical transport model (CTM) MOCAGE <xref ref-type="bibr" rid="bib1.bibx30" id="paren.52"/> is used in this study. A global configuration with a horizontal resolution of <inline-formula><mml:math id="M89" display="inline"><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup><mml:mo>×</mml:mo><mml:mn mathvariant="normal">2</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula> and 60 hybrid sigma-pressure levels up to 0.1 hPa has been used. The vertical resolution varies from about 100 m in the planetary boundary layer to about 700 m in the upper troposphere, decreasing further to approximately 2 km in the upper stratosphere. Chemical mechanism, emissions and physical parameterizations follow the setup used for operational air-quality forecasts <xref ref-type="bibr" rid="bib1.bibx34" id="paren.53"/>, which includes about 100 species and 300 chemical reactions.  A similar configuration has been employed by <xref ref-type="bibr" rid="bib1.bibx2" id="text.54"/> to assimilate IASI <inline-formula><mml:math id="M90" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> columns over Europe but with a lower model top at 5 hPa. Other authors favoured a simplified chemistry scheme but with a model top at 0.1 hPa to assimilate satellite <inline-formula><mml:math id="M91" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> products globally <xref ref-type="bibr" rid="bib1.bibx15 bib1.bibx46" id="paren.55"/>.</p>
      <p id="d1e1942">For this study we considered the highest available model top because we need to simulate the full atmosphere to compute radiances. In addition, the 0.1 hPa top matches with the vertical grid used for SOFRID retrievals (Sect. <xref ref-type="sec" rid="Ch1.S2.SS1.SSS2"/>), making the comparison of the two assimilation approaches (radiances versus L2) stricter. The full chemical scheme is chosen instead of a simplified chemistry to reduce biases of the modelled <inline-formula><mml:math id="M92" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> in the troposphere as much as possible. The main intent of this study is in fact to evaluate the impact of dynamical and accurate <inline-formula><mml:math id="M93" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> prior information on assimilation results.</p>
      <p id="d1e1969">The meteorological forcing comes from the ECMWF IFS, from which we retrieved the forecast (type “fc”) initialized with the analysis at 00:00 UTC each day. The NWP fields are interpolated on the horizontal grid of MOCAGE (<inline-formula><mml:math id="M94" display="inline"><mml:mrow><mml:mn mathvariant="normal">2</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup><mml:mo>×</mml:mo><mml:mn mathvariant="normal">2</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula>) during the retrieval process and stored with a time step of 3 h. During the integration of MOCAGE, the meteorological forcing is linearly interpolated at the advection time step of MOCAGE (hourly) and on the CTM's vertical grid.</p>
</sec>
<?pagebreak page3968?><sec id="Ch1.S3.SS2">
  <label>3.2</label><title>Radiative transfer model</title>
      <p id="d1e2000">RTTOV <xref ref-type="bibr" rid="bib1.bibx50" id="paren.56"/> is a community RTM developed for operational NWP models. One of its main advantages is computational efficiency, which is achieved by running accurate but costly line-by-line RT simulations for a large number of satellite sensors, observation geometries and atmospheres and storing the corresponding coefficients in large lookup tables. RTTOV provides application programming interfaces (APIs) for the direct RT computations plus the tangent linear and adjoint model, which are needed in variational assimilation systems.</p>
      <?pagebreak page3969?><p id="d1e2006">Version 11.3 of RTTOV <xref ref-type="bibr" rid="bib1.bibx51" id="paren.57"/> has been used in this study for the L1 assimilation. This version includes coefficients for the IASI TIR channels computed using a fine atmospheric grid (101 vertical levels). The SST, 2 m temperature, 2 m pressure and 2 m wind vector are taken from high-resolution (<inline-formula><mml:math id="M95" display="inline"><mml:mrow><mml:mn mathvariant="normal">0.125</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup><mml:mo>×</mml:mo><mml:mn mathvariant="normal">0.125</mml:mn><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula>) global IFS forecasts initialized with the analysis at 00:00 UTC each day and co-located (nearest neighbour) with satellite ground pixels prior to data assimilation. A linear interpolation from the 3 h forecast steps to the closest hour of the IASI observations is also performed for these fields. The surface emissivity is based on the RTTOV monthly TIR emissivity atlas <xref ref-type="bibr" rid="bib1.bibx5" id="paren.58"/>. Only clear-sky RT computations are performed for this study, and no aerosols have been prescribed. The RTM configuration is summarized in Table <xref ref-type="table" rid="Ch1.T2"/>. Due to the different processing chains, the auxiliary inputs of RTTOV could not be set exactly equal for L1 assimilation and L2 retrievals (Table <xref ref-type="table" rid="Ch1.T2"/>). The potential impact of these residual differences is discussed in Sect. <xref ref-type="sec" rid="Ch1.S4.SS1"/>.</p>
</sec>
<sec id="Ch1.S3.SS3">
  <label>3.3</label><title>Assimilation algorithm</title>
      <p id="d1e2050">The assimilation suite for MOCAGE is based on a variational algorithm and was developed initially within the ASSET (Assimilation of Envisat data) project <xref ref-type="bibr" rid="bib1.bibx31" id="paren.59"/>. The objective was to assimilate satellite products at a global scale, and a 3-D-FGAT implementation was chosen. It evolved later to provide air-quality reanalyses at the surface based on a 3D-Var implementation <xref ref-type="bibr" rid="bib1.bibx29" id="paren.60"/> and was extended to 4D-Var when employing linearized chemistry schemes <xref ref-type="bibr" rid="bib1.bibx37 bib1.bibx15" id="paren.61"/>. In all cases the minimization of the variational cost function is performed using the limited-memory Broyden–Fletcher–Goldfarb–Shanno (BFGS) algorithm <xref ref-type="bibr" rid="bib1.bibx32" id="paren.62"/>. In this study we used a 3D-Var algorithm with hourly assimilation windows and with <inline-formula><mml:math id="M96" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> as the control variable.</p>
      <p id="d1e2076">The 3-D background error covariance is modelled through a diffusion operator <xref ref-type="bibr" rid="bib1.bibx56" id="paren.63"/> and allows the specification of heterogeneous correlation length scales. Compared to previous studies using the MOCAGE assimilation suite, a new vertical correlation operator has been employed here: the vertical error correlation is now assigned by explicitly filling a positive definite matrix using the Gaussian formulation of <xref ref-type="bibr" rid="bib1.bibx45" id="text.64"/> and by numerically computing its square root. This avoids difficulties encountered with diffusion-based operators concerning the normalization in the presence of boundaries (e.g. the surface) and heterogeneity <xref ref-type="bibr" rid="bib1.bibx41" id="paren.65"/>. Since the vertical dimension of the model grid is relatively small, this choice does not impact the numerical cost and the memory requirements significantly with respect to the previous implementation based on diffusion.</p>
      <p id="d1e2088">The observation operator of MOCAGE allows a large number of measurements to be assimilated, spanning from columns of gases <xref ref-type="bibr" rid="bib1.bibx35" id="paren.66"/> to aerosol optical depth <xref ref-type="bibr" rid="bib1.bibx52" id="paren.67"/>. Next, we give some details of the implementation used in this study to assimilate vertical profiles and radiances.</p>
      <p id="d1e2097">After the horizontal and temporal interpolation of the model fields at the satellite ground-pixel position, modelled profiles are linearly interpolated to the retrieval's vertical grid. When the averaging kernels are used (i.e. for SOFRID assimilation), the linear estimation equation <xref ref-type="bibr" rid="bib1.bibx3" id="paren.68"/> is used to remove the impact of the prior information from the innovation vector. The ensemble of these operations is stored as coefficients of a large sparse matrix and done through its multiplication by the model 3-D field. This approach is practical since numerous applications of the linearized and adjoint operator are needed during the minimization of the variational cost function. Differently from all previous studies involving IASI <inline-formula><mml:math id="M97" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> assimilation <xref ref-type="bibr" rid="bib1.bibx35 bib1.bibx15 bib1.bibx46" id="paren.69"/>, in which L2 profiles were first reduced to total or partial columns prior to assimilation, here we assimilate the full L2 profiles directly (43 levels). This avoids any loss of information and allows a fairer comparison between L2 and radiance assimilation. The error covariance matrix of the profile-type observations is diagonal in the latitude–longitude dimensions, but off-diagonal terms are allowed along the vertical dimension. Alternative approaches exist to optimally reduce the<?pagebreak page3970?> dimension of the L2 observation space based on the DOF of the retrievals <xref ref-type="bibr" rid="bib1.bibx40 bib1.bibx43" id="paren.70"/>, which are of interest to further reduce the numerical cost of SOFRID assimilation without loss of accuracy. However, this is left for future work.</p>
      <p id="d1e2121">To compute modelled radiances we employ the same horizontal and temporal interpolation as in the case of profile observations, except for the vertical interpolation. In fact, the RTTOV vertical interpolator is used for radiance computations instead of the MOCAGE one. All model levels (60) and corresponding pressure levels are given as input to RTTOV, which performs the vertical interpolation to the IASI coefficient levels internally. Since the model vertical resolution is lower than the one available in RTTOV for IASI coefficients (101 levels), we used the default option based on <xref ref-type="bibr" rid="bib1.bibx48" id="text.71"/>. Also, <inline-formula><mml:math id="M98" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> profiles above the CTM top (0.1 hPa) are completed using RTTOV climatological profiles.
Auxiliary inputs for the radiance computation include the pressure, temperature and water vapour profiles, which are interpolated from the corresponding MOCAGE fields.</p>
      <p id="d1e2138">The MOCAGE control vector has been extended to include the SST, as in the SOFRID retrieval scheme. This proved to be important since small errors in the SST translate in significant differences between modelled and measured radiances. Not accounting for this would produce incorrect <inline-formula><mml:math id="M99" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> analyses. The SST does not belong to the MOCAGE prognostic fields, nor is it prescribed on the MOCAGE grid. Hence, the SST analysis is not propagated in time, and no spatial covariance model has been implemented so far. In this regard the treatment of the SST is equivalent to that done in L2 retrievals. In the context of MOCAGE 3D-Var, it can be interpreted as a variational bias correction term in the observation space <xref ref-type="bibr" rid="bib1.bibx10" id="paren.72"/>, with prior values given by the NWP model (IFS; see Sect. <xref ref-type="sec" rid="Ch1.S3.SS2"/>).</p>
</sec>
<sec id="Ch1.S3.SS4">
  <label>3.4</label><title>Setup of the experiments</title>
      <p id="d1e2166">We performed numerical experiments for the month of July 2010, which corresponds to the typical presence of summer <inline-formula><mml:math id="M100" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> maxima in the Northern Hemisphere linked to photochemical pollution. July 2010 is also interesting due to the development of a strong La Niña episode <xref ref-type="bibr" rid="bib1.bibx46" id="paren.73"/>. The main difference between assimilating L2 and L1 data consists in using a climatological (L2 assimilation) versus a dynamical a priori profile (L1 assimilation) for the inversion of the radiative transfer problem. The chosen period presents large local deviations of the <inline-formula><mml:math id="M101" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> field from climatological values. Therefore, it provides an interesting benchmark period with respect to the objective of this study.</p>
      <p id="d1e2194">The CTM was initialized on 1 June 2010 with a zonal climatology and run for a 1-month period (spin-up) to provide chemically balanced initial conditions on 1 July 2010 for all simulations.</p>
      <p id="d1e2197">The observation error covariance matrix (<inline-formula><mml:math id="M102" display="inline"><mml:mi mathvariant="bold">R</mml:mi></mml:math></inline-formula>) is prescribed according to the choices adopted in SOFRID V3.0. When the radiances are assimilated, a diagonal matrix (i.e. with no inter-channel correlation) is used, with a constant standard deviation of to 0.7 mW m<inline-formula><mml:math id="M103" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">2</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> sr<inline-formula><mml:math id="M104" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> cm for all channels. This is a simplified although common setting for most IASI <inline-formula><mml:math id="M105" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> retrievals <xref ref-type="bibr" rid="bib1.bibx3 bib1.bibx6" id="paren.74"/>. The SST, which is controlled as well within radiance assimilation, has a prescribed standard deviation of 4 <inline-formula><mml:math id="M106" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>C for all ground pixels. When L2 profiles are assimilated we used the full non-diagonal error covariance matrix provided by SOFRID or MLS retrievals.</p>
      <p id="d1e2255">We considered a dynamical rejection of observations based on the relative differences between simulated and measured values with respect to simulated values. It avoids assimilating observations with departures from the corresponding model background that are too large. The threshold values are set to 12 % for L1 radiances and 2000 % for L2 profiles, and trespassing the threshold for any particular channel or profile level rejects the entire spectrum or profile. The strong difference between the two thresholds is a consequence of the very different nature of assimilated observations: the exponential shape of <inline-formula><mml:math id="M107" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> profiles can produce very large departures when the gradient is the steepest (tropopause), and a small rejection threshold would filter out most of the profile observations. This is not the case for radiances, which vary on a linear scale. Threshold values have been chosen based on misfit histograms in order to remove abnormal tails. As a consequence, L1 and L2 pixels that pass the selection and are further assimilated could differ. However, the relative number of rejected observations for the entire month of July is quite limited in both cases (3 % for L1, 6 % for L2), thus not affecting the results statistically.</p>
      <p id="d1e2270">The setup of the background error covariance (<inline-formula><mml:math id="M108" display="inline"><mml:mi mathvariant="bold">B</mml:mi></mml:math></inline-formula>) is a critical step both for L2 retrievals and data assimilation. We did benefit from past experiences using MOCAGE, IASI and MLS <inline-formula><mml:math id="M109" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> <xref ref-type="bibr" rid="bib1.bibx37 bib1.bibx15 bib1.bibx46" id="paren.75"/> to define a first guess of <inline-formula><mml:math id="M110" display="inline"><mml:mi mathvariant="bold">B</mml:mi></mml:math></inline-formula>, and we tried to further derive an optimal parameterization for this study. Note that the <inline-formula><mml:math id="M111" display="inline"><mml:mi mathvariant="bold">B</mml:mi></mml:math></inline-formula> matrix (3-D) used in data assimilation is by definition different with respect to the one specified within SOFRID (1-D), but the same 3-D <inline-formula><mml:math id="M112" display="inline"><mml:mi mathvariant="bold">B</mml:mi></mml:math></inline-formula> is used for all data assimilation experiments (L1 and L2).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F3" specific-use="star"><?xmltex \currentcnt{3}?><label>Figure 3</label><caption><p id="d1e2318">Relative root mean square error (RMSE) of the control simulation with respect to radiosoundings (solid lines) and MLS (dotted lines) averaged globally (first plot) and for five separate latitude bands (90–60<inline-formula><mml:math id="M113" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> S, 60–30<inline-formula><mml:math id="M114" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> S, 30<inline-formula><mml:math id="M115" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> S–30<inline-formula><mml:math id="M116" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N, 30–60<inline-formula><mml:math id="M117" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N, 60–90<inline-formula><mml:math id="M118" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N). To compute the percentage, the RMSE statistics have been divided by the corresponding average profile of the observations (radiosoundings or MLS) for each band.</p></caption>
          <?xmltex \igopts{width=341.433071pt}?><graphic xlink:href="https://amt.copernicus.org/articles/12/3963/2019/amt-12-3963-2019-f03.png"/>

        </fig>

      <p id="d1e2382">Concerning the standard deviation, <xref ref-type="bibr" rid="bib1.bibx15" id="text.76"/> and <xref ref-type="bibr" rid="bib1.bibx46" id="text.77"/> employed vertically varying errors expressed as percentages of the background <inline-formula><mml:math id="M119" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> profile, with larger relative errors in the troposphere and smaller in the stratosphere. Since we use a more detailed chemistry model here (Sect. <xref ref-type="sec" rid="Ch1.S3.SS1"/>), we evaluated the root mean square error (RMSE) of the free model simulation (control) against ozonesondes and MLS profiles (Fig. <xref ref-type="fig" rid="Ch1.F3"/>). We remark that the model's RMSE reproduces the vertical features observed in previous studies, with smaller errors in the stratosphere (between 20 and 50 hPa), larger errors in the free troposphere and highest errors close to the tropopause and within the planetary boundary layer. Note also the zonal variability of the maxima, which appear to be linked to the variability<?pagebreak page3971?> of the tropopause height. Thanks to the detailed chemical mechanism, biases (Fig. <xref ref-type="fig" rid="Ch1.F4"/>) are generally smaller than in the studies cited previously but remain significant compared to standard deviation values (Fig. <xref ref-type="fig" rid="Ch1.F5"/>), especially around the tropopause. Interestingly, RMSE and standard deviation values computed against MLS are generally smaller than those evaluated against ozonesondes, whereas biases are more consistent between the two datasets. We attribute this effect to the larger number of MLS observations (Table <xref ref-type="table" rid="Ch1.T1"/>), which provides more robust standard deviation statistics.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F4" specific-use="star"><?xmltex \currentcnt{4}?><label>Figure 4</label><caption><p id="d1e2415">Relative bias of the control simulation with respect to radiosoundings (solid lines) and MLS (dotted lines). Same plots as in Fig <xref ref-type="fig" rid="Ch1.F3"/>.</p></caption>
          <?xmltex \igopts{width=341.433071pt}?><graphic xlink:href="https://amt.copernicus.org/articles/12/3963/2019/amt-12-3963-2019-f04.png"/>

        </fig>

      <p id="d1e2426">The background standard deviation is prescribed through a smooth step function that takes values of 2 % above 50 hPa and 10 % below to reproduce roughly the patterns observed in Fig. <xref ref-type="fig" rid="Ch1.F5"/>. Values are smaller than those in Fig. <xref ref-type="fig" rid="Ch1.F5"/> to account for the error reduction during the assimilation, which is particularly strong when MLS observations are used (see Sect. <xref ref-type="sec" rid="Ch1.S4.SS3"/>). Also, neglecting error correlations between IASI channels within <inline-formula><mml:math id="M120" display="inline"><mml:mi mathvariant="bold">R</mml:mi></mml:math></inline-formula> leads to a strong weight towards the observations: reducing the background standard deviation compensates in part for this effect. All the choices made to define <inline-formula><mml:math id="M121" display="inline"><mml:mi mathvariant="bold">B</mml:mi></mml:math></inline-formula> are a result of a large number of assimilation evaluations, in which different options were considered. For example, setting values of 5 % and 25 % leads to less accurate results for both L1 and L2 assimilation (not reported). The percent profile is multiplied by the hourly <inline-formula><mml:math id="M122" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> field of the control simulation once for the entire period and not at every forecast time step. Therefore, all assimilation experiments presented in this study are based on the same <inline-formula><mml:math id="M123" display="inline"><mml:mi mathvariant="bold">B</mml:mi></mml:math></inline-formula> matrix. This choice was made to permit a stricter comparison between L1 and L2 assimilation experiments.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F5" specific-use="star"><?xmltex \currentcnt{5}?><label>Figure 5</label><caption><p id="d1e2471">Relative standard deviation of the control simulation with respect to radiosoundings (solid lines) and MLS (dotted lines). Same plots as in Fig. <xref ref-type="fig" rid="Ch1.F3"/>.</p></caption>
          <?xmltex \igopts{width=341.433071pt}?><graphic xlink:href="https://amt.copernicus.org/articles/12/3963/2019/amt-12-3963-2019-f05.png"/>

        </fig>

      <p id="d1e2482">The vertical error correlation diffuses the assimilation increments between model levels and has been found to significantly impact the quality of <inline-formula><mml:math id="M124" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> analyses with current model vertical resolutions (not shown). In general, small values of vertical correlation are favoured in the stratosphere due to the stratification and to avoid injection of large stratospheric <inline-formula><mml:math id="M125" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> increments in the troposphere, whereas larger values are expected within the troposphere due to vertical mixing. In this study a constant value of one model level defines the length scale of the Gaussian correlation (Sect. <xref ref-type="sec" rid="Ch1.S3.SS3"/>). Different<?pagebreak page3972?> choices for the stratosphere and troposphere did not lead to particular improvements (not shown).</p>
      <p id="d1e2509">Finally, the exponential scale of the horizontal error correlation is set to be equal to 200 km, with the zonal component that is reduced towards the poles to account for the increasing resolution of the model's grid <xref ref-type="bibr" rid="bib1.bibx15" id="paren.78"/>.</p>
      <p id="d1e2515">The choice of the background and observation errors is relatively simplistic in this study. Further improvements of the <inline-formula><mml:math id="M126" display="inline"><mml:mi mathvariant="bold">B</mml:mi></mml:math></inline-formula> parameterization could be achieved by diagnosing the forecast errors hourly <xref ref-type="bibr" rid="bib1.bibx12" id="paren.79"/> or using ensembles of model forecasts. However, more complex and costly estimations do not always improve the results of chemical assimilation systematically and significantly <xref ref-type="bibr" rid="bib1.bibx37" id="paren.80"/>. Moreover, a good estimation of <inline-formula><mml:math id="M127" display="inline"><mml:mi mathvariant="bold">B</mml:mi></mml:math></inline-formula> cannot be done independently of that of <inline-formula><mml:math id="M128" display="inline"><mml:mi mathvariant="bold">R</mml:mi></mml:math></inline-formula>, which is kept fixed here on purpose. Additional research is needed in this regard, which is beyond the scope of this study.</p>
</sec>
</sec>
<sec id="Ch1.S4">
  <label>4</label><title>Results</title>
      <p id="d1e2554">A total of six simulations for the month of July 2010 have been performed (Table <xref ref-type="table" rid="Ch1.T3"/>), starting on 1 July: a free model simulation (control) and five 3D-Var analyses assimilating SOFRID L2 profiles (named L2a), IASI L1 radiances (L1a), MLS L2 profiles (MLSa), MLS plus SOFRID L2 profiles (MLS <inline-formula><mml:math id="M129" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L2a) and MLS plus L1 radiances (MLS <inline-formula><mml:math id="M130" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L1a).
The first three simulations (control, L2a and L1a) are discussed in Sect. <xref ref-type="sec" rid="Ch1.S4.SS1"/>. The control simulation and the three analyses that include MLS are discussed in Sect. <xref ref-type="sec" rid="Ch1.S4.SS3"/>. All simulations have been validated against ozonesondes profiles to elucidate the differences of the resulting <inline-formula><mml:math id="M131" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> vertical distribution. A total of 219 radiosoundings are available globally for July 2010 (Table <xref ref-type="table" rid="Ch1.T1"/>). The co-location of ozonesonde profiles with model fields in time and space is performed through the MOCAGE observation operator (Sect. <xref ref-type="sec" rid="Ch1.S3"/>).</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T3"><?xmltex \currentcnt{3}?><label>Table 3</label><caption><p id="d1e2596">Names of experiments and assimilated data.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="4">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:colspec colnum="4" colname="col4" align="left"/>
     <oasis:thead>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">Experiment's name</oasis:entry>
         <oasis:entry colname="col2">IASI L1</oasis:entry>
         <oasis:entry colname="col3">IASI L2</oasis:entry>
         <oasis:entry colname="col4">MLS L2</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>
         <oasis:entry colname="col1">Control</oasis:entry>
         <oasis:entry colname="col2">no</oasis:entry>
         <oasis:entry colname="col3">no</oasis:entry>
         <oasis:entry colname="col4">no</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">L1a</oasis:entry>
         <oasis:entry colname="col2">yes</oasis:entry>
         <oasis:entry colname="col3">no</oasis:entry>
         <oasis:entry colname="col4">no</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">L2a</oasis:entry>
         <oasis:entry colname="col2">no</oasis:entry>
         <oasis:entry colname="col3">yes</oasis:entry>
         <oasis:entry colname="col4">no</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">MLSa</oasis:entry>
         <oasis:entry colname="col2">no</oasis:entry>
         <oasis:entry colname="col3">no</oasis:entry>
         <oasis:entry colname="col4">yes</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">MLS <inline-formula><mml:math id="M132" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L1a</oasis:entry>
         <oasis:entry colname="col2">yes</oasis:entry>
         <oasis:entry colname="col3">no</oasis:entry>
         <oasis:entry colname="col4">yes</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">MLS <inline-formula><mml:math id="M133" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L2a</oasis:entry>
         <oasis:entry colname="col2">no</oasis:entry>
         <oasis:entry colname="col3">yes</oasis:entry>
         <oasis:entry colname="col4">yes</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

<sec id="Ch1.S4.SS1">
  <label>4.1</label><title>IASI assimilation</title>
      <p id="d1e2746">The average <inline-formula><mml:math id="M134" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> values of the control simulation are displayed in Fig. <xref ref-type="fig" rid="Ch1.F6"/>. <inline-formula><mml:math id="M135" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> fields have been first interpolated vertically from the model grid to a selection of pressure levels, covering both the stratosphere and the troposphere, and averaged afterwards. The maps show well known properties of the <inline-formula><mml:math id="M136" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> distribution such as the strong zonal gradients in the stratosphere and the presence of local minima in the tropical<?pagebreak page3973?> free troposphere due to deep convection. The average difference between the control simulation and the fixed a priori profile used in SOFRID retrievals (Sect. <xref ref-type="sec" rid="Ch1.S2.SS1.SSS2"/>) is displayed in Fig. <xref ref-type="fig" rid="Ch1.F7"/>. Large differences (<inline-formula><mml:math id="M137" display="inline"><mml:mrow><mml:mo>&gt;</mml:mo><mml:mn mathvariant="normal">100</mml:mn></mml:mrow></mml:math></inline-formula> %) are found at low latitudes both in the lower stratosphere and in the troposphere, with largest values close to the tropical tropopause (150 hPa). This is expected since the SOFRID a priori profile is based on a global ozonesonde climatology that is more representative of mid-latitude <inline-formula><mml:math id="M138" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> profiles (Sect. <xref ref-type="sec" rid="Ch1.S2.SS1.SSS2"/>).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F6" specific-use="star"><?xmltex \currentcnt{6}?><label>Figure 6</label><caption><p id="d1e2814">Average <inline-formula><mml:math id="M139" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> values of the control simulation in units of parts per billion (ppb) for July 2010. From left to right, different pressure levels are displayed covering the stratosphere <bold>(a, b, c)</bold> and the free troposphere <bold>(d, e, f)</bold>. Average, maximum and minimum values of the displayed fields are given above each map.</p></caption>
          <?xmltex \igopts{width=369.885827pt}?><graphic xlink:href="https://amt.copernicus.org/articles/12/3963/2019/amt-12-3963-2019-f06.png"/>

        </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F7" specific-use="star"><?xmltex \currentcnt{7}?><label>Figure 7</label><caption><p id="d1e2842">Relative average differences between the control simulation and the SOFRID a priori profile on July 2010. Values are given as percentages (%) of the control simulation (Fig. <xref ref-type="fig" rid="Ch1.F6"/>). Same plots as in Fig. <xref ref-type="fig" rid="Ch1.F6"/>.</p></caption>
          <?xmltex \igopts{width=369.885827pt}?><graphic xlink:href="https://amt.copernicus.org/articles/12/3963/2019/amt-12-3963-2019-f07.png"/>

        </fig>

      <?pagebreak page3974?><p id="d1e2856"><?xmltex \hack{\newpage}?>We discuss the geographical differences between L1a and L2a analyses by looking at the monthly bias between the two experiments, divided by the average <inline-formula><mml:math id="M140" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> of the control simulation (Fig. <xref ref-type="fig" rid="Ch1.F6"/>). Relative differences are displayed in Fig. <xref ref-type="fig" rid="Ch1.F8"/>. First, we remark that differences are generally significant both in the stratosphere and in the troposphere, with absolute values that can exceed 50 % of the <inline-formula><mml:math id="M141" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> field locally and global averages as high as to 20 %. Largest differences in the stratosphere are found at tropical latitudes, L1a showing larger <inline-formula><mml:math id="M142" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> values than L2a at 20 hPa and lower at 70 hPa. In the troposphere the strongest positive differences are still found in the tropics, especially over central Africa, eastern Asia, South America and Middle East regions. Differences become smaller when moving down to 750 hPa and tend to disappear at lower altitudes (not shown), which is normal considering the vertical sensitivity of IASI. At mid-latitudes and high latitudes, relative differences are smaller than at the tropics. This behaviour is consistent with the fact that the SOFRID prior information is much less accurate for tropical latitudes than for mid-latitudes and high latitudes (Fig. <xref ref-type="fig" rid="Ch1.F7"/>). Overall, these plots suggest that when the L2 a priori profile is strongly biased (<inline-formula><mml:math id="M143" display="inline"><mml:mrow><mml:mo>&gt;</mml:mo><mml:mn mathvariant="normal">100</mml:mn></mml:mrow></mml:math></inline-formula> %), the equivalence between L1 and L2 assimilation in the thermal infrared is not verified for <inline-formula><mml:math id="M144" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>, even when the averaging kernels are employed.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F8" specific-use="star"><?xmltex \currentcnt{8}?><label>Figure 8</label><caption><p id="d1e2923">Relative average differences (%) between radiances and Level 2 assimilation (L1a minus L2a divided by the corresponding <inline-formula><mml:math id="M145" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> values of the control simulation in Fig. <xref ref-type="fig" rid="Ch1.F6"/>) for July 2010. Same plots as in Fig. <xref ref-type="fig" rid="Ch1.F6"/>.</p></caption>
          <?xmltex \igopts{width=369.885827pt}?><graphic xlink:href="https://amt.copernicus.org/articles/12/3963/2019/amt-12-3963-2019-f08.png"/>

        </fig>

      <p id="d1e2947">To confirm that the observed differences are not a consequence of the slightly different NWP inputs used in L1 assimilation and L2 retrievals (Table <xref ref-type="table" rid="Ch1.T2"/>) we rerun the L1a simulation using exactly the same SST a priori values used in SOFRID retrievals. Since we cannot use the same water vapour and temperature profiles of SOFRID within L1a due to the different vertical grids, a different approach has been used: we repeated all assimilation experiments but using ERA Interim <xref ref-type="bibr" rid="bib1.bibx11" id="paren.81"/> instead of the NWP forecasts as meteorological forcing for the CTM. This increases potential differences between the L1 and L2 assimilation, due to the different configurations of operational NWP and ERA Interim (model resolution, assimilated instruments, etc.). In all the above cases we obtained very similar results to those presented in Fig. <xref ref-type="fig" rid="Ch1.F8"/> (not shown), which suggests that differences between L1a and L2a discussed previously do not depend on the auxiliary RTM inputs.</p>
      <?pagebreak page3975?><p id="d1e2957">To further verify which one out of the L1a and L2a experiments reproduces the measured <inline-formula><mml:math id="M146" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> profiles better, we validated the three simulations against radiosoundings. Figure <xref ref-type="fig" rid="Ch1.F9"/> reports the RMSE differences computed globally and for five different latitude bands. The displayed values are the differences between the RMSE of the assimilation experiment and the corresponding value for the control simulation (Fig. <xref ref-type="fig" rid="Ch1.F3"/>). Negative values in Fig. <xref ref-type="fig" rid="Ch1.F9"/> indicate that the assimilation improved the <inline-formula><mml:math id="M147" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> field and decreased the relative RMSE with respect to ozonesondes by the amount displayed on the plot. Looking at the global averages we remark that below 70 hPa the gain is similar for both L1a and L2a experiments and quite significant at 200 hPa (20 %). Note, however, the strong similarity between the global and 30–60<inline-formula><mml:math id="M148" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N statistics, due to the over-representation of ozonesondes for the Northern Hemisphere (NH) mid-latitudes (63 % of the total).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F9" specific-use="star"><?xmltex \currentcnt{9}?><label>Figure 9</label><caption><p id="d1e3000">Relative difference of RMSE (<inline-formula><mml:math id="M149" display="inline"><mml:mi mathvariant="normal">Δ</mml:mi></mml:math></inline-formula>RMSE) with respect to radiosoundings for L1a (blue) and L2a (red). The difference is computed by subtracting the RMSE of L1a (L2a) from the RMSE of the control simulation (Fig. <xref ref-type="fig" rid="Ch1.F3"/>). Negative values mean that the assimilation improved (decreased) the RMSE of the control simulation, and positive values indicate degradation (increase) of the RMSE. The statistics are computed for the same latitudes as in Fig. <xref ref-type="fig" rid="Ch1.F3"/>.</p></caption>
          <?xmltex \igopts{width=369.885827pt}?><graphic xlink:href="https://amt.copernicus.org/articles/12/3963/2019/amt-12-3963-2019-f09.png"/>

        </fig>

      <p id="d1e3021">In the NH the RMSE of the control simulation is effectively reduced between 70 and 300 hPa (up to 20 %). L1a shows a slightly better gain than L2a between 150 and 300 hPa. Interestingly, both L1a and L2a display increased RMSE between 300 and 400 hPa. This behaviour is also confirmed when the vertical error correlation is switched off in the 3D-Var <inline-formula><mml:math id="M150" display="inline"><mml:mi mathvariant="bold">B</mml:mi></mml:math></inline-formula> and with different choices for the vertical interpolation of <inline-formula><mml:math id="M151" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> optical coefficients within RTTOV (log-linear or Rochon, not shown). Since large negative biases were present in the control simulation (as low as <inline-formula><mml:math id="M152" display="inline"><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">30</mml:mn></mml:mrow></mml:math></inline-formula> %; see Fig. <xref ref-type="fig" rid="Ch1.F4"/>), a possible explanation is that part of the strong positive correction of <inline-formula><mml:math id="M153" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> between 100 and 300 hPa is propagated downwards, where both absolute <inline-formula><mml:math id="M154" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> concentrations and relative biases are much lower. This can degrade the analysis accuracy below 300 hPa. Whether this propagation is carried out by the Jacobian matrix of the observation operator (either through the RTM or the retrieval's AK) or by vertical <inline-formula><mml:math id="M155" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> transport is not yet elucidated and would need further investigation. Also, other possible factors affecting the accuracy of the RTM exist, like inadequate vertical resolution close to the tropopause or uncertainties in meteorological profiles or in the impact of aerosols. Nonetheless, these errors impact both L1a and L2a in our study: further optimization of the L1 assimilation configuration with respect to the L2 retrievals is left for a future study. The RMSE is reduced again at about 500 hPa between 30 and 60<inline-formula><mml:math id="M156" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N, although not very significantly. The assimilation increases the RMSE of the tropospheric profile (350–1000 hPa) at northern latitudes (60–90<inline-formula><mml:math id="M157" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N). In general, the validation confirms that L1a and L2a have a very similar accuracy in NH at mid-latitudes and high latitudes, as also suggested previously by Fig. <xref ref-type="fig" rid="Ch1.F8"/>. However, the strongest positive corrections are confined to the UTLS.</p>
      <p id="d1e3108">At the tropics (30<inline-formula><mml:math id="M158" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> S–30<inline-formula><mml:math id="M159" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N) the results differ more significantly. In the troposphere (below 100 hPa), both L1a and L2a reduced the RMSE of the control simulation, although by a smaller amount than in the NH (5 %). Note also that L1a RMSE reduction is larger than L2a between 400 and 600 hPa, whereas it is the other way around at about 250 and 800 hPa. Above 100 hPa we observe an increase of RMSE that peaks at 60 hPa with L2a and at 30 hPa with L1a but smaller in magnitude for L1a. This behaviour might be linked to the strong differences that exist between the SOFRID prior information and the modelled <inline-formula><mml:math id="M160" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> at the tropical tropopause, to some other factor affecting the RT computations, to overestimation of the background error covariances or to a complex combination of all previous causes. A full satisfactory explanation has not been found yet.</p>
      <?pagebreak page3976?><p id="d1e3140">Results in the Southern Hemisphere (SH) (30–90<inline-formula><mml:math id="M161" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> S) are again similar: a lower RMSE than for the control simulation is found for both L1a and L2a in the upper and lower stratosphere (between 30 and 100 hPa and between 150 and 300 hPa). An improvement is also found in the troposphere (400–600 hPa) at mid-latitudes (30–60<inline-formula><mml:math id="M162" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> S), but the low number of ozonesondes available in this band (Table <xref ref-type="table" rid="Ch1.T1"/>) requires a more careful interpretation.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F10" specific-use="star"><?xmltex \currentcnt{10}?><label>Figure 10</label><caption><p id="d1e3165">Relative difference of RMSE (<inline-formula><mml:math id="M163" display="inline"><mml:mi mathvariant="normal">Δ</mml:mi></mml:math></inline-formula>RMSE) with respect to MLS profiles for L1a (blue) and L2a (red). Same plots as in Fig. <xref ref-type="fig" rid="Ch1.F9"/>.</p></caption>
          <?xmltex \igopts{width=369.885827pt}?><graphic xlink:href="https://amt.copernicus.org/articles/12/3963/2019/amt-12-3963-2019-f10.png"/>

        </fig>

      <p id="d1e3183">Since radiosoundings do not provide a uniform global coverage, and vertical coverage is also lacking in the vicinity of the <inline-formula><mml:math id="M164" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> maximum, we validated the three simulations against MLS measurements. The RMSE differences for stratospheric profiles can be found in Fig. <xref ref-type="fig" rid="Ch1.F10"/>. These statistics are based on more than 10<inline-formula><mml:math id="M165" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">5</mml:mn></mml:msup></mml:math></inline-formula> profiles for the global average and between 15 000 and 30 000 for zonal averages, depending on the latitude band (Table <xref ref-type="table" rid="Ch1.T1"/>). The patterns observed in the stratosphere with respect to ozonesondes are also confirmed with MLS. The only exceptions are a smaller RMSE degradation at 50 hPa for L2a in the tropics and for both L1a and L2a at 150 hPa in the 30–60<inline-formula><mml:math id="M166" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> S band. Higher confidence should be given to the RMSE values provided by MLS than those obtained with radiosoundings (see also Fig. <xref ref-type="fig" rid="Ch1.F3"/> and the relative discussion in Sect. <xref ref-type="sec" rid="Ch1.S3.SS4"/>). However, a similar RMSE behaviour is observed overall, and this bolsters the robustness of the conclusions derived with the radiosoundings in the troposphere.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F11" specific-use="star"><?xmltex \currentcnt{11}?><label>Figure 11</label><caption><p id="d1e3227">Relative average differences between MLS <inline-formula><mml:math id="M167" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L1a and MLS <inline-formula><mml:math id="M168" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L2a (MLS <inline-formula><mml:math id="M169" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L1a minus MLS <inline-formula><mml:math id="M170" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L2a divided by the corresponding <inline-formula><mml:math id="M171" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> values of the control simulation in Fig. <xref ref-type="fig" rid="Ch1.F6"/>) for July 2010. Same plots as in Fig. <xref ref-type="fig" rid="Ch1.F8"/>.</p></caption>
          <?xmltex \igopts{width=369.885827pt}?><graphic xlink:href="https://amt.copernicus.org/articles/12/3963/2019/amt-12-3963-2019-f11.png"/>

        </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F12" specific-use="star"><?xmltex \currentcnt{12}?><label>Figure 12</label><caption><p id="d1e3282">Relative difference of RMSE (<inline-formula><mml:math id="M172" display="inline"><mml:mi mathvariant="normal">Δ</mml:mi></mml:math></inline-formula>RMSE) with respect to radiosoundings for MLSa (teal), MLS <inline-formula><mml:math id="M173" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L1a (dark blue) and MLS <inline-formula><mml:math id="M174" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L2a (red). Same plots as in Fig. <xref ref-type="fig" rid="Ch1.F9"/>.</p></caption>
          <?xmltex \igopts{width=369.885827pt}?><graphic xlink:href="https://amt.copernicus.org/articles/12/3963/2019/amt-12-3963-2019-f12.png"/>

        </fig>

</sec>
<sec id="Ch1.S4.SS2">
  <label>4.2</label><title>Computational cost</title>
      <p id="d1e3323">The computational cost of L1 assimilation is necessarily higher than for L2 assimilation. Additional CPU time is due not only to online RTM computations but also to a higher number of iterations needed by the minimizer to converge. For a typical 24 h long simulation performed on Intel Xeon E5-2680 V3 CPU, the total CPU time is 3.9 CPU hours for<?pagebreak page3977?> L2a and 13.2 CPU hours for L1a. Note that the L2a time does not include the cost of the L1 to L2 processor but only the cost of the 3D-Var assimilation plus the model forecasts. Most of the CPU time for L1a is spent on the linearized and adjoint calls of the RTM (50 % of the total CPU time), whereas the corresponding time spent for the observation operator within the L2a experiment is about 1 %. However, the total CPU time can be significantly decreased by reducing the maximum number of iterations of the minimizer. A simulation with a halved number of iterations (75) showed very similar results to the ones that have been reported (150 iterations) and could be considered if computation time is a critical factor. Moreover, with standard high-performance computers, and thanks to the parallel nature of the observation operator and the RTM, we could obtain a speed-up of about 24 on the 24 CPU cores. This reduces the runtime of L1a to about 36 min for the 24 h long simulation versus 13 min for L2a. The extra cost of L1 assimilation therefore also seems acceptable for operational applications.</p>
</sec>
<sec id="Ch1.S4.SS3">
  <label>4.3</label><title>IASI and MLS assimilation</title>
      <p id="d1e3334">Some issues were identified in the previous section in the stratosphere, especially at tropical latitudes. Among possible reasons, one is that inversion of TIR measurements might be particularly sensitive to the vertical distribution of <inline-formula><mml:math id="M175" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> in the tropical stratosphere. We consider assimilating MLS L2 profiles in combination with IASI here to correct the model stratosphere and troposphere simultaneously, as also done in previous studies <xref ref-type="bibr" rid="bib1.bibx15 bib1.bibx46" id="paren.82"/>. When the radiances are assimilated, the RT problem is solved for the entire atmospheric column within the iterations of the variational algorithm. Therefore, enhanced and better synergies could be observed than when only L2 products are assimilated.</p>
      <p id="d1e3351">We report in Fig. <xref ref-type="fig" rid="Ch1.F11"/> the impact of assimilating MLS in combination with IASI L1 and L2 by computing the average differences between MLS <inline-formula><mml:math id="M176" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L1a and MLS <inline-formula><mml:math id="M177" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L2a. We remark that the differences in the stratosphere are highly reduced with respect to Fig. <xref ref-type="fig" rid="Ch1.F8"/>, which is expected due to the<?pagebreak page3978?> direct constraint of MLS observations. Significant differences (<inline-formula><mml:math id="M178" display="inline"><mml:mrow><mml:mo>&gt;</mml:mo><mml:mn mathvariant="normal">10</mml:mn></mml:mrow></mml:math></inline-formula> %) remain below 150 hPa, with patterns and sign similar to those in Fig. <xref ref-type="fig" rid="Ch1.F8"/>. The amplitude of the differences is, however, also slightly reduced at 300 and 500 hPa.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F13" specific-use="star"><?xmltex \currentcnt{13}?><label>Figure 13</label><caption><p id="d1e3387">Taylor diagrams of modelled tropospheric ozone columns (340–750 hPa) for the Control simulation (green), MLSa (violet), MLS <inline-formula><mml:math id="M179" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L1a (grey) and MLS <inline-formula><mml:math id="M180" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L2a (yellow) averaged globally and for five separate latitude bands. The Taylor statistics are computed against radiosoundings.</p></caption>
          <?xmltex \igopts{width=369.885827pt}?><graphic xlink:href="https://amt.copernicus.org/articles/12/3963/2019/amt-12-3963-2019-f13.png"/>

        </fig>

      <p id="d1e3411">We compared the RMSE of MLSa, MLS <inline-formula><mml:math id="M181" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L1a and MLS <inline-formula><mml:math id="M182" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L2a computed against ozonesondes (Fig. <xref ref-type="fig" rid="Ch1.F12"/>) to evaluate if the joint assimilation improves the overall <inline-formula><mml:math id="M183" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> distribution. MLSa provides particularly accurate results down to 200 or 300 hPa, depending on the latitude, with a robust reduction of the RMSE with respect to the control simulation. The only exception is in the SH mid-latitudes below 250 hPa, where the MLSa RMSE increases. We suspect that this might be linked again to the combination of strong <inline-formula><mml:math id="M184" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> gradients at the tropopause height and the negative bias of the control simulation above the tropopause (see Sect. <xref ref-type="sec" rid="Ch1.S4.SS1"/>). Overall MLSa confirms results found in past studies <xref ref-type="bibr" rid="bib1.bibx37 bib1.bibx15" id="paren.83"/> and represents much better prior information for assimilation of radiances or retrievals.</p>
      <p id="d1e3458">We remark that MLS <inline-formula><mml:math id="M185" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L1a and MLS <inline-formula><mml:math id="M186" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L2a now provide closer results in the NH and in the tropics compared to Fig. <xref ref-type="fig" rid="Ch1.F9"/>. The stratospheric <inline-formula><mml:math id="M187" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> gain is much more significant with MLS <inline-formula><mml:math id="M188" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L1a and MLS <inline-formula><mml:math id="M189" display="inline"><mml:mo>+</mml:mo></mml:math></inline-formula> L2a than with L1a and L2a and remains very close to MLSa, demonstrating that assimilating accurate stratospheric profiles remains essential for <inline-formula><mml:math id="M190" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> reanalyses. The only region where IASI further improves the UTLS profile with respect to MLSa is in the NH: a positive, albeit small, effect of assimilating IASI in combination with MLS is found between 150 and 300 hPa. On the other hand, below 300 hPa, the addition of MLS (Fig. <xref ref-type="fig" rid="Ch1.F12"/>) does not bring further improvements with respect to IASI alone (Fig. <xref ref-type="fig" rid="Ch1.F9"/>). We can conclude that MLS corrects most of the errors introduced by IASI assimilation in the stratosphere (Fig. <xref ref-type="fig" rid="Ch1.F9"/>), but no particular synergy is observed in the case of MLS and L1 assimilation in the troposphere.</p>
      <p id="d1e3520">In Fig. <xref ref-type="fig" rid="Ch1.F13"/> we report the Taylor plots concerning the free troposphere <inline-formula><mml:math id="M191" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> column (340–750 hPa), to  further evaluate the skills of the assimilation experiments in terms of variability. We examine the free troposphere here since it is where the direct impact of IASI assimilation is the largest and the impact of MLS the smallest (except for the 30–60<inline-formula><mml:math id="M192" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> S band). IASI assimilation improves the variability of the modelled <inline-formula><mml:math id="M193" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> field when looking at global averages, but this conclusion varies as a function of the latitude band. Robust and significant improvements are only found at the tropics and in the SH polar region; mixed results are obtained elsewhere. This confirms previous findings obtained with L2 assimilation <xref ref-type="bibr" rid="bib1.bibx15" id="paren.84"/> and adds the conclusion that better prior information does not necessarily solve all issues related to the assimilation of TIR measurements at mid-latitudes and high latitudes. Nevertheless, the assimilation of radiances provides slightly better results at all latitudes in general and permits more variability to be extracted from IASI spectra, especially at tropical latitudes.</p>
</sec>
</sec>
<sec id="Ch1.S5" sec-type="conclusions">
  <label>5</label><title>Conclusions</title>
      <?pagebreak page3979?><p id="d1e3569">In this study we addressed the following question: what are the differences between the direct assimilation of IASI radiances (Level 1) and the assimilation of Level 2 products for <inline-formula><mml:math id="M194" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> analyses and reanalyses? We used an experimental setup in which differences between the L2 retrieval and the L1 assimilation have been minimized as much as possible, for example by using the same RTM (RTTOV) and control vector (<inline-formula><mml:math id="M195" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> and SST) in both approaches. This allowed the impact of the <inline-formula><mml:math id="M196" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> prior information and its error covariance on the quality of the analysis to be delved into.</p>
      <p id="d1e3605">We performed twin assimilation experiments with the MOCAGE CTM and the SOFRID <inline-formula><mml:math id="M197" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> retrievals, using the same IASI ground pixels for both L1 and L2 assimilation, named L1a and L2a respectively. We compared the obtained analyses against each other and against ozonesondes and MLS profiles for the month of July 2010.</p>
      <p id="d1e3619">The results suggest that the accuracy of the <inline-formula><mml:math id="M198" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> prior information used in the L2 retrievals can influence the analysis, even when the averaging kernels are employed within the assimilation. When the <inline-formula><mml:math id="M199" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> prior information is strongly biased (at low latitudes in this study), L1a and L2a differ significantly (<inline-formula><mml:math id="M200" display="inline"><mml:mrow><mml:mo>&gt;</mml:mo><mml:mn mathvariant="normal">10</mml:mn></mml:mrow></mml:math></inline-formula> %) and the analysis shows a better variability when assimilating directly L1 radiances instead of L2 profiles. L1a and L2a are otherwise very similar at mid-latitudes and high latitudes, where the SOFRID prior information is closer to the true <inline-formula><mml:math id="M201" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> profile.</p>
      <p id="d1e3665">We conclude that particular care should be taken before assimilating satellite retrievals with prior information that can, in some circumstances, differ significantly from the local ozone profile. Computing retrievals using an a priori profile issued from a model could be relevant in improving current IASI <inline-formula><mml:math id="M202" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> L2 products and might reduce the differences between L2a and L1a observed in our study. Preliminary results with SOFRID based on a modelled a priori profile also show significant differences with the original product (Brice Barret, personal communication,  2019), with patterns similar to those presented in this study. However, when the final purpose is data assimilation, the L1 approach is more practical and statistically consistent, especially in the case that the observations need to be assimilated within the same forecast model that was used to compute L2 retrievals.</p>
      <p id="d1e3680">A positive impact has been found when assimilating MLS profiles and IASI simultaneously (either L1 or L2), which corrected stratospheric biases due to IASI assimilation alone. Differences between L1 and L2 assimilation are globally<?pagebreak page3980?> reduced by MLS in the stratosphere but remain significant (<inline-formula><mml:math id="M203" display="inline"><mml:mrow><mml:mo>&gt;</mml:mo><mml:mn mathvariant="normal">10</mml:mn></mml:mrow></mml:math></inline-formula> %) in the tropical troposphere. Also, MLS assimilation strongly improves the model's accuracy down to 200 hPa, and a clear added value of IASI assimilation (L1 or L2) can only be observed in the tropical troposphere. These results remind us that the information brought by limb sounders like MLS into the DA system remains essential to improve upper stratosphere <inline-formula><mml:math id="M204" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>. Interesting perspectives for future work are to (i) verify whether the assimilation of <inline-formula><mml:math id="M205" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> retrievals from UV spectrometers like GOME-2 or TROPOMI also shows issues related to the a priori dependence and (ii) examine if UV assimilation could replace MLS when assimilated jointly with IASI and provide similar performances in the stratosphere. This will be important to ensure the capacity to carry out accurate <inline-formula><mml:math id="M206" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula> reanalyses when the MLS instrument is phased out.</p>
      <p id="d1e3726">We reckon that L1 assimilation requires the full atmosphere to be modelled, which may not be available to some models, for example those conceived exclusively for tropospheric applications. Moreover, Level 2 products can be aggregated vertically to correct some model layers selectively and averaged spatially to fit models with coarser resolution than the satellite ground-pixel size. This cannot easily be done with radiances and should be addressed in future research.</p>
      <p id="d1e3729">In this study the observations, their error covariance and the RTM auxiliary inputs were kept almost identical between L1 and L2 assimilation on purpose. Further research is needed to address issues that are common to L1 and L2 assimilation, e.g. increased errors close to the tropopause in the NH or in the tropical stratosphere. Improvements are expected, for example, by increasing the vertical resolution of the model, including modelled aerosols within the RT or using more realistic observation error covariances. Including more modelled variables among the RTM inputs is in particular of interest in the context of the evolution towards ESMs, for which hyper-spectral sounders like IASI can provide very valuable constraints for multi-variate reanalyses (atmosphere plus surface). Including inter-channel and ground-pixel correlations in the observation error covariance matrix seems necessary to correctly weight very dense IASI observations within higher-resolution models than the one used in this study. All these aspects deserve further research.</p>
</sec>

      
      </body>
    <back><notes notes-type="dataavailability"><title>Data availability</title>

      <?pagebreak page3981?><p id="d1e3736">The input data used in this study are freely accessible through the web pages reported in the paper, if not stated differently. Access to operational ECMWF (<uri>https://www.ecmwf.int/en/forecasts/accessing-forecasts</uri>, last access: 18 July 2019) analyses and forecasts used to run the chemical transport model is subject to some particular conditions. All results are available upon request to the author.</p>
  </notes><notes notes-type="authorcontribution"><title>Author contributions</title>

      <p id="d1e3745">EE performed the numerical experiments and wrote the manuscript. BB and EF computed SOFRID retrievals used as input for some of the experiments. DC helped with the setup of the chemistry transport model.</p>
  </notes><notes notes-type="competinginterests"><title>Competing interests</title>

      <p id="d1e3751">The authors declare that they have no conflict of interest.</p>
  </notes><ack><title>Acknowledgements</title><p id="d1e3757">We acknowledge EUMETSAT for providing IASI L1C data, WOUDC for providing ozonesondes data and the NASA Jet Propulsion Laboratory for the availability of Aura MLS Level 2 <inline-formula><mml:math id="M207" display="inline"><mml:mrow class="chem"><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn mathvariant="normal">3</mml:mn></mml:msub></mml:mrow></mml:math></inline-formula>. We also thanks the MOCAGE team at Météo-France for providing the chemical transport model, the RTTOV team for the radiative transfer model and Andrea Piacentini and Gabriel Jonville for their help with technical developments of the assimilation code. This work was possible thanks to the financial support from the Région Midi-Pyrénées, who sponsored the preliminary work of Hélène Peiro on the subject, and CNES (Centre  National  d'Études Spatiales), through the TOSCA program.</p></ack><notes notes-type="reviewstatement"><title>Review statement</title>

      <p id="d1e3773">This paper was edited by Mark Weber and reviewed by two anonymous referees.</p>
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<abstract-html><p>The prior information used for Level 2 (L2) retrievals in the thermal infrared can influence the quality of the retrievals themselves and, therefore, their further assimilation in atmospheric composition models. In this study we evaluate the differences between assimilating L2 ozone profiles and Level 1 (L1) radiances from the Infrared Atmospheric Sounding Interferometer (IASI). We minimized potential differences between the two approaches by employing the same radiative transfer code (Radiative Transfer for TOVS, RTTOV) and a very similar setup for both the L2 retrievals (1D-Var) and the L1 assimilation (3D-Var). We computed hourly 3D-Var analyses assimilating L1 and L2 data in the chemical transport model MOCAGE and compared the resulting O<sub>3</sub> fields among each other and against ozonesondes. We also evaluated the joint assimilation of limb measurements from the Microwave Limb Sounder (MLS) in combination with IASI to assess the impact of stratospheric O<sub>3</sub> on tropospheric analyses. Results indicate that significant differences can arise between L2 and L1 assimilation, especially in regions where the L2 prior information is strongly biased (at low latitudes in this study). In these regions the L1 assimilation provides a better variability of the free-troposphere ozone column. L1 and L2 assimilation instead give very similar results at high latitudes, especially when MLS measurements are used to constrain the stratospheric O<sub>3</sub> column. A critical analysis of the potential benefits and drawbacks of L1 assimilation is given in the conclusions. We also list remaining issues that are common to both the L1 and L2 approaches and that deserve further research.</p></abstract-html>
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