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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Panorama: A Targeted Proteomics
Knowledge Base</title><author><name sortKey="Sharma, Vagisha" sort="Sharma, Vagisha" uniqKey="Sharma V" first="Vagisha" last="Sharma">Vagisha Sharma</name><affiliation><nlm:aff id="aff1"><institution>University of Washington</institution>, Seattle, Washington 98195,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Eckels, Josh" sort="Eckels, Josh" uniqKey="Eckels J" first="Josh" last="Eckels">Josh Eckels</name><affiliation><nlm:aff id="aff2"><institution>LabKey Software</institution>, San Diego, California 92101,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Taylor, Greg K" sort="Taylor, Greg K" uniqKey="Taylor G" first="Greg K." last="Taylor">Greg K. Taylor</name><affiliation><nlm:aff id="aff2"><institution>LabKey Software</institution>, San Diego, California 92101,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Shulman, Nicholas X0a J" sort="Shulman, Nicholas X0a J" uniqKey="Shulman N" first="Nicholas X0a J." last="Shulman">Nicholas X0a J. Shulman</name><affiliation><nlm:aff id="aff1"><institution>University of Washington</institution>, Seattle, Washington 98195,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Stergachis, Andrew B" sort="Stergachis, Andrew B" uniqKey="Stergachis A" first="Andrew B." last="Stergachis">Andrew B. Stergachis</name><affiliation><nlm:aff id="aff1"><institution>University of Washington</institution>, Seattle, Washington 98195,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Joyner, Shannon A" sort="Joyner, Shannon A" uniqKey="Joyner S" first="Shannon A." last="Joyner">Shannon A. Joyner</name><affiliation><nlm:aff id="aff3"><institution>Carnegie Melon University</institution>, Pittsburgh, Pennsylvania 15213,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Yan, Ping" sort="Yan, Ping" uniqKey="Yan P" first="Ping" last="Yan">Ping Yan</name><affiliation><nlm:aff id="aff4"><institution>Fred Hutchinson Cancer Research Center</institution>, Seattle, Washington 98109,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Whiteaker, Jeffrey R" sort="Whiteaker, Jeffrey R" uniqKey="Whiteaker J" first="Jeffrey R." last="Whiteaker">Jeffrey R. Whiteaker</name><affiliation><nlm:aff id="aff4"><institution>Fred Hutchinson Cancer Research Center</institution>, Seattle, Washington 98109,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Halusa, Goran N" sort="Halusa, Goran N" uniqKey="Halusa G" first="Goran N." last="Halusa">Goran N. Halusa</name><affiliation><nlm:aff id="aff5"><institution>Leidos Biomedical Research, Inc.</institution>, Frederick, Maryland 21702,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Schilling, Birgit" sort="Schilling, Birgit" uniqKey="Schilling B" first="Birgit" last="Schilling">Birgit Schilling</name><affiliation><nlm:aff id="aff6"><institution>Buck Institute for Research on Aging</institution>, Novato, California 94945,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Gibson, Bradford W" sort="Gibson, Bradford W" uniqKey="Gibson B" first="Bradford W." last="Gibson">Bradford W. Gibson</name><affiliation><nlm:aff id="aff6"><institution>Buck Institute for Research on Aging</institution>, Novato, California 94945,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Colangelo, Christopher M" sort="Colangelo, Christopher M" uniqKey="Colangelo C" first="Christopher M." last="Colangelo">Christopher M. Colangelo</name><affiliation><nlm:aff id="aff7"><institution>Yale University</institution>, New Haven, Connecticut 06520,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Paulovich, Amanda G" sort="Paulovich, Amanda G" uniqKey="Paulovich A" first="Amanda G." last="Paulovich">Amanda G. Paulovich</name><affiliation><nlm:aff id="aff4"><institution>Fred Hutchinson Cancer Research Center</institution>, Seattle, Washington 98109,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Carr, Steven X0a A" sort="Carr, Steven X0a A" uniqKey="Carr S" first="Steven X0a A." last="Carr">Steven X0a A. Carr</name><affiliation><nlm:aff id="aff8"><institution>The Broad Institute</institution>, Cambridge, Massachusetts 02142,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Jaffe, Jacob D" sort="Jaffe, Jacob D" uniqKey="Jaffe J" first="Jacob D." last="Jaffe">Jacob D. Jaffe</name><affiliation><nlm:aff id="aff8"><institution>The Broad Institute</institution>, Cambridge, Massachusetts 02142,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Maccoss, Michael J" sort="Maccoss, Michael J" uniqKey="Maccoss M" first="Michael J." last="Maccoss">Michael J. Maccoss</name><affiliation><nlm:aff id="aff1"><institution>University of Washington</institution>, Seattle, Washington 98195,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Maclean, Brendan" sort="Maclean, Brendan" uniqKey="Maclean B" first="Brendan" last="Maclean">Brendan Maclean</name><affiliation><nlm:aff id="aff1"><institution>University of Washington</institution>, Seattle, Washington 98195,<country>United States</country></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25102069</idno><idno type="pmc">4156235</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156235</idno><idno type="RBID">PMC:4156235</idno><idno type="doi">10.1021/pr5006636</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000280</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000280</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Panorama: A Targeted Proteomics
Knowledge Base</title><author><name sortKey="Sharma, Vagisha" sort="Sharma, Vagisha" uniqKey="Sharma V" first="Vagisha" last="Sharma">Vagisha Sharma</name><affiliation><nlm:aff id="aff1"><institution>University of Washington</institution>, Seattle, Washington 98195,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Eckels, Josh" sort="Eckels, Josh" uniqKey="Eckels J" first="Josh" last="Eckels">Josh Eckels</name><affiliation><nlm:aff id="aff2"><institution>LabKey Software</institution>, San Diego, California 92101,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Taylor, Greg K" sort="Taylor, Greg K" uniqKey="Taylor G" first="Greg K." last="Taylor">Greg K. Taylor</name><affiliation><nlm:aff id="aff2"><institution>LabKey Software</institution>, San Diego, California 92101,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Shulman, Nicholas X0a J" sort="Shulman, Nicholas X0a J" uniqKey="Shulman N" first="Nicholas X0a J." last="Shulman">Nicholas X0a J. Shulman</name><affiliation><nlm:aff id="aff1"><institution>University of Washington</institution>, Seattle, Washington 98195,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Stergachis, Andrew B" sort="Stergachis, Andrew B" uniqKey="Stergachis A" first="Andrew B." last="Stergachis">Andrew B. Stergachis</name><affiliation><nlm:aff id="aff1"><institution>University of Washington</institution>, Seattle, Washington 98195,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Joyner, Shannon A" sort="Joyner, Shannon A" uniqKey="Joyner S" first="Shannon A." last="Joyner">Shannon A. Joyner</name><affiliation><nlm:aff id="aff3"><institution>Carnegie Melon University</institution>, Pittsburgh, Pennsylvania 15213,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Yan, Ping" sort="Yan, Ping" uniqKey="Yan P" first="Ping" last="Yan">Ping Yan</name><affiliation><nlm:aff id="aff4"><institution>Fred Hutchinson Cancer Research Center</institution>, Seattle, Washington 98109,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Whiteaker, Jeffrey R" sort="Whiteaker, Jeffrey R" uniqKey="Whiteaker J" first="Jeffrey R." last="Whiteaker">Jeffrey R. Whiteaker</name><affiliation><nlm:aff id="aff4"><institution>Fred Hutchinson Cancer Research Center</institution>, Seattle, Washington 98109,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Halusa, Goran N" sort="Halusa, Goran N" uniqKey="Halusa G" first="Goran N." last="Halusa">Goran N. Halusa</name><affiliation><nlm:aff id="aff5"><institution>Leidos Biomedical Research, Inc.</institution>, Frederick, Maryland 21702,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Schilling, Birgit" sort="Schilling, Birgit" uniqKey="Schilling B" first="Birgit" last="Schilling">Birgit Schilling</name><affiliation><nlm:aff id="aff6"><institution>Buck Institute for Research on Aging</institution>, Novato, California 94945,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Gibson, Bradford W" sort="Gibson, Bradford W" uniqKey="Gibson B" first="Bradford W." last="Gibson">Bradford W. Gibson</name><affiliation><nlm:aff id="aff6"><institution>Buck Institute for Research on Aging</institution>, Novato, California 94945,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Colangelo, Christopher M" sort="Colangelo, Christopher M" uniqKey="Colangelo C" first="Christopher M." last="Colangelo">Christopher M. Colangelo</name><affiliation><nlm:aff id="aff7"><institution>Yale University</institution>, New Haven, Connecticut 06520,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Paulovich, Amanda G" sort="Paulovich, Amanda G" uniqKey="Paulovich A" first="Amanda G." last="Paulovich">Amanda G. Paulovich</name><affiliation><nlm:aff id="aff4"><institution>Fred Hutchinson Cancer Research Center</institution>, Seattle, Washington 98109,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Carr, Steven X0a A" sort="Carr, Steven X0a A" uniqKey="Carr S" first="Steven X0a A." last="Carr">Steven X0a A. Carr</name><affiliation><nlm:aff id="aff8"><institution>The Broad Institute</institution>, Cambridge, Massachusetts 02142,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Jaffe, Jacob D" sort="Jaffe, Jacob D" uniqKey="Jaffe J" first="Jacob D." last="Jaffe">Jacob D. Jaffe</name><affiliation><nlm:aff id="aff8"><institution>The Broad Institute</institution>, Cambridge, Massachusetts 02142,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Maccoss, Michael J" sort="Maccoss, Michael J" uniqKey="Maccoss M" first="Michael J." last="Maccoss">Michael J. Maccoss</name><affiliation><nlm:aff id="aff1"><institution>University of Washington</institution>, Seattle, Washington 98195,<country>United States</country></nlm:aff></affiliation></author><author><name sortKey="Maclean, Brendan" sort="Maclean, Brendan" uniqKey="Maclean B" first="Brendan" last="Maclean">Brendan Maclean</name><affiliation><nlm:aff id="aff1"><institution>University of Washington</institution>, Seattle, Washington 98195,<country>United States</country></nlm:aff></affiliation></author></analytic><series><title level="j">Journal of Proteome Research</title><idno type="ISSN">1535-3893</idno><idno type="eISSN">1535-3907</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p content-type="toc-graphic"><graphic xlink:href="pr-2014-006636_0004" id="ab-tgr1"></graphic></p><p>Panorama
is a web application for storing, sharing, analyzing,
and reusing targeted assays created and refined with Skyline,1 an increasingly popular Windows client software
tool for targeted proteomics experiments. Panorama allows laboratories
to store and organize curated results contained in Skyline documents
with fine-grained permissions, which facilitates distributed collaboration
and secure sharing of published and unpublished data via a web-browser
interface. It is fully integrated with the Skyline workflow and supports
publishing a document directly to a Panorama server from the Skyline
user interface. Panorama captures the complete Skyline document information
content in a relational database schema. Curated results published
to Panorama can be aggregated and exported as chromatogram libraries.
These libraries can be used in Skyline to pick optimal targets in
new experiments and to validate peak identification of target peptides.
Panorama is open-source and freely available. It is distributed as
part of LabKey Server,2 an open source
biomedical research data management system. Laboratories and organizations
can set up Panorama locally by downloading and installing the software
on their own servers. They can also request freely hosted projects
on <uri xlink:href="https://panoramaweb.org">https://panoramaweb.org</uri>, a Panorama server maintained
by the Department of Genome Sciences at the University of Washington.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Maclean, B" uniqKey="Maclean B">B. MacLean</name></author><author><name sortKey="Tomazela, D M" uniqKey="Tomazela D">D. M. Tomazela</name></author><author><name sortKey="Shulman, N" uniqKey="Shulman N">N. Shulman</name></author><author><name sortKey="Chambers, M" uniqKey="Chambers M">M. Chambers</name></author><author><name sortKey="Finney, G L" uniqKey="Finney G">G. L. Finney</name></author><author><name sortKey="Frewen, B" uniqKey="Frewen B">B. Frewen</name></author><author><name sortKey="Kern, R" uniqKey="Kern R">R. Kern</name></author><author><name sortKey="Tabb, D L" uniqKey="Tabb D">D. L. Tabb</name></author><author><name sortKey="Liebler, D C" uniqKey="Liebler D">D. C. Liebler</name></author><author><name sortKey="Maccoss, M J" uniqKey="Maccoss M">M. J. MacCoss</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nelson, E K" uniqKey="Nelson E">E. K. Nelson</name></author><author><name sortKey="Piehler, B" uniqKey="Piehler B">B. Piehler</name></author><author><name sortKey="Eckels, J" uniqKey="Eckels J">J. Eckels</name></author><author><name sortKey="Rauch, A" uniqKey="Rauch A">A. Rauch</name></author><author><name sortKey="Bellew, M" uniqKey="Bellew M">M. Bellew</name></author><author><name sortKey="Hussey, P" uniqKey="Hussey P">P. Hussey</name></author><author><name sortKey="Ramsay, S" uniqKey="Ramsay S">S. Ramsay</name></author><author><name sortKey="Nathe, C" uniqKey="Nathe C">C. Nathe</name></author><author><name sortKey="Lum, K" uniqKey="Lum K">K. Lum</name></author><author><name sortKey="Krouse, K" uniqKey="Krouse K">K. Krouse</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marx, V" uniqKey="Marx V">V. Marx</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Picotti, P" uniqKey="Picotti P">P. Picotti</name></author><author><name sortKey="Bodenmiller, B" uniqKey="Bodenmiller B">B. Bodenmiller</name></author><author><name sortKey="Aebersold, R" uniqKey="Aebersold R">R. Aebersold</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gillette, M A" uniqKey="Gillette M">M. A. Gillette</name></author><author><name sortKey="Carr, S A" uniqKey="Carr S">S. A. Carr</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schilling, B" uniqKey="Schilling B">B. Schilling</name></author><author><name sortKey="Rardin, M J" uniqKey="Rardin M">M. J. Rardin</name></author><author><name sortKey="Maclean, B X" uniqKey="Maclean B">B. X. MacLean</name></author><author><name sortKey="Zawadzka, A M" uniqKey="Zawadzka A">A. M. Zawadzka</name></author><author><name sortKey="Frewen, B E" uniqKey="Frewen B">B. E. Frewen</name></author><author><name sortKey="Cusack, M P" uniqKey="Cusack M">M. P. Cusack</name></author><author><name sortKey="Sorensen, D J" uniqKey="Sorensen D">D. J. Sorensen</name></author><author><name sortKey="Bereman, M S" uniqKey="Bereman M">M. S. Bereman</name></author><author><name sortKey="Jing, E" uniqKey="Jing E">E. Jing</name></author><author><name sortKey="Wu, C C" uniqKey="Wu C">C. C. Wu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sherrod, S D" uniqKey="Sherrod S">S. D. Sherrod</name></author><author><name sortKey="Myers, M V" uniqKey="Myers M">M. V. Myers</name></author><author><name sortKey="Li, M" uniqKey="Li M">M. Li</name></author><author><name sortKey="Myers, J S" uniqKey="Myers J">J. S. Myers</name></author><author><name sortKey="Carpenter, K L" uniqKey="Carpenter K">K. L. Carpenter</name></author><author><name sortKey="Maclean, B" uniqKey="Maclean B">B. Maclean</name></author><author><name sortKey="Maccoss, M J" uniqKey="Maccoss M">M. J. Maccoss</name></author><author><name sortKey="Liebler, D C" uniqKey="Liebler D">D. C. Liebler</name></author><author><name sortKey="Ham, A J L" uniqKey="Ham A">A.-J. L. Ham</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Peterson, A C" uniqKey="Peterson A">A. C. Peterson</name></author><author><name sortKey="Russell, J D" uniqKey="Russell J">J. D. Russell</name></author><author><name sortKey="Bailey, D J" uniqKey="Bailey D">D. J. Bailey</name></author><author><name sortKey="Westphall, M S" uniqKey="Westphall M">M. S. Westphall</name></author><author><name sortKey="Coon, J J" uniqKey="Coon J">J. J. Coon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Venable, J D" uniqKey="Venable J">J. D. Venable</name></author><author><name sortKey="Dong, M Q" uniqKey="Dong M">M.-Q. Dong</name></author><author><name sortKey="Wohlschlegel, J" uniqKey="Wohlschlegel J">J. Wohlschlegel</name></author><author><name sortKey="Dillin, A" uniqKey="Dillin A">A. Dillin</name></author><author><name sortKey="Yates, J R" uniqKey="Yates J">J. R. Yates</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gillet, L C" uniqKey="Gillet L">L. C. Gillet</name></author><author><name sortKey="Navarro, P" uniqKey="Navarro P">P. Navarro</name></author><author><name sortKey="Tate, S" uniqKey="Tate S">S. Tate</name></author><author><name sortKey="Rost, H" uniqKey="Rost H">H. Rost</name></author><author><name sortKey="Selevsek, N" uniqKey="Selevsek N">N. Selevsek</name></author><author><name sortKey="Reiter, L" uniqKey="Reiter L">L. Reiter</name></author><author><name sortKey="Bonner, R" uniqKey="Bonner R">R. Bonner</name></author><author><name sortKey="Aebersold, R" uniqKey="Aebersold R">R. Aebersold</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Farrah, T" uniqKey="Farrah T">T. Farrah</name></author><author><name sortKey="Deutsch, E W" uniqKey="Deutsch E">E. W. Deutsch</name></author><author><name sortKey="Kreisberg, R" uniqKey="Kreisberg R">R. Kreisberg</name></author><author><name sortKey="Sun, Z" uniqKey="Sun Z">Z. Sun</name></author><author><name sortKey="Campbell, D S" uniqKey="Campbell D">D. S. Campbell</name></author><author><name sortKey="Mendoza, L" uniqKey="Mendoza L">L. Mendoza</name></author><author><name sortKey="Kusebauch, U" uniqKey="Kusebauch U">U. Kusebauch</name></author><author><name sortKey="Brusniak, M Y" uniqKey="Brusniak M">M.-Y. Brusniak</name></author><author><name sortKey="Huttenhain, R" uniqKey="Huttenhain R">R. Hüttenhain</name></author><author><name sortKey="Schiess, R" uniqKey="Schiess R">R. Schiess</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cham, J A" uniqKey="Cham J">J. A. Cham</name></author><author><name sortKey="Bianco, L" uniqKey="Bianco L">L. Bianco</name></author><author><name sortKey="Barton, C" uniqKey="Barton C">C. Barton</name></author><author><name sortKey="Bessant, C" uniqKey="Bessant C">C. Bessant</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Prakash, A" uniqKey="Prakash A">A. Prakash</name></author><author><name sortKey="Tomazela, D M" uniqKey="Tomazela D">D. M. Tomazela</name></author><author><name sortKey="Frewen, B" uniqKey="Frewen B">B. Frewen</name></author><author><name sortKey="Maclean, B" uniqKey="Maclean B">B. Maclean</name></author><author><name sortKey="Merrihew, G" uniqKey="Merrihew G">G. Merrihew</name></author><author><name sortKey="Peterman, S" uniqKey="Peterman S">S. Peterman</name></author><author><name sortKey="Maccoss, M J" uniqKey="Maccoss M">M. J. Maccoss</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mallick, P" uniqKey="Mallick P">P. Mallick</name></author><author><name sortKey="Schirle, M" uniqKey="Schirle M">M. Schirle</name></author><author><name sortKey="Chen, S S" uniqKey="Chen S">S. S. Chen</name></author><author><name sortKey="Flory, M R" uniqKey="Flory M">M. R. Flory</name></author><author><name sortKey="Lee, H" uniqKey="Lee H">H. Lee</name></author><author><name sortKey="Martin, D" uniqKey="Martin D">D. Martin</name></author><author><name sortKey="Ranish, J" uniqKey="Ranish J">J. Ranish</name></author><author><name sortKey="Raught, B" uniqKey="Raught B">B. Raught</name></author><author><name sortKey="Schmitt, R" uniqKey="Schmitt R">R. Schmitt</name></author><author><name sortKey="Werner, T" uniqKey="Werner T">T. Werner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bereman, M S" uniqKey="Bereman M">M. S. Bereman</name></author><author><name sortKey="Maclean, B" uniqKey="Maclean B">B. MacLean</name></author><author><name sortKey="Tomazela, D M" uniqKey="Tomazela D">D. M. Tomazela</name></author><author><name sortKey="Liebler, D C" uniqKey="Liebler D">D. C. Liebler</name></author><author><name sortKey="Maccoss, M J" uniqKey="Maccoss M">M. J. MacCoss</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stergachis, A B" uniqKey="Stergachis A">A. B. Stergachis</name></author><author><name sortKey="Maclean, B" uniqKey="Maclean B">B. MacLean</name></author><author><name sortKey="Lee, K" uniqKey="Lee K">K. Lee</name></author><author><name sortKey="Stamatoyannopoulos, J A" uniqKey="Stamatoyannopoulos J">J. A. Stamatoyannopoulos</name></author><author><name sortKey="Maccoss, M J" uniqKey="Maccoss M">M. J. MacCoss</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Abbatiello, S E" uniqKey="Abbatiello S">S. E. Abbatiello</name></author><author><name sortKey="Mani, D R" uniqKey="Mani D">D. R. Mani</name></author><author><name sortKey="Keshishian, H" uniqKey="Keshishian H">H. Keshishian</name></author><author><name sortKey="Carr, S A" uniqKey="Carr S">S. A. Carr</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Escher, C" uniqKey="Escher C">C. Escher</name></author><author><name sortKey="Reiter, L" uniqKey="Reiter L">L. Reiter</name></author><author><name sortKey="Maclean, B" uniqKey="Maclean B">B. MacLean</name></author><author><name sortKey="Ossola, R" uniqKey="Ossola R">R. Ossola</name></author><author><name sortKey="Herzog, F" uniqKey="Herzog F">F. Herzog</name></author><author><name sortKey="Chilton, J" uniqKey="Chilton J">J. Chilton</name></author><author><name sortKey="Maccoss, M J" uniqKey="Maccoss M">M. J. MacCoss</name></author><author><name sortKey="Rinner, O" uniqKey="Rinner O">O. Rinner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Maclean, B" uniqKey="Maclean B">B. Maclean</name></author><author><name sortKey="Tomazela, D M" uniqKey="Tomazela D">D. M. Tomazela</name></author><author><name sortKey="Abbatiello, S E" uniqKey="Abbatiello S">S. E. Abbatiello</name></author><author><name sortKey="Zhang, S" uniqKey="Zhang S">S. Zhang</name></author><author><name sortKey="Whiteaker, J R" uniqKey="Whiteaker J">J. R. Whiteaker</name></author><author><name sortKey="Paulovich, A G" uniqKey="Paulovich A">A. G. Paulovich</name></author><author><name sortKey="Carr, S A" uniqKey="Carr S">S. A. Carr</name></author><author><name sortKey="Maccoss, M J" uniqKey="Maccoss M">M. J. Maccoss</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Whiteaker, J R" uniqKey="Whiteaker J">J. R. Whiteaker</name></author><author><name sortKey="Halusa, G N" uniqKey="Halusa G">G. N. Halusa</name></author><author><name sortKey="Hoofnagle, A N" uniqKey="Hoofnagle A">A. N. Hoofnagle</name></author><author><name sortKey="Sharma, V" uniqKey="Sharma V">V. Sharma</name></author><author><name sortKey="Maclean, B" uniqKey="Maclean B">B. MacLean</name></author><author><name sortKey="Yan, P" uniqKey="Yan P">P. Yan</name></author><author><name sortKey="Wrobel, J A" uniqKey="Wrobel J">J. A. Wrobel</name></author><author><name sortKey="Kennedy, J" uniqKey="Kennedy J">J. Kennedy</name></author><author><name sortKey="Mani, D R" uniqKey="Mani D">D. R. Mani</name></author><author><name sortKey="Zimmerman, L J" uniqKey="Zimmerman L">L. J. Zimmerman</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="brief-report" xml:lang="EN"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">J Proteome Res</journal-id><journal-id journal-id-type="iso-abbrev">J. Proteome Res</journal-id><journal-id journal-id-type="publisher-id">pr</journal-id><journal-id journal-id-type="coden">jprobs</journal-id><journal-title-group><journal-title>Journal of Proteome Research</journal-title></journal-title-group><issn pub-type="ppub">1535-3893</issn><issn pub-type="epub">1535-3907</issn><publisher><publisher-name>American Chemical
Society</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25102069</article-id><article-id pub-id-type="pmc">4156235</article-id><article-id pub-id-type="doi">10.1021/pr5006636</article-id><article-categories><subj-group><subject>Technical Note</subject></subj-group></article-categories><title-group><article-title>Panorama: A Targeted Proteomics
Knowledge Base</article-title></title-group><contrib-group><contrib contrib-type="author" id="ath1"><name><surname>Sharma</surname><given-names>Vagisha</given-names></name><xref rid="aff1" ref-type="aff">†</xref></contrib><contrib contrib-type="author" id="ath2"><name><surname>Eckels</surname><given-names>Josh</given-names></name><xref rid="aff2" ref-type="aff">‡</xref></contrib><contrib contrib-type="author" id="ath3"><name><surname>Taylor</surname><given-names>Greg K.</given-names></name><xref rid="aff2" ref-type="aff">‡</xref></contrib><contrib contrib-type="author" id="ath4"><name><surname>Shulman</surname><given-names>Nicholas
J.</given-names></name><xref rid="aff1" ref-type="aff">†</xref></contrib><contrib contrib-type="author" id="ath5"><name><surname>Stergachis</surname><given-names>Andrew B.</given-names></name><xref rid="aff1" ref-type="aff">†</xref></contrib><contrib contrib-type="author" id="ath6"><name><surname>Joyner</surname><given-names>Shannon A.</given-names></name><xref rid="aff3" ref-type="aff">§</xref></contrib><contrib contrib-type="author" id="ath7"><name><surname>Yan</surname><given-names>Ping</given-names></name><xref rid="aff4" ref-type="aff">∥</xref></contrib><contrib contrib-type="author" id="ath8"><name><surname>Whiteaker</surname><given-names>Jeffrey R.</given-names></name><xref rid="aff4" ref-type="aff">∥</xref></contrib><contrib contrib-type="author" id="ath9"><name><surname>Halusa</surname><given-names>Goran N.</given-names></name><xref rid="aff5" ref-type="aff">⊥</xref></contrib><contrib contrib-type="author" id="ath10"><name><surname>Schilling</surname><given-names>Birgit</given-names></name><xref rid="aff6" ref-type="aff">#</xref></contrib><contrib contrib-type="author" id="ath11"><name><surname>Gibson</surname><given-names>Bradford W.</given-names></name><xref rid="aff6" ref-type="aff">#</xref></contrib><contrib contrib-type="author" id="ath12"><name><surname>Colangelo</surname><given-names>Christopher M.</given-names></name><xref rid="aff7" ref-type="aff">○</xref></contrib><contrib contrib-type="author" id="ath13"><name><surname>Paulovich</surname><given-names>Amanda G.</given-names></name><xref rid="aff4" ref-type="aff">∥</xref></contrib><contrib contrib-type="author" id="ath14"><name><surname>Carr</surname><given-names>Steven
A.</given-names></name><xref rid="aff8" ref-type="aff">∇</xref></contrib><contrib contrib-type="author" id="ath15"><name><surname>Jaffe</surname><given-names>Jacob D.</given-names></name><xref rid="aff8" ref-type="aff">∇</xref></contrib><contrib contrib-type="author" id="ath16"><name><surname>MacCoss</surname><given-names>Michael J.</given-names></name><xref rid="aff1" ref-type="aff">†</xref></contrib><contrib contrib-type="author" corresp="yes" id="ath17"><name><surname>MacLean</surname><given-names>Brendan</given-names></name><xref rid="cor1" ref-type="other">*</xref><xref rid="aff1" ref-type="aff">†</xref></contrib><aff id="aff1"><label>†</label><institution>University of Washington</institution>, Seattle, Washington 98195,<country>United States</country></aff><aff id="aff2"><label>‡</label><institution>LabKey Software</institution>, San Diego, California 92101,<country>United States</country></aff><aff id="aff3"><label>§</label><institution>Carnegie Melon University</institution>, Pittsburgh, Pennsylvania 15213,<country>United States</country></aff><aff id="aff4"><label>∥</label><institution>Fred Hutchinson Cancer Research Center</institution>, Seattle, Washington 98109,<country>United States</country></aff><aff id="aff5"><label>⊥</label><institution>Leidos Biomedical Research, Inc.</institution>, Frederick, Maryland 21702,<country>United States</country></aff><aff id="aff6"><label>#</label><institution>Buck Institute for Research on Aging</institution>, Novato, California 94945,<country>United States</country></aff><aff id="aff7"><label>○</label><institution>Yale University</institution>, New Haven, Connecticut 06520,<country>United States</country></aff><aff id="aff8"><label>∇</label><institution>The Broad Institute</institution>, Cambridge, Massachusetts 02142,<country>United States</country></aff></contrib-group><author-notes><corresp id="cor1"><label>*</label>E-mail: <email>brendanx@uw.edu</email>. Phone: <phone>(206) 616-9023</phone>. Fax: <fax>(206) 685-7301</fax>.</corresp></author-notes><pub-date pub-type="pmc-release"><day>07</day><month>08</month><year>2015</year></pub-date><pub-date pub-type="epub"><day>07</day><month>08</month><year>2014</year></pub-date><pub-date pub-type="ppub"><day>05</day><month>09</month><year>2014</year></pub-date><volume>13</volume><issue>9</issue><fpage>4205</fpage><lpage>4210</lpage><history><date date-type="received"><day>29</day><month>06</month><year>2014</year></date></history><permissions><copyright-statement>Copyright © 2014 American Chemical Society</copyright-statement><copyright-year>2014</copyright-year><copyright-holder>American Chemical Society</copyright-holder><license><license-p><ext-link ext-link-type="uri" xlink:href="http://pubs.acs.org/page/policy/authorchoice_termsofuse.html">Terms of Use</ext-link></license-p></license></permissions><abstract><p content-type="toc-graphic"><graphic xlink:href="pr-2014-006636_0004" id="ab-tgr1"></graphic></p><p>Panorama
is a web application for storing, sharing, analyzing,
and reusing targeted assays created and refined with Skyline,1 an increasingly popular Windows client software
tool for targeted proteomics experiments. Panorama allows laboratories
to store and organize curated results contained in Skyline documents
with fine-grained permissions, which facilitates distributed collaboration
and secure sharing of published and unpublished data via a web-browser
interface. It is fully integrated with the Skyline workflow and supports
publishing a document directly to a Panorama server from the Skyline
user interface. Panorama captures the complete Skyline document information
content in a relational database schema. Curated results published
to Panorama can be aggregated and exported as chromatogram libraries.
These libraries can be used in Skyline to pick optimal targets in
new experiments and to validate peak identification of target peptides.
Panorama is open-source and freely available. It is distributed as
part of LabKey Server,2 an open source
biomedical research data management system. Laboratories and organizations
can set up Panorama locally by downloading and installing the software
on their own servers. They can also request freely hosted projects
on <uri xlink:href="https://panoramaweb.org">https://panoramaweb.org</uri>, a Panorama server maintained
by the Department of Genome Sciences at the University of Washington.</p></abstract><kwd-group><kwd>Software</kwd><kwd>knowledge base</kwd><kwd>mass spectrometry</kwd><kwd>targeted proteomics</kwd><kwd>SRM</kwd><kwd>MRM</kwd><kwd>chromatogram
libraries</kwd><kwd>skyline</kwd></kwd-group><funding-group><funding-statement><funding-source>National Institutes of Health, United States</funding-source></funding-statement></funding-group><custom-meta-group><custom-meta><meta-name>document-id-old-9</meta-name><meta-value>pr5006636</meta-value></custom-meta><custom-meta><meta-name>document-id-new-14</meta-name><meta-value>pr-2014-006636</meta-value></custom-meta><custom-meta><meta-name>ccc-price</meta-name><meta-value></meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec sec-type="intro" id="sec1"><label>1</label><title>Introduction</title><p>In recent years, targeted
proteomics has emerged as a mainstream
technology to detect and quantify protein and peptide abundances in
complex biological samples.<sup><xref ref-type="bibr" rid="ref3">3</xref>−<xref ref-type="bibr" rid="ref5">5</xref></sup> This popularity has, in part,
been fueled by the introduction and broad adoption of the enabling
Skyline software tool.<sup><xref ref-type="bibr" rid="ref1">1</xref>,<xref ref-type="bibr" rid="ref3">3</xref></sup> Skyline is a freely available
Windows client application that has become a valuable tool for building
and optimizing selected reaction monitoring (SRM) assays. Skyline
works across instrument platforms, and its intuitive user interface
and rich set of graphs simplifies the development and refinement of
targeted methods and also makes it easy for users to visually assess
data quality. In addition to being the most commonly used tool for
analyzing data acquired on triple quadrupole instruments, Skyline
is now widely used for data analysis and method development in experiments
that involve TOF and ion trap mass spectrometers, spanning the techniques
of data-dependent acquisition (DDA),<sup><xref ref-type="bibr" rid="ref6">6</xref></sup> targeted
MS/MS<sup><xref ref-type="bibr" rid="ref7">7</xref></sup> (also referred to as parallel reaction
monitoring or PRM),<sup><xref ref-type="bibr" rid="ref8">8</xref></sup> and data-independent
acquisition DIA.<sup><xref ref-type="bibr" rid="ref9">9</xref>,<xref ref-type="bibr" rid="ref10">10</xref></sup> The growth in adoption of Skyline
for targeted proteomics experiments has resulted in an increasing
accumulation of Skyline documents across various laboratories and
organizations. These documents represent a large body of work to develop
targeted assays for precise quantitative measurement of proteins and
peptides across a range of experimental protocols, which have the
potential to become a resource of experimental information. Organizing
these documents into a database is essential to make it possible to
review and explore larger sets of well-annotated experimental data
in aggregate and to enable use of the accumulated knowledge to inform
targeted measurement in future experiments.</p><p>Panorama was developed
with the goals of data integrity, security,
sharing, scalability, and ease-of-use. It allows laboratories and
organizations to aggregate curated results contained in Skyline documents,
without loss of information. The Panorama schema provides a relational
database storage format for the complete Skyline document data model.
Panorama is designed both to facilitate sharing results among lab
members, external collaborators, and with the general public and to
keep private data secure during multiple experiment studies and the
peer-review process. The rich security model of LabKey Server combined
with its support for installation on private servers, as well as the
availability of professional paid support, has allowed Panorama adoption
even among large pharmaceutical companies. Panorama has been tightly
integrated with Skyline, allowing users to publish their documents
to Panorama directly from Skyline and also to query results exported
from Panorama when designing new methods in Skyline (Figure <xref rid="fig1" ref-type="fig">1</xref>).</p><fig id="fig1" position="float"><label>Figure 1</label><caption><p>Skyline–Panorama dataflow. Users publish documents
containing
refined targeted methods from Skyline to a Panorama server, where
they are stored in a relational database. Data uploaded to Panorama
can be viewed, searched and analyzed in a web-browser interface. Documents
published to Panorama as well as chromatogram libraries exported from
library folders can be downloaded to view and use in Skyline.</p></caption><graphic xlink:href="pr-2014-006636_0002" id="gr1" position="float"></graphic></fig><p>Existing repositories, such as
the Peptide Atlas SRM Experiment Library (PASSEL)<sup><xref ref-type="bibr" rid="ref11">11</xref></sup> and MRMaid-DB,<sup><xref ref-type="bibr" rid="ref12">12</xref></sup> provide a place
for collecting and exploring experimental SRM data and transitions
that have already been published. These repositories are public and
do not provide mechanisms for secure data sharing with internal and
external collaborators prior to publication. They also lack a local
installation option for organizations and laboratories that may prefer
to manage their own repositories. They require the submission of RAW
data and transition lists and do not yet have support for importing
the rich information about the data curation and analysis process
or custom annotations available in Skyline documents. In contrast,
Panorama supports a knowledge base environment for continued interaction
with and analysis of large sets of targeted proteomics data in public
or private circles. Knowledge accumulated over time can be used to
create chromatogram libraries tailored to specific biological and
experimental conditions. These libraries can be used to select the
most suitable peptides and product ions to monitor in a targeted experiment,
and the stored chromatograms may also be used to increase confidence
in chromatogram peak picking.</p></sec><sec id="sec2"><label>2</label><title>Design and Implementation</title><p>Panorama has been implemented as a module in LabKey Server,<sup><xref ref-type="bibr" rid="ref2">2</xref></sup> a bioinformatics data management platform with
rich support for proteomics data. Both LabKey Server and the Panorama
module are available as open-source software under the Apache 2.0
license. The complete source code can be downloaded from <uri xlink:href="https://www.labkey.org/wiki/home/Documentation/page.view?name=sourceCode">https://www.labkey.org/wiki/home/Documentation/page.view?name=sourceCode</uri>. LabKey Server is a web application that is implemented in Java
and runs on the Apache Tomcat web server. It comes with core customizable
features for file management, data organization and security, role-based
permissions, integration with analysis tools like R, and client APIs
for retrieving and interacting with data.</p><p>At the heart of the
Panorama module is a comprehensive database
schema that closely matches the Skyline document data model for capturing
the variety of information contained in Skyline files. A web-browser
interface (Figure <xref rid="fig2" ref-type="fig">2</xref>) lets the user explore
and interrogate results contained in uploaded Skyline documents, including
chromatogram views, peak area graphs, and an interactive viewer for
MS/MS spectra (<xref rid="notes-1" ref-type="notes">Supporting Information Note 1</xref>). Users can upload Skyline documents to a hierarchical folder structure
and view the precursors and transitions measured in a Skyline document
(<xref rid="notes-1" ref-type="notes">Supporting Information Figure 1</xref>). More
detailed views are available for the proteins (<xref rid="notes-1" ref-type="notes">Supporting Information Figure 2</xref>) and peptides (<xref rid="notes-1" ref-type="notes">Supporting Information Figure 3</xref>) contained in
each document. An enhanced search interface allows searching for a
protein, peptide, or specific modifications contained in the documents
published to a folder and, optionally, its subfolders (<xref rid="notes-1" ref-type="notes">Supporting Information Figure 4</xref>).</p><fig id="fig2" position="float"><label>Figure 2</label><caption><p>Panorama web-browser
interface showing the precursor list in a
Skyline document. Clicking on one of the peptide sequences provides
a more detailed view for the peptide that includes chromatograms for
the precursors in all of the replicates. A graph showing the peak
areas for the peptide measured in individual replicates is also displayed.
Peak areas can be grouped by a replicate annotation, as shown above
for the annotation “Condition” (Disease and Healthy).
The source document can be downloaded via a DOWNLOAD link for viewing
in Skyline.</p></caption><graphic xlink:href="pr-2014-006636_0003" id="gr2" position="float"></graphic></fig><sec id="sec2.1"><label>2.1</label><title>Data
Organization, Sharing, and Security</title><p>LabKey Server, developed
over the past decade primarily by the
programmers at LabKey Software, is a data management platform that
provides the ability to organize data into a customizable workspace
with a hierarchical folder structure. Data can be separated into folders
by organism, biological matrix, MS instrumentation, and so on, which
allows users to identify and organize experiments over a period of
time. Panorama users can control access to the data in each folder
by configuring the permission settings to keep the data completely
private or can provide access to select collaborators or journal reviewers
prior to publication (<xref rid="notes-1" ref-type="notes">Supporting Information Note
1</xref>). Upon publication, or whenever the data owners choose, making
a simple change to the security settings can make the data available
to the general public. The comprehensive access control model implemented
in LabKey Server makes Panorama a viable option for individual laboratories,
companies, and other organizations that want secure and flexible management
of their accumulated targeted assay data.</p><p>Data in a Panorama
database can be accessed through client libraries available in several
programming languages, including R, JavaScript, Java, Perl, and Python.
Programmatic access to the data facilitates building external applications
for data analysis and designing custom user interfaces.</p></sec><sec id="sec2.2"><label>2.2</label><title>Chromatogram Libraries</title><p>Selected reaction
monitoring (SRM) has been recognized as a method for detecting and
quantifying proteins of interest in a given sample with high sensitivity
and specificity.<sup><xref ref-type="bibr" rid="ref3">3</xref></sup> A key requirement in
developing an SRM assay is selecting peptides that uniquely identify
a protein and have physicochemical properties that make them readily
detectable in a mass spectrometer. Also important is the selection
of candidate fragment ions for each of the peptides of interest. Current
approaches use a combination of spectral libraries from shotgun experiments<sup><xref ref-type="bibr" rid="ref13">13</xref></sup> and de novo prediction algorithms<sup><xref ref-type="bibr" rid="ref14">14</xref></sup> or broad measurement and subsequent method refinement<sup><xref ref-type="bibr" rid="ref15">15</xref></sup> to guide the selection of peptides. The former
assumes that peptides most frequently observed in shotgun experiments
will produce a good response in a targeted proteomics setting, and
the latter necessitates concerted effort for each new method developed.
Although spectrum libraries can accurately predict which fragment
ions will produce the most intense signal on a triple quadrupole instrument,<sup><xref ref-type="bibr" rid="ref13">13</xref></sup> these libraries do not always have adequate
coverage of the entire proteome, especially low-abundance proteins
such as human transcription factors and kinases.<sup><xref ref-type="bibr" rid="ref16">16</xref></sup> Even the fragment ion measurements in these libraries may
differ from targeted measurements due to instrument differences or
interference that goes undetected in spectrum measurement. To overcome
these limitations, assay development efforts may measure all precursor
and product ions for proteins of interest, under experimental conditions
with safeguards like reference standard peptides, and then iteratively
refine assays.<sup><xref ref-type="bibr" rid="ref15">15</xref>,<xref ref-type="bibr" rid="ref17">17</xref></sup> Once an assay has been established,
it can be used to guide the selection of peptides and product ions
to measure in any new experiment under similar conditions. This benefit,
however, is frequently lost or cumbersome without organized storage
and recall.</p><p>Panorama solves this problem by providing the option
of organizing assay results in special chromatogram library folders
(<xref rid="notes-1" ref-type="notes">Supporting Information Note 2</xref>). Assays
that have been curated in Skyline can be published to designated library
folders in Panorama, where they may be subsequently downloaded as
a chromatogram library file. The library download is updated with
new assays each time a Skyline document is published to the library
folder. Users can create library folders for each biological source,
sample matrix, experimental protocol, and mass spectrometer type used
in any experiment. This makes these libraries as specific to a given
experimental setup as necessary and the assays reproducible under
similar settings. Chromatogram libraries can be downloaded for use
in Skyline to pick optimal peptides for proteins and optimal product
ions for precursors in a new experiment. Chromatogram libraries also
contain representative chromatograms and peak areas for each precursor
that can be compared with newly acquired data for validation of peptide
identification (<xref rid="notes-1" ref-type="notes">Supporting Information Figure
5 and Supporting Information Note 2</xref>).</p></sec><sec id="sec2.3"><label>2.3</label><title>Integration
with Skyline</title><p>Skyline
captures extensive information about the targeted proteomics methods
it is used to design as well as the acquired results imported and
curated within its user interface. This information is stored in the
Skyline document, a human readable XML format file, and a companion
binary data file. The relational database schema in which Panorama
stores data was designed to mirror closely the Skyline data model
and to include the full information content it contains, such as complex
peptide modification information, normalized retention times (iRT),<sup><xref ref-type="bibr" rid="ref18">18</xref></sup> optimized collision energy,<sup><xref ref-type="bibr" rid="ref19">19</xref></sup> and declustering potential. Panorama is fully integrated
into the Skyline user interface, allowing users to configure one or
more Panorama servers in Skyline and to publish documents to a folder
within a server of choice through a point-and-click user interface
(<xref rid="notes-1" ref-type="notes">Supporting Information Figure 6 and Supporting
Information Note 1</xref>). All documents published to Panorama may
be downloaded again through a web-browser link and reviewed within
Skyline. Documents published to designated library folders in Panorama
can be combined into library files and used in Skyline to pick optimal
peptides and product ions, as well as to compare acquired data to
results contained in Panorama for peak identification confidence.
Panorama development keeps pace with Skyline development to include
new features added to Skyline such as replicate annotations and mass
errors in chromatograms extracted from high-resolution mass spectra.</p></sec><sec id="sec2.4"><label>2.4</label><title>Installation Options</title><p>Panorama can
be installed on a server in a lab by following one of the installation
options available for LabKey Server. The latest release of LabKey
Server, with the Panorama module, can be downloaded from <uri xlink:href="http://labkey.com/download-labkey-server">http://labkey.com/download-labkey-server</uri>, and commercial support is available to assist server setup. For
laboratories without the resources, expertise, or interest to maintain
their own Panorama server, a public server, PanoramaWeb, is hosted
at the University of Washington by the MacCoss lab (<uri xlink:href="https://panoramaweb.org">https://panoramaweb.org</uri>). Anyone can request a free project in which they will have full
administrative rights. These rights includes the ability to configure
the project workspace with the desired folder hierarchy, project membership,
and access control policies, as one would on any private installation.
PanoramaWeb currently hosts projects for 66 different laboratories,
and a total of 779 Skyline documents have been uploaded to the server.
Latest figures on PanoramaWeb usage can be viewed at the following
link: <uri xlink:href="https://panoramaweb.org/labkey/wiki/home/page.view?name=Dashboard">https://panoramaweb.org/labkey/wiki/home/page.view?name=Dashboard</uri>.</p></sec></sec><sec id="sec3"><label>3</label><title>Use Cases and Public Implementations That Enable
Collaboration</title><p>Panorama facilitates collaborative, targeted
proteomics projects
that use the Skyline software. In addition to the ability to configure
access permissions to suit the needs of a project, Panorama leverages
a variety of components and features available in LabKey Server to
provide an environment that facilitates collaboration and data sharing.
This includes the availability of client libraries in several programming
languages that allow external applications to programmatically access
the data in a Panorama database. These libraries can also be used
on the Panorama server to design custom interfaces. The comprehensive
Panorama database schema is exposed to the user to enable creating
custom views of the data or even writing custom SQL scripts. Data
analysis can be performed within Panorama using familiar tools such
as the R software environment for statistical computing. PanoramaWeb
(<uri xlink:href="https://panoramaweb.org">https://panoramaweb.org</uri><underline>)</underline>, the public
Panorama server maintained by the Department of Genome Sciences at
the University of Washington, hosts several multilab projects that
showcase the suitability of the platform as a solution for collaborative
targeted proteomics efforts.</p><p>The Clinical Proteomic Tumor Analysis
Consortium (CPTAC) Assay
Portal (<uri xlink:href="https://assays.cancer.gov/">https://assays.cancer.gov/</uri>),<sup><xref ref-type="bibr" rid="ref20">20</xref></sup> designed to disseminate high-quality proteomics assays,
is tied to the CPTAC Assay Portal project (<uri xlink:href="https://daily.panoramaweb.org/labkey/CPTAC_Assays.url">https://daily.panoramaweb.org/labkey/CPTAC_Assays.url</uri>) on PanoramaWeb. CPTAC members have published detailed assay characterization
data, contained in Skyline documents, to this project. The CPTAC-hosted
web portal uses the LabKey Server programmatic interfaces to request
data from the PanoramaWeb database. Several analysis scripts, written
in the R programming language, were developed by CPTAC members to
ensure data quality and to evaluate assay performance. These scripts
were integrated into their PanoramaWeb project (<xref rid="notes-1" ref-type="notes">Supporting Information Figure 7</xref>), and the results from running
these scripts are displayed in the CPTAC-hosted portal. As new assays
are submitted, these scripts are executed on PanormaWeb via programmatic
requests, and the results are imported into the assay portal database.</p><p>PanoramaWeb was chosen as the repository for the American Biomedical
Research Foundation (ABRF) Standards Proteomics Research Group (sPRG)
2013 study in which over 40 anonymized laboratories published their
results to a PanoramaWeb project. Panorama also has the ability to
import Excel spreadsheets, allowing results from participants that
did not use Skyline for data processing to be added to the same project
(<xref rid="notes-1" ref-type="notes">Supporting Information Figure 8</xref>). In addition,
a custom summary table was uploaded to PanoramaWeb (<xref rid="notes-1" ref-type="notes">Supporting Information Figure 9</xref>), enabling results from all
of the participants to be captured in one overview table with hyperlinks
leading to the results for individual participants. Results from analysis
scripts, developed by the sPRG members to assess data quality, were
added to each participant’s folder on PanoramaWeb (<xref rid="notes-1" ref-type="notes">Supporting Information Figure 10</xref>). The project
benefitted from the data management and organization features of Panorama,
and data analysis was greatly simplified by the ability to easily
access results from multiple participating laboratories. Processed
data as well as analysis scripts and their results are available in
the ABRF sPRG project on PanoramaWeb (<uri xlink:href="https://panoramaweb.org/labkey/ABRF-sPRG-2013.url">https://panoramaweb.org/labkey/ABRF-sPRG-2013.url</uri>).</p><p>PanoramaWeb also hosts targeted phosphoproteomics data from
an
assay developed under the auspices of the Library of Integrated Network-based
Cellular Signatures (LINCS) project (<uri xlink:href="http://www.lincsproject.org">www.lincsproject.org</uri>). The LINCS consortium engages several centers that generate molecular
phenotypic data for cellular perturbations using different assay technologies.
It is extremely important that data provenance, traceability, and
interoperability are maintained and available to consortium members
and other consumers of the data. PanoramaWeb was the logical choice
for deposition of all LINCS targeted proteomics data.</p><p>This particular
use case illustrates the flexibility and system
interoperability that PanoramaWeb creates. Execution of a multicenter
consortium project requires rigorous attention to sample and assay
annotation with appropriate metadata to promote reuse of the data
that is generated. The Skyline document model allows faithful assignment
of dozens of pieces of metadata to hundreds of samples in individual
studies. After publishing LINCS data to PanoramaWeb at <uri xlink:href="https://daily.panoramaweb.org/labkey/LINCS.url">https://daily.panoramaweb.org/labkey/LINCS.url</uri>, the combination of quantitative MS data with sample metadata annotations
allow automated creation of data formats that can then be leveraged
by other components of the consortium. Using the R programming language
interface, Panorama enables complete data processing from a Skyline
document, including normalization, outlier removal, probe failure
detection, and summarization, to exporting results in the Gene Cluster
Text (GCT) file format (<xref rid="notes-1" ref-type="notes">Supporting Information
Figure 11</xref>), a recognized standard for analysis of gene expression
data. This allows compatibility with a number of other downstream
tools such as the GENE-E visualization and analysis platform (<uri xlink:href="http://www.broadinstitute.org/cancer/software/GENE-E/index.html">http://www.broadinstitute.org/cancer/software/GENE-E/index.html</uri>) and allows direct import into the LINCS Connectivity Map portal
(<uri xlink:href="http://www.lincscloud.org">http://www.lincscloud.org</uri>).</p></sec><sec sec-type="conclusions" id="sec4"><label>4</label><title>Conclusions</title><p>Panorama addresses the need to archive and share an increasing
number of documents being generated by the growing adoption of Skyline
in targeted proteomics workflows. Over time, experiments stored in
a Panorama server can serve as a knowledge base of curated targeted
assays for the proteomics research community. Development of Panorama
has been a collaborative process to enable the implementation of components
and features useful to end users and to identify and explore its potential
beyond a data archival system. We have described several multilab
collaborative projects hosted on PanoramaWeb that are using Panorama
not only for storing and sharing Skyline documents but also for analyzing
large data sets and presenting results to the broader community.</p></sec></body><back><notes id="notes-1" notes-type="si"><title>Supporting Information Available</title><p>Supporting Information
provides more details of the Panorama user
interface as well as tutorials describing a broad range of Panorama
features and use cases. This material is available free of charge
via the Internet at <uri xlink:href="http://pubs.acs.org">http://pubs.acs.org</uri>.</p></notes><sec sec-type="supplementary-material"><title>Supplementary Material</title><supplementary-material content-type="local-data" id="sifile1"><media xlink:href="pr5006636_si_001.pdf"><caption><p>pr5006636_si_001.pdf</p></caption></media></supplementary-material></sec><notes id="NOTES-d3570e656-autogenerated" notes-type="conflict-of-interest"><p>The authors
declare no
competing financial interest.</p></notes><ack><title>Acknowledgments</title><p>The authors would
like to acknowledge financial support from
National Institute of Health grants R01 GM103551 (to M.J.M.), U01
CA164186 (to J.D.J.), U24 CA160034 from the National Cancer Institute
Clinical Proteomics Tumor Analysis Consortium Initiative (to S.A.C.
and A.G.P.) and grants HHSN268201000033C and R01HL096738 from the
National Heart, Lung, and Blood Institute (to S.A.C.), as well as
funding from the Broad Institute of MIT and Harvard.</p></ack><ref-list><title>References</title><ref id="ref1"><mixed-citation publication-type="journal" id="cit1"><name><surname>MacLean</surname><given-names>B.</given-names></name>; <name><surname>Tomazela</surname><given-names>D. M.</given-names></name>; <name><surname>Shulman</surname><given-names>N.</given-names></name>; <name><surname>Chambers</surname><given-names>M.</given-names></name>; <name><surname>Finney</surname><given-names>G. L.</given-names></name>; <name><surname>Frewen</surname><given-names>B.</given-names></name>; <name><surname>Kern</surname><given-names>R.</given-names></name>; <name><surname>Tabb</surname><given-names>D. L.</given-names></name>; <name><surname>Liebler</surname><given-names>D. C.</given-names></name>; <name><surname>MacCoss</surname><given-names>M. J.</given-names></name><article-title>Skyline: an open source document editor for creating
and analyzing targeted proteomics experiments</article-title>. <source>Bioinformatics</source><year>2010</year>, <volume>26</volume>, <fpage>966</fpage>–<lpage>968</lpage>.<pub-id pub-id-type="pmid">20147306</pub-id></mixed-citation></ref><ref id="ref2"><mixed-citation publication-type="journal" id="cit2"><name><surname>Nelson</surname><given-names>E. K.</given-names></name>; <name><surname>Piehler</surname><given-names>B.</given-names></name>; <name><surname>Eckels</surname><given-names>J.</given-names></name>; <name><surname>Rauch</surname><given-names>A.</given-names></name>; <name><surname>Bellew</surname><given-names>M.</given-names></name>; <name><surname>Hussey</surname><given-names>P.</given-names></name>; <name><surname>Ramsay</surname><given-names>S.</given-names></name>; <name><surname>Nathe</surname><given-names>C.</given-names></name>; <name><surname>Lum</surname><given-names>K.</given-names></name>; <name><surname>Krouse</surname><given-names>K.</given-names></name>; et al. <article-title>LabKey Server: an open source platform for scientific
data integration, analysis and collaboration</article-title>. <source>BMC Bioinf.</source><year>2011</year>, <volume>12</volume>, <fpage>71</fpage>.</mixed-citation></ref><ref id="ref3"><mixed-citation publication-type="journal" id="cit3"><name><surname>Marx</surname><given-names>V.</given-names></name><article-title>Targeted proteomics</article-title>. <source>Nat. Methods</source><year>2013</year>, <volume>10</volume>, <fpage>19</fpage>–<lpage>22</lpage>.<pub-id pub-id-type="pmid">23547293</pub-id></mixed-citation></ref><ref id="ref4"><mixed-citation publication-type="journal" id="cit4"><name><surname>Picotti</surname><given-names>P.</given-names></name>; <name><surname>Bodenmiller</surname><given-names>B.</given-names></name>; <name><surname>Aebersold</surname><given-names>R.</given-names></name><article-title>Proteomics meets the scientific method</article-title>. <source>Nat. Methods</source><year>2013</year>, <volume>10</volume>, <fpage>24</fpage>–<lpage>27</lpage>.<pub-id pub-id-type="pmid">23269373</pub-id></mixed-citation></ref><ref id="ref5"><mixed-citation publication-type="journal" id="cit5"><name><surname>Gillette</surname><given-names>M. A.</given-names></name>; <name><surname>Carr</surname><given-names>S. A.</given-names></name><article-title>Quantitative analysis of peptides and proteins in biomedicine
by targeted mass spectrometry</article-title>. <source>Nat. Methods</source><year>2013</year>, <volume>10</volume>, <fpage>28</fpage>–<lpage>34</lpage>.<pub-id pub-id-type="pmid">23269374</pub-id></mixed-citation></ref><ref id="ref6"><mixed-citation publication-type="journal" id="cit6"><name><surname>Schilling</surname><given-names>B.</given-names></name>; <name><surname>Rardin</surname><given-names>M. J.</given-names></name>; <name><surname>MacLean</surname><given-names>B. X.</given-names></name>; <name><surname>Zawadzka</surname><given-names>A. M.</given-names></name>; <name><surname>Frewen</surname><given-names>B. E.</given-names></name>; <name><surname>Cusack</surname><given-names>M. P.</given-names></name>; <name><surname>Sorensen</surname><given-names>D. J.</given-names></name>; <name><surname>Bereman</surname><given-names>M. S.</given-names></name>; <name><surname>Jing</surname><given-names>E.</given-names></name>; <name><surname>Wu</surname><given-names>C. C.</given-names></name>; et al. <article-title>Platform-independent
and label-free quantitation of
proteomic data using MS1 extracted ion chromatograms in skyline: application
to protein acetylation and phosphorylation</article-title>. <source>Mol. Cell. Proteomics</source><year>2012</year>, <volume>11</volume>, <fpage>202</fpage>–<lpage>214</lpage>.<pub-id pub-id-type="pmid">22454539</pub-id></mixed-citation></ref><ref id="ref7"><mixed-citation publication-type="journal" id="cit7"><name><surname>Sherrod</surname><given-names>S. D.</given-names></name>; <name><surname>Myers</surname><given-names>M. V.</given-names></name>; <name><surname>Li</surname><given-names>M.</given-names></name>; <name><surname>Myers</surname><given-names>J. S.</given-names></name>; <name><surname>Carpenter</surname><given-names>K. L.</given-names></name>; <name><surname>Maclean</surname><given-names>B.</given-names></name>; <name><surname>Maccoss</surname><given-names>M. J.</given-names></name>; <name><surname>Liebler</surname><given-names>D. C.</given-names></name>; <name><surname>Ham</surname><given-names>A.-J. L.</given-names></name><article-title>Label-free
quantitation of protein modifications by pseudo selected reaction
monitoring with internal reference peptides</article-title>. <source>J. Proteome Res.</source><year>2012</year>, <volume>11</volume>, <fpage>3467</fpage>–<lpage>3479</lpage>.<pub-id pub-id-type="pmid">22559222</pub-id></mixed-citation></ref><ref id="ref8"><mixed-citation publication-type="journal" id="cit8"><name><surname>Peterson</surname><given-names>A. C.</given-names></name>; <name><surname>Russell</surname><given-names>J. D.</given-names></name>; <name><surname>Bailey</surname><given-names>D. J.</given-names></name>; <name><surname>Westphall</surname><given-names>M. S.</given-names></name>; <name><surname>Coon</surname><given-names>J. J.</given-names></name><article-title>Parallel reaction monitoring for high resolution and
high mass accuracy quantitative, targeted proteomics</article-title>. <source>Mol. Cell. Proteomics</source><year>2012</year>, <volume>11</volume>, <fpage>1475</fpage>–<lpage>1488</lpage>.<pub-id pub-id-type="pmid">22865924</pub-id></mixed-citation></ref><ref id="ref9"><mixed-citation publication-type="journal" id="cit9"><name><surname>Venable</surname><given-names>J. D.</given-names></name>; <name><surname>Dong</surname><given-names>M.-Q.</given-names></name>; <name><surname>Wohlschlegel</surname><given-names>J.</given-names></name>; <name><surname>Dillin</surname><given-names>A.</given-names></name>; <name><surname>Yates</surname><given-names>J. R.</given-names></name><article-title>Automated
approach for quantitative analysis of complex peptide mixtures from
tandem mass spectra</article-title>. <source>Nat. Methods</source><year>2004</year>, <volume>1</volume>, <fpage>39</fpage>–<lpage>45</lpage>.<pub-id pub-id-type="pmid">15782151</pub-id></mixed-citation></ref><ref id="ref10"><mixed-citation publication-type="journal" id="cit10"><name><surname>Gillet</surname><given-names>L. C.</given-names></name>; <name><surname>Navarro</surname><given-names>P.</given-names></name>; <name><surname>Tate</surname><given-names>S.</given-names></name>; <name><surname>Rost</surname><given-names>H.</given-names></name>; <name><surname>Selevsek</surname><given-names>N.</given-names></name>; <name><surname>Reiter</surname><given-names>L.</given-names></name>; <name><surname>Bonner</surname><given-names>R.</given-names></name>; <name><surname>Aebersold</surname><given-names>R.</given-names></name><article-title>Targeted data
extraction of the MS/MS spectra generated by data-independent acquisition:
a new concept for consistent and accurate proteome analysis</article-title>. <source>Mol. Cell. Proteomics</source><year>2012</year>, <volume>11</volume>, <fpage>O111.016717</fpage>.<pub-id pub-id-type="pmid">22261725</pub-id></mixed-citation></ref><ref id="ref11"><mixed-citation publication-type="journal" id="cit11"><name><surname>Farrah</surname><given-names>T.</given-names></name>; <name><surname>Deutsch</surname><given-names>E. W.</given-names></name>; <name><surname>Kreisberg</surname><given-names>R.</given-names></name>; <name><surname>Sun</surname><given-names>Z.</given-names></name>; <name><surname>Campbell</surname><given-names>D. S.</given-names></name>; <name><surname>Mendoza</surname><given-names>L.</given-names></name>; <name><surname>Kusebauch</surname><given-names>U.</given-names></name>; <name><surname>Brusniak</surname><given-names>M.-Y.</given-names></name>; <name><surname>Hüttenhain</surname><given-names>R.</given-names></name>; <name><surname>Schiess</surname><given-names>R.</given-names></name>; et al. <article-title>PASSEL: the PeptideAtlas SRM experiment library</article-title>. <source>Proteomics</source><year>2012</year>, <volume>12</volume>, <fpage>1170</fpage>–<lpage>1175</lpage>.<pub-id pub-id-type="pmid">22318887</pub-id></mixed-citation></ref><ref id="ref12"><mixed-citation publication-type="journal" id="cit12"><name><surname>Cham</surname><given-names>J. A.</given-names></name>; <name><surname>Bianco</surname><given-names>L.</given-names></name>; <name><surname>Barton</surname><given-names>C.</given-names></name>; <name><surname>Bessant</surname><given-names>C.</given-names></name><article-title>MRMaid-DB: a repository
of published SRM transitions</article-title>. <source>J. Proteome Res.</source><year>2010</year>, <volume>9</volume>, <fpage>620</fpage>–<lpage>625</lpage>.<pub-id pub-id-type="pmid">19908920</pub-id></mixed-citation></ref><ref id="ref13"><mixed-citation publication-type="journal" id="cit13"><name><surname>Prakash</surname><given-names>A.</given-names></name>; <name><surname>Tomazela</surname><given-names>D. M.</given-names></name>; <name><surname>Frewen</surname><given-names>B.</given-names></name>; <name><surname>Maclean</surname><given-names>B.</given-names></name>; <name><surname>Merrihew</surname><given-names>G.</given-names></name>; <name><surname>Peterman</surname><given-names>S.</given-names></name>; <name><surname>Maccoss</surname><given-names>M. J.</given-names></name><article-title>Expediting
the development of targeted
SRM assays: using data from shotgun proteomics to automate method
development</article-title>. <source>J. Proteome Res.</source><year>2009</year>, <volume>8</volume>, <fpage>2733</fpage>–<lpage>2739</lpage>.<pub-id pub-id-type="pmid">19326923</pub-id></mixed-citation></ref><ref id="ref14"><mixed-citation publication-type="journal" id="cit14"><name><surname>Mallick</surname><given-names>P.</given-names></name>; <name><surname>Schirle</surname><given-names>M.</given-names></name>; <name><surname>Chen</surname><given-names>S. S.</given-names></name>; <name><surname>Flory</surname><given-names>M. R.</given-names></name>; <name><surname>Lee</surname><given-names>H.</given-names></name>; <name><surname>Martin</surname><given-names>D.</given-names></name>; <name><surname>Ranish</surname><given-names>J.</given-names></name>; <name><surname>Raught</surname><given-names>B.</given-names></name>; <name><surname>Schmitt</surname><given-names>R.</given-names></name>; <name><surname>Werner</surname><given-names>T.</given-names></name>; et al. <article-title>Computational
prediction of proteotypic peptides for
quantitative proteomics</article-title>. <source>Nat. Biotechnol.</source><year>2007</year>, <volume>25</volume>, <fpage>125</fpage>–<lpage>131</lpage>.<pub-id pub-id-type="pmid">17195840</pub-id></mixed-citation></ref><ref id="ref15"><mixed-citation publication-type="journal" id="cit15"><name><surname>Bereman</surname><given-names>M. S.</given-names></name>; <name><surname>MacLean</surname><given-names>B.</given-names></name>; <name><surname>Tomazela</surname><given-names>D. M.</given-names></name>; <name><surname>Liebler</surname><given-names>D. C.</given-names></name>; <name><surname>MacCoss</surname><given-names>M. J.</given-names></name><article-title>The development
of selected reaction monitoring methods for targeted proteomics via
empirical refinement</article-title>. <source>Proteomics</source><year>2012</year>, <volume>12</volume>, <fpage>1134</fpage>–<lpage>1141</lpage>.<pub-id pub-id-type="pmid">22577014</pub-id></mixed-citation></ref><ref id="ref16"><mixed-citation publication-type="journal" id="cit16"><name><surname>Stergachis</surname><given-names>A. B.</given-names></name>; <name><surname>MacLean</surname><given-names>B.</given-names></name>; <name><surname>Lee</surname><given-names>K.</given-names></name>; <name><surname>Stamatoyannopoulos</surname><given-names>J. A.</given-names></name>; <name><surname>MacCoss</surname><given-names>M. J.</given-names></name><article-title>Rapid empirical
discovery of optimal peptides for targeted
proteomics</article-title>. <source>Nat. Methods</source><year>2011</year>, <volume>8</volume>, <fpage>1041</fpage>–<lpage>1043</lpage>.<pub-id pub-id-type="pmid">22056677</pub-id></mixed-citation></ref><ref id="ref17"><mixed-citation publication-type="journal" id="cit17"><name><surname>Abbatiello</surname><given-names>S. E.</given-names></name>; <name><surname>Mani</surname><given-names>D. R.</given-names></name>; <name><surname>Keshishian</surname><given-names>H.</given-names></name>; <name><surname>Carr</surname><given-names>S. A.</given-names></name><article-title>Automated detection
of inaccurate and imprecise transitions in peptide quantification
by multiple reaction monitoring mass spectrometry</article-title>. <source>Clin. Chem.</source><year>2010</year>, <volume>56</volume>, <fpage>291</fpage>–<lpage>305</lpage>.<pub-id pub-id-type="pmid">20022980</pub-id></mixed-citation></ref><ref id="ref18"><mixed-citation publication-type="journal" id="cit18"><name><surname>Escher</surname><given-names>C.</given-names></name>; <name><surname>Reiter</surname><given-names>L.</given-names></name>; <name><surname>MacLean</surname><given-names>B.</given-names></name>; <name><surname>Ossola</surname><given-names>R.</given-names></name>; <name><surname>Herzog</surname><given-names>F.</given-names></name>; <name><surname>Chilton</surname><given-names>J.</given-names></name>; <name><surname>MacCoss</surname><given-names>M. J.</given-names></name>; <name><surname>Rinner</surname><given-names>O.</given-names></name><article-title>Using iRT, a normalized
retention time for more targeted measurement of peptides</article-title>. <source>Proteomics</source><year>2012</year>, <volume>12</volume>, <fpage>1111</fpage>–<lpage>1121</lpage>.<pub-id pub-id-type="pmid">22577012</pub-id></mixed-citation></ref><ref id="ref19"><mixed-citation publication-type="journal" id="cit19"><name><surname>Maclean</surname><given-names>B.</given-names></name>; <name><surname>Tomazela</surname><given-names>D. M.</given-names></name>; <name><surname>Abbatiello</surname><given-names>S. E.</given-names></name>; <name><surname>Zhang</surname><given-names>S.</given-names></name>; <name><surname>Whiteaker</surname><given-names>J. R.</given-names></name>; <name><surname>Paulovich</surname><given-names>A. G.</given-names></name>; <name><surname>Carr</surname><given-names>S. A.</given-names></name>; <name><surname>Maccoss</surname><given-names>M. J.</given-names></name><article-title>Effect of collision
energy optimization on the measurement of peptides by selected reaction
monitoring (SRM) mass spectrometry</article-title>. <source>Anal. Chem.</source><year>2010</year>, <volume>82</volume>, <fpage>10116</fpage>–<lpage>10124</lpage>.<pub-id pub-id-type="pmid">21090646</pub-id></mixed-citation></ref><ref id="ref20"><mixed-citation publication-type="journal" id="cit20"><name><surname>Whiteaker</surname><given-names>J. R.</given-names></name>; <name><surname>Halusa</surname><given-names>G. N.</given-names></name>; <name><surname>Hoofnagle</surname><given-names>A. N.</given-names></name>; <name><surname>Sharma</surname><given-names>V.</given-names></name>; <name><surname>MacLean</surname><given-names>B.</given-names></name>; <name><surname>Yan</surname><given-names>P.</given-names></name>; <name><surname>Wrobel</surname><given-names>J. A.</given-names></name>; <name><surname>Kennedy</surname><given-names>J.</given-names></name>; <name><surname>Mani</surname><given-names>D. R.</given-names></name>; <name><surname>Zimmerman</surname><given-names>L. J.</given-names></name>; et al. <article-title>CPTAC Assay Portal: a repository of targeted proteomic assays</article-title>. <source>Nat. Methods</source><year>2014</year>, <volume>11</volume>, <fpage>703</fpage>–<lpage>704</lpage>.<pub-id pub-id-type="pmid">24972168</pub-id></mixed-citation></ref></ref-list></back></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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