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<!DOCTYPE html>
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<div class="csl-bib-body" style="line-height: 2; ">
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">1.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Keller, A., Nesvizhskii, A. I., Kolker, E. & Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. <i>Anal. Chem.</i> <b>74</b>, 5383–5392 (2002).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Empirical%20statistical%20model%20to%20estimate%20the%20accuracy%20of%20peptide%20identifications%20made%20by%20MS%2FMS%20and%20database%20search&rft.jtitle=Anal.%20Chem.&rft.volume=74&rft.issue=20&rft.aufirst=A.&rft.aulast=Keller&rft.au=A.%20Keller&rft.au=A.%20I.%20Nesvizhskii&rft.au=E.%20Kolker&rft.au=R.%20Aebersold&rft.date=2002-10&rft.pages=5383%E2%80%935392"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">2.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Keller, A. <i>et al.</i> Experimental protein mixture for validating tandem mass spectral analysis. <i>OMICS</i> <b>6</b>, 207–212 (2002).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Experimental%20protein%20mixture%20for%20validating%20tandem%20mass%20spectral%20analysis&rft.jtitle=OMICS&rft.volume=6&rft.issue=2&rft.aufirst=A.&rft.aulast=Keller&rft.au=A.%20Keller&rft.au=S.%20Purvine&rft.au=A.%20I.%20Nesvizhskii&rft.au=S.%20Stolyar&rft.au=D.%20R.%20Goodlett&rft.au=E.%20Kolker&rft.date=2002&rft.pages=207%E2%80%93212"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">3.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Kolker, E. <i>et al.</i> Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. <i>J. Bacteriol.</i> <b>185</b>, 4593–4602 (2003).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Initial%20proteome%20analysis%20of%20model%20microorganism%20Haemophilus%20influenzae%20strain%20Rd%20KW20&rft.jtitle=J.%20Bacteriol.&rft.volume=185&rft.issue=15&rft.aufirst=E.&rft.aulast=Kolker&rft.au=E.%20Kolker&rft.au=S.%20Purvine&rft.au=M.%20Y.%20Galperin&rft.au=S.%20Stolyar&rft.au=D.%20R.%20Goodlett&rft.au=A.%20I.%20Nesvizhskii&rft.au=A.%20Keller&rft.au=T.%20Xie&rft.au=J.%20K.%20Eng&rft.au=E.%20Yi&rft.au=L.%20Hood&rft.au=A.%20F.%20Picone&rft.au=T.%20Cherny&rft.au=B.%20C.%20Tjaden&rft.au=A.%20F.%20Siegel&rft.au=T.%20J.%20Reilly&rft.au=K.%20S.%20Makarova&rft.au=B.%20O.%20Palsson&rft.au=A.%20L.%20Smith&rft.date=2003-08&rft.pages=4593%E2%80%934602"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">4.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Nesvizhskii, A. I., Keller, A., Kolker, E. & Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry. <i>Anal. Chem.</i> <b>75</b>, 4646–4658 (2003).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=A%20statistical%20model%20for%20identifying%20proteins%20by%20tandem%20mass%20spectrometry&rft.jtitle=Anal.%20Chem.&rft.volume=75&rft.issue=17&rft.aufirst=A.%20I.&rft.aulast=Nesvizhskii&rft.au=A.%20I.%20Nesvizhskii&rft.au=A.%20Keller&rft.au=E.%20Kolker&rft.au=R.%20Aebersold&rft.date=2003-09&rft.pages=4646%E2%80%934658"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">5.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">von Haller, P. D. <i>et al.</i> The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT and tandem mass spectrometry to proteins copurifying with T cell lipid rafts. <i>Mol. Cell Proteomics</i> <b>2</b>, 426–427 (2003).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=The%20application%20of%20new%20software%20tools%20to%20quantitative%20protein%20profiling%20via%20isotope-coded%20affinity%20tag%20(ICAT)%20and%20tandem%20mass%20spectrometry%3A%20I.%20Statistically%20annotated%20datasets%20for%20peptide%20sequences%20and%20proteins%20identified%20via%20the%20application%20of%20ICAT%20and%20tandem%20mass%20spectrometry%20to%20proteins%20copurifying%20with%20T%20cell%20lipid%20rafts&rft.jtitle=Mol.%20Cell%20Proteomics&rft.volume=2&rft.issue=7&rft.aufirst=P.%20D.&rft.aulast=von%20Haller&rft.au=P.%20D.%20von%20Haller&rft.au=E.%20Yi&rft.au=S.%20Donohoe&rft.au=K.%20Vaughn&rft.au=A.%20Keller&rft.au=A.%20I.%20Nesvizhskii&rft.au=J.%20Eng&rft.au=X.%20J.%20Li&rft.au=D.%20R.%20Goodlett&rft.au=R.%20Aebersold&rft.au=J.%20D.%20Watts&rft.date=2003-07&rft.pages=426%E2%80%93427"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">6.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">von Haller, P. D. <i>et al.</i> The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the application of statistical tools for data analysis and interpretation. <i>Mol. Cell Proteomics</i> <b>2</b>, 428–442 (2003).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=The%20application%20of%20new%20software%20tools%20to%20quantitative%20protein%20profiling%20via%20isotope-coded%20affinity%20tag%20(ICAT)%20and%20tandem%20mass%20spectrometry%3A%20II.%20Evaluation%20of%20tandem%20mass%20spectrometry%20methodologies%20for%20large-scale%20protein%20analysis%2C%20and%20the%20application%20of%20statistical%20tools%20for%20data%20analysis%20and%20interpretation&rft.jtitle=Mol.%20Cell%20Proteomics&rft.volume=2&rft.issue=7&rft.aufirst=P.%20D.&rft.aulast=von%20Haller&rft.au=P.%20D.%20von%20Haller&rft.au=E.%20Yi&rft.au=S.%20Donohoe&rft.au=K.%20Vaughn&rft.au=A.%20Keller&rft.au=A.%20I.%20Nesvizhskii&rft.au=J.%20Eng&rft.au=X.%20J.%20Li&rft.au=D.%20R.%20Goodlett&rft.au=R.%20Aebersold&rft.au=J.%20D.%20Watts&rft.date=2003-07&rft.pages=428%E2%80%93442"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">7.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Carr, S. <i>et al.</i> The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. <i>Mol. Cell Proteomics</i> <b>3</b>, 531–533 (2004).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=The%20need%20for%20guidelines%20in%20publication%20of%20peptide%20and%20protein%20identification%20data%3A%20Working%20Group%20on%20Publication%20Guidelines%20for%20Peptide%20and%20Protein%20Identification%20Data&rft.jtitle=Mol.%20Cell%20Proteomics&rft.volume=3&rft.issue=6&rft.aufirst=S.&rft.aulast=Carr&rft.au=S.%20Carr&rft.au=R.%20Aebersold&rft.au=M.%20Baldwin&rft.au=A.%20Burlingame&rft.au=K.%20Clauser&rft.au=A.%20Nesvizhskii&rft.date=2004-06&rft.pages=531%E2%80%93533"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">8.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Marelli, M. <i>et al.</i> Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane. <i>J. Cell Biol.</i> <b>167</b>, 1099–1112 (2004).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Quantitative%20mass%20spectrometry%20reveals%20a%20role%20for%20the%20GTPase%20Rho1p%20in%20actin%20organization%20on%20the%20peroxisome%20membrane&rft.jtitle=J.%20Cell%20Biol.&rft.volume=167&rft.issue=6&rft.aufirst=M.&rft.aulast=Marelli&rft.au=M.%20Marelli&rft.au=J.%20J.%20Smith&rft.au=S.%20Jung&rft.au=E.%20Yi&rft.au=A.%20I.%20Nesvizhskii&rft.au=R.%20H.%20Christmas&rft.au=R.%20A.%20Saleem&rft.au=Y.%20Y.%20Tam&rft.au=A.%20Fagarasanu&rft.au=D.%20R.%20Goodlett&rft.au=R.%20Aebersold&rft.au=R.%20A.%20Rachubinski&rft.au=J.%20D.%20Aitchison&rft.date=2004-12&rft.pages=1099%E2%80%931112"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">9.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Nesvizhskii, A. I. & Aebersold, R. Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS. <i>Drug Discov. Today</i> <b>9</b>, 173–181 (2004).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Analysis%2C%20statistical%20validation%20and%20dissemination%20of%20large-scale%20proteomics%20datasets%20generated%20by%20tandem%20MS&rft.jtitle=Drug%20Discov.%20Today&rft.volume=9&rft.issue=4&rft.aufirst=A.%20I.&rft.aulast=Nesvizhskii&rft.au=A.%20I.%20Nesvizhskii&rft.au=R.%20Aebersold&rft.date=2004-02&rft.pages=173%E2%80%93181"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">10.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Wollscheid, B. <i>et al.</i> Lipid raft proteins and their identification in T lymphocytes. <i>Subcell. Biochem.</i> <b>37</b>, 121–152 (2004).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Lipid%20raft%20proteins%20and%20their%20identification%20in%20T%20lymphocytes&rft.jtitle=Subcell.%20Biochem.&rft.volume=37&rft.aufirst=B.&rft.aulast=Wollscheid&rft.au=B.%20Wollscheid&rft.au=P.%20D.%20von%20Haller&rft.au=E.%20Yi&rft.au=S.%20Donohoe&rft.au=K.%20Vaughn&rft.au=A.%20Keller&rft.au=A.%20I.%20Nesvizhskii&rft.au=J.%20Eng&rft.au=X.%20J.%20Li&rft.au=D.%20R.%20Goodlett&rft.au=R.%20Aebersold&rft.au=J.%20D.%20Watts&rft.date=2004&rft.pages=121%E2%80%93152"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">11.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Desiere, F. <i>et al.</i> Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. <i>Genome Biol.</i> <b>6</b>, R9 (2005).</div>
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<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Integration%20with%20the%20human%20genome%20of%20peptide%20sequences%20obtained%20by%20high-throughput%20mass%20spectrometry&rft.jtitle=Genome%20Biol.&rft.volume=6&rft.issue=1&rft.aufirst=F.&rft.aulast=Desiere&rft.au=F.%20Desiere&rft.au=E.%20W.%20Deutsch&rft.au=A.%20I.%20Nesvizhskii&rft.au=P.%20Mallick&rft.au=N.%20L.%20King&rft.au=J.%20K.%20Eng&rft.au=A.%20Aderem&rft.au=R.%20Boyle&rft.au=E.%20Brunner&rft.au=S.%20Donohoe&rft.au=N.%20Fausto&rft.au=E.%20Hafen&rft.au=L.%20Hood&rft.au=M.%20G.%20Katze&rft.au=K.%20A.%20Kennedy&rft.au=F.%20Kregenow&rft.au=H.%20Lee&rft.au=B.%20Lin&rft.au=D.%20Martin&rft.au=J.%20A.%20Ranish&rft.au=D.%20J.%20Rawlings&rft.au=L.%20E.%20Samelson&rft.au=Y.%20Shiio&rft.au=J.%20D.%20Watts&rft.au=B.%20Wollscheid&rft.au=M.%20E.%20Wright&rft.au=W.%20Yan&rft.au=L.%20Yang&rft.au=E.%20C.%20Yi&rft.au=H.%20Zhang&rft.au=R.%20Aebersold&rft.date=2005&rft.pages=R9"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">12.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Deutsch, E. W. <i>et al.</i> Human Plasma PeptideAtlas. <i>Proteomics</i> <b>5</b>, 3497–3500 (2005).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Human%20Plasma%20PeptideAtlas&rft.jtitle=Proteomics&rft.volume=5&rft.issue=13&rft.aufirst=E.%20W.&rft.aulast=Deutsch&rft.au=E.%20W.%20Deutsch&rft.au=J.%20K.%20Eng&rft.au=H.%20Zhang&rft.au=N.%20L.%20King&rft.au=A.%20I.%20Nesvizhskii&rft.au=B.%20Lin&rft.au=H.%20Lee&rft.au=E.%20C.%20Yi&rft.au=R.%20Ossola&rft.au=R.%20Aebersold&rft.date=2005-08&rft.pages=3497%E2%80%933500"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">13.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Martens, L. <i>et al.</i> Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories. <i>Proteomics</i> <b>5</b>, 3501–3505 (2005).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Do%20we%20want%20our%20data%20raw%3F%20Including%20binary%20mass%20spectrometry%20data%20in%20public%20proteomics%20data%20repositories&rft.jtitle=Proteomics&rft.volume=5&rft.issue=13&rft.aufirst=L.&rft.aulast=Martens&rft.au=L.%20Martens&rft.au=A.%20I.%20Nesvizhskii&rft.au=H.%20Hermjakob&rft.au=M.%20Adamski&rft.au=G.%20S.%20Omenn&rft.au=J.%20Vandekerckhove&rft.au=K.%20Gevaert&rft.date=2005-08&rft.pages=3501%E2%80%933505"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">14.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Martin, D. B., Eng, J. K., Nesvizhskii, A. I., Gemmill, A. & Aebersold, R. Investigation of neutral loss during collision-induced dissociation of peptide ions. <i>Anal. Chem.</i> <b>77</b>, 4870–4882 (2005).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Investigation%20of%20neutral%20loss%20during%20collision-induced%20dissociation%20of%20peptide%20ions&rft.jtitle=Anal.%20Chem.&rft.volume=77&rft.issue=15&rft.aufirst=D.%20B.&rft.aulast=Martin&rft.au=D.%20B.%20Martin&rft.au=J.%20K.%20Eng&rft.au=A.%20I.%20Nesvizhskii&rft.au=A.%20Gemmill&rft.au=R.%20Aebersold&rft.date=2005-08&rft.pages=4870%E2%80%934882"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">15.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Nesvizhskii, A. I. & Aebersold, R. Interpretation of shotgun proteomic data: the protein inference problem. <i>Mol. Cell Proteomics</i> <b>4</b>, 1419–1440 (2005).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Interpretation%20of%20shotgun%20proteomic%20data%3A%20the%20protein%20inference%20problem&rft.jtitle=Mol.%20Cell%20Proteomics&rft.volume=4&rft.issue=10&rft.aufirst=A.%20I.&rft.aulast=Nesvizhskii&rft.au=A.%20I.%20Nesvizhskii&rft.au=R.%20Aebersold&rft.date=2005-10&rft.pages=1419%E2%80%931440"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">16.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Desiere, F. <i>et al.</i> The PeptideAtlas project. <i>Nucleic Acids Res.</i> <b>34</b>, D655–658 (2006).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=The%20PeptideAtlas%20project&rft.jtitle=Nucleic%20Acids%20Res.&rft.volume=34&rft.issue=Database%20issue&rft.aufirst=F.&rft.aulast=Desiere&rft.au=F.%20Desiere&rft.au=E.%20W.%20Deutsch&rft.au=N.%20L.%20King&rft.au=A.%20I.%20Nesvizhskii&rft.au=P.%20Mallick&rft.au=J.%20Eng&rft.au=S.%20Chen&rft.au=J.%20Eddes&rft.au=S.%20N.%20Loevenich&rft.au=R.%20Aebersold&rft.date=2006-01&rft.pages=D655%E2%80%93658"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">17.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">King, N. L. <i>et al.</i> Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. <i>Genome Biol.</i> <b>7</b>, R106 (2006).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Analysis%20of%20the%20Saccharomyces%20cerevisiae%20proteome%20with%20PeptideAtlas&rft.jtitle=Genome%20Biol.&rft.volume=7&rft.issue=11&rft.aufirst=N.%20L.&rft.aulast=King&rft.au=N.%20L.%20King&rft.au=E.%20W.%20Deutsch&rft.au=J.%20A.%20Ranish&rft.au=A.%20I.%20Nesvizhskii&rft.au=J.%20S.%20Eddes&rft.au=P.%20Mallick&rft.au=J.%20Eng&rft.au=F.%20Desiere&rft.au=M.%20Flory&rft.au=D.%20B.%20Martin&rft.au=B.%20Kim&rft.au=H.%20Lee&rft.au=B.%20Raught&rft.au=R.%20Aebersold&rft.date=2006&rft.pages=R106"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">18.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Malmstrom, J. <i>et al.</i> Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis. <i>J. Proteome Res.</i> <b>5</b>, 2241–2249 (2006).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Optimized%20peptide%20separation%20and%20identification%20for%20mass%20spectrometry%20based%20proteomics%20via%20free-flow%20electrophoresis&rft.jtitle=J.%20Proteome%20Res.&rft.volume=5&rft.issue=9&rft.aufirst=J.&rft.aulast=Malmstrom&rft.au=J.%20Malmstrom&rft.au=H.%20Lee&rft.au=A.%20I.%20Nesvizhskii&rft.au=D.%20Shteynberg&rft.au=S.%20Mohanty&rft.au=E.%20Brunner&rft.au=M.%20Ye&rft.au=G.%20Weber&rft.au=C.%20Eckerskorn&rft.au=R.%20Aebersold&rft.date=2006-09&rft.pages=2241%E2%80%932249"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">19.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Nesvizhskii, A. I. <i>et al.</i> Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. <i>Mol. Cell Proteomics</i> <b>5</b>, 652–670 (2006).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Dynamic%20spectrum%20quality%20assessment%20and%20iterative%20computational%20analysis%20of%20shotgun%20proteomic%20data%3A%20toward%20more%20efficient%20identification%20of%20post-translational%20modifications%2C%20sequence%20polymorphisms%2C%20and%20novel%20peptides&rft.jtitle=Mol.%20Cell%20Proteomics&rft.volume=5&rft.issue=4&rft.aufirst=A.%20I.&rft.aulast=Nesvizhskii&rft.au=A.%20I.%20Nesvizhskii&rft.au=F.%20F.%20Roos&rft.au=J.%20Grossmann&rft.au=M.%20Vogelzang&rft.au=J.%20S.%20Eddes&rft.au=W.%20Gruissem&rft.au=S.%20Baginsky&rft.au=R.%20Aebersold&rft.date=2006-04&rft.pages=652%E2%80%93670"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">20.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Kim, B. <i>et al.</i> The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes. <i>Proc. Natl. Acad. Sci. U.S.A.</i> <b>104</b>, 16068–16073 (2007).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=The%20transcription%20elongation%20factor%20TFIIS%20is%20a%20component%20of%20RNA%20polymerase%20II%20preinitiation%20complexes&rft.jtitle=Proc.%20Natl.%20Acad.%20Sci.%20U.S.A.&rft.volume=104&rft.issue=41&rft.aufirst=B.&rft.aulast=Kim&rft.au=B.%20Kim&rft.au=A.%20I.%20Nesvizhskii&rft.au=P.%20G.%20Rani&rft.au=S.%20Hahn&rft.au=R.%20Aebersold&rft.au=J.%20A.%20Ranish&rft.date=2007-10&rft.pages=16068%E2%80%9316073"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">21.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Mueller, D. <i>et al.</i> A role for the MLL fusion partner ENL in transcriptional elongation and chromatin modification. <i>Blood</i> <b>110</b>, 4445–4454 (2007).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=A%20role%20for%20the%20MLL%20fusion%20partner%20ENL%20in%20transcriptional%20elongation%20and%20chromatin%20modification&rft.jtitle=Blood&rft.volume=110&rft.issue=13&rft.aufirst=D.&rft.aulast=Mueller&rft.au=D.%20Mueller&rft.au=C.%20Bach&rft.au=D.%20Zeisig&rft.au=M.%20P.%20Garcia-Cuellar&rft.au=S.%20Monroe&rft.au=A.%20Sreekumar&rft.au=R.%20Zhou&rft.au=A.%20Nesvizhskii&rft.au=A.%20Chinnaiyan&rft.au=J.%20L.%20Hess&rft.au=R.%20K.%20Slany&rft.date=2007-12&rft.pages=4445%E2%80%934454"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">22.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Nesvizhskii, A. I. Protein identification by tandem mass spectrometry and sequence database searching. <i>Methods Mol. Biol.</i> <b>367</b>, 87–119 (2007).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Protein%20identification%20by%20tandem%20mass%20spectrometry%20and%20sequence%20database%20searching&rft.jtitle=Methods%20Mol.%20Biol.&rft.volume=367&rft.aufirst=A.%20I.&rft.aulast=Nesvizhskii&rft.au=A.%20I.%20Nesvizhskii&rft.date=2007&rft.pages=87%E2%80%93119"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">23.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Nesvizhskii, A. I., Vitek, O. & Aebersold, R. Analysis and validation of proteomic data generated by tandem mass spectrometry. <i>Nat. Methods</i> <b>4</b>, 787–797 (2007).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Analysis%20and%20validation%20of%20proteomic%20data%20generated%20by%20tandem%20mass%20spectrometry&rft.jtitle=Nat.%20Methods&rft.volume=4&rft.issue=10&rft.aufirst=A.%20I.&rft.aulast=Nesvizhskii&rft.au=A.%20I.%20Nesvizhskii&rft.au=O.%20Vitek&rft.au=R.%20Aebersold&rft.date=2007-10&rft.pages=787%E2%80%93797"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">24.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Yoo, C. <i>et al.</i> Comprehensive analysis of proteins of pH fractionated samples using monolithic LC/MS/MS, intact MW measurement and MALDI-QIT-TOF MS. <i>J Mass Spectrom</i> <b>42</b>, 312–334 (2007).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Comprehensive%20analysis%20of%20proteins%20of%20pH%20fractionated%20samples%20using%20monolithic%20LC%2FMS%2FMS%2C%20intact%20MW%20measurement%20and%20MALDI-QIT-TOF%20MS&rft.jtitle=J%20Mass%20Spectrom&rft.volume=42&rft.issue=3&rft.aufirst=C.&rft.aulast=Yoo&rft.au=C.%20Yoo&rft.au=T.%20H.%20Patwa&rft.au=P.%20Kreunin&rft.au=F.%20R.%20Miller&rft.au=C.%20G.%20Huber&rft.au=A.%20I.%20Nesvizhskii&rft.au=D.%20M.%20Lubman&rft.date=2007-03&rft.pages=312%E2%80%93334"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">25.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Cao, X. & Nesvizhskii, A. I. Improved sequence tag generation method for peptide identification in tandem mass spectrometry. <i>J. Proteome Res.</i> <b>7</b>, 4422–4434 (2008).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Improved%20sequence%20tag%20generation%20method%20for%20peptide%20identification%20in%20tandem%20mass%20spectrometry&rft.jtitle=J.%20Proteome%20Res.&rft.volume=7&rft.issue=10&rft.aufirst=X.&rft.aulast=Cao&rft.au=X.%20Cao&rft.au=A.%20I.%20Nesvizhskii&rft.date=2008-10&rft.pages=4422%E2%80%934434"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">26.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Choi, H., Fermin, D. & Nesvizhskii, A. I. Significance analysis of spectral count data in label-free shotgun proteomics. <i>Mol. Cell Proteomics</i> <b>7</b>, 2373–2385 (2008).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Significance%20analysis%20of%20spectral%20count%20data%20in%20label-free%20shotgun%20proteomics&rft.jtitle=Mol.%20Cell%20Proteomics&rft.volume=7&rft.issue=12&rft.aufirst=H.&rft.aulast=Choi&rft.au=H.%20Choi&rft.au=D.%20Fermin&rft.au=A.%20I.%20Nesvizhskii&rft.date=2008-12&rft.pages=2373%E2%80%932385"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">27.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Choi, H., Ghosh, D. & Nesvizhskii, A. I. Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. <i>J. Proteome Res.</i> <b>7</b>, 286–292 (2008).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Statistical%20validation%20of%20peptide%20identifications%20in%20large-scale%20proteomics%20using%20the%20target-decoy%20database%20search%20strategy%20and%20flexible%20mixture%20modeling&rft.jtitle=J.%20Proteome%20Res.&rft.volume=7&rft.issue=1&rft.aufirst=H.&rft.aulast=Choi&rft.au=H.%20Choi&rft.au=D.%20Ghosh&rft.au=A.%20I.%20Nesvizhskii&rft.date=2008-01&rft.pages=286%E2%80%93292"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">28.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Choi, H. & Nesvizhskii, A. I. False discovery rates and related statistical concepts in mass spectrometry-based proteomics. <i>J. Proteome Res.</i> <b>7</b>, 47–50 (2008).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=False%20discovery%20rates%20and%20related%20statistical%20concepts%20in%20mass%20spectrometry-based%20proteomics&rft.jtitle=J.%20Proteome%20Res.&rft.volume=7&rft.issue=1&rft.aufirst=H.&rft.aulast=Choi&rft.au=H.%20Choi&rft.au=A.%20I.%20Nesvizhskii&rft.date=2008-01&rft.pages=47%E2%80%9350"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">29.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Choi, H. & Nesvizhskii, A. I. Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics. <i>J. Proteome Res.</i> <b>7</b>, 254–265 (2008).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Semisupervised%20model-based%20validation%20of%20peptide%20identifications%20in%20mass%20spectrometry-based%20proteomics&rft.jtitle=J.%20Proteome%20Res.&rft.volume=7&rft.issue=1&rft.aufirst=H.&rft.aulast=Choi&rft.au=H.%20Choi&rft.au=A.%20I.%20Nesvizhskii&rft.date=2008-01&rft.pages=254%E2%80%93265"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">30.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Ding, Y., Choi, H. & Nesvizhskii, A. I. Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics. <i>J. Proteome Res.</i> <b>7</b>, 4878–4889 (2008).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Adaptive%20discriminant%20function%20analysis%20and%20reranking%20of%20MS%2FMS%20database%20search%20results%20for%20improved%20peptide%20identification%20in%20shotgun%20proteomics&rft.jtitle=J.%20Proteome%20Res.&rft.volume=7&rft.issue=11&rft.aufirst=Y.&rft.aulast=Ding&rft.au=Y.%20Ding&rft.au=H.%20Choi&rft.au=A.%20I.%20Nesvizhskii&rft.date=2008-11&rft.pages=4878%E2%80%934889"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">31.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Marelli, M., Nesvizhskii, A. I. & Aitchison, J. D. Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions : an example in peroxisomes. <i>Methods Mol. Biol.</i> <b>432</b>, 357–371 (2008).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Identifying%20bona%20fide%20components%20of%20an%20organelle%20by%20isotope-coded%20labeling%20of%20subcellular%20fractions%20%3A%20an%20example%20in%20peroxisomes&rft.jtitle=Methods%20Mol.%20Biol.&rft.volume=432&rft.aufirst=M.&rft.aulast=Marelli&rft.au=M.%20Marelli&rft.au=A.%20I.%20Nesvizhskii&rft.au=J.%20D.%20Aitchison&rft.date=2008&rft.pages=357%E2%80%93371"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">32.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Searle, B. C., Turner, M. & Nesvizhskii, A. I. Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies. <i>J. Proteome Res.</i> <b>7</b>, 245–253 (2008).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Improving%20sensitivity%20by%20probabilistically%20combining%20results%20from%20multiple%20MS%2FMS%20search%20methodologies&rft.jtitle=J.%20Proteome%20Res.&rft.volume=7&rft.issue=1&rft.aufirst=B.%20C.&rft.aulast=Searle&rft.au=B.%20C.%20Searle&rft.au=M.%20Turner&rft.au=A.%20I.%20Nesvizhskii&rft.date=2008-01&rft.pages=245%E2%80%93253"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">33.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Taylor, B. S. <i>et al.</i> Humoral response profiling reveals pathways to prostate cancer progression. <i>Mol. Cell Proteomics</i> <b>7</b>, 600–611 (2008).</div>
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<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Humoral%20response%20profiling%20reveals%20pathways%20to%20prostate%20cancer%20progression&rft.jtitle=Mol.%20Cell%20Proteomics&rft.volume=7&rft.issue=3&rft.aufirst=B.%20S.&rft.aulast=Taylor&rft.au=B.%20S.%20Taylor&rft.au=M.%20Pal&rft.au=J.%20Yu&rft.au=B.%20Laxman&rft.au=S.%20Kalyana-Sundaram&rft.au=R.%20Zhao&rft.au=A.%20Menon&rft.au=J.%20T.%20Wei&rft.au=A.%20I.%20Nesvizhskii&rft.au=D.%20Ghosh&rft.au=G.%20S.%20Omenn&rft.au=D.%20M.%20Lubman&rft.au=A.%20M.%20Chinnaiyan&rft.au=A.%20Sreekumar&rft.date=2008-03&rft.pages=600%E2%80%93611"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">34.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Ulintz, P. J., Bodenmiller, B., Andrews, P. C., Aebersold, R. & Nesvizhskii, A. I. Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence. <i>Mol. Cell Proteomics</i> <b>7</b>, 71–87 (2008).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Investigating%20MS2%2FMS3%20matching%20statistics%3A%20a%20model%20for%20coupling%20consecutive%20stage%20mass%20spectrometry%20data%20for%20increased%20peptide%20identification%20confidence&rft.jtitle=Mol.%20Cell%20Proteomics&rft.volume=7&rft.issue=1&rft.aufirst=P.%20J.&rft.aulast=Ulintz&rft.au=P.%20J.%20Ulintz&rft.au=B.%20Bodenmiller&rft.au=P.%20C.%20Andrews&rft.au=R.%20Aebersold&rft.au=A.%20I.%20Nesvizhskii&rft.date=2008-01&rft.pages=71%E2%80%9387"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">35.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Choi, H., Nesvizhskii, A. I., Ghosh, D. & Qin, Z. S. Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data. <i>Bioinformatics</i> <b>25</b>, 1715–1721 (2009).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Hierarchical%20hidden%20Markov%20model%20with%20application%20to%20joint%20analysis%20of%20ChIP-chip%20and%20ChIP-seq%20data&rft.jtitle=Bioinformatics&rft.volume=25&rft.issue=14&rft.aufirst=H.&rft.aulast=Choi&rft.au=H.%20Choi&rft.au=A.%20I.%20Nesvizhskii&rft.au=D.%20Ghosh&rft.au=Z.%20S.%20Qin&rft.date=2009-07&rft.pages=1715%E2%80%931721"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">36.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Goudreault, M. <i>et al.</i> A PP2A phosphatase high density interaction network identifies a novel striatin-interacting phosphatase and kinase complex linked to the cerebral cavernous malformation 3 (CCM3) protein. <i>Mol. Cell Proteomics</i> <b>8</b>, 157–171 (2009).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=A%20PP2A%20phosphatase%20high%20density%20interaction%20network%20identifies%20a%20novel%20striatin-interacting%20phosphatase%20and%20kinase%20complex%20linked%20to%20the%20cerebral%20cavernous%20malformation%203%20(CCM3)%20protein&rft.jtitle=Mol.%20Cell%20Proteomics&rft.volume=8&rft.issue=1&rft.aufirst=M.&rft.aulast=Goudreault&rft.au=M.%20Goudreault&rft.au=L.%20M.%20D'Ambrosio&rft.au=M.%20J.%20Kean&rft.au=M.%20J.%20Mullin&rft.au=B.%20G.%20Larsen&rft.au=A.%20Sanchez&rft.au=S.%20Chaudhry&rft.au=G.%20I.%20Chen&rft.au=F.%20Sicheri&rft.au=A.%20I.%20Nesvizhskii&rft.au=R.%20Aebersold&rft.au=B.%20Raught&rft.au=A.%20C.%20Gingras&rft.date=2009-01&rft.pages=157%E2%80%93171"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">37.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Ho, L. <i>et al.</i> An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. <i>Proc. Natl. Acad. Sci. U.S.A.</i> <b>106</b>, 5181–5186 (2009).</div>
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<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=An%20embryonic%20stem%20cell%20chromatin%20remodeling%20complex%2C%20esBAF%2C%20is%20essential%20for%20embryonic%20stem%20cell%20self-renewal%20and%20pluripotency&rft.jtitle=Proc.%20Natl.%20Acad.%20Sci.%20U.S.A.&rft.volume=106&rft.issue=13&rft.aufirst=L.&rft.aulast=Ho&rft.au=L.%20Ho&rft.au=J.%20L.%20Ronan&rft.au=J.%20Wu&rft.au=B.%20T.%20Staahl&rft.au=L.%20Chen&rft.au=A.%20Kuo&rft.au=J.%20Lessard&rft.au=A.%20I.%20Nesvizhskii&rft.au=J.%20Ranish&rft.au=G.%20R.%20Crabtree&rft.date=2009-03&rft.pages=5181%E2%80%935186"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">38.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Rodriguez, H. <i>et al.</i> Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. <i>J. Proteome Res.</i> <b>8</b>, 3689–3692 (2009).</div>
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<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">39.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Ulintz, P. J. <i>et al.</i> Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification. <i>J. Proteome Res.</i> <b>8</b>, 887–899 (2009).</div>
</div>
<span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rfr_id=info%3Asid%2Fzotero.org%3A2&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Comparison%20of%20MS(2)-only%2C%20MSA%2C%20and%20MS(2)%2FMS(3)%20methodologies%20for%20phosphopeptide%20identification&rft.jtitle=J.%20Proteome%20Res.&rft.volume=8&rft.issue=2&rft.aufirst=P.%20J.&rft.aulast=Ulintz&rft.au=P.%20J.%20Ulintz&rft.au=A.%20K.%20Yocum&rft.au=B.%20Bodenmiller&rft.au=R.%20Aebersold&rft.au=P.%20C.%20Andrews&rft.au=A.%20I.%20Nesvizhskii&rft.date=2009-02&rft.pages=887%E2%80%93899"></span>
<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">40.</div>
<div class="csl-right-inline" style="margin: 0 .4em 0 2.5em;">Vellaichamy, A. <i>et al.</i> Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases. <i>PLoS ONE</i> <b>4</b>, e7075 (2009).</div>
</div>
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<div class="csl-entry" style="clear: left; ">
<div class="csl-left-margin" style="float: left; padding-right: 0.5em;text-align: right; width: 2em;">41.</div>
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