Show simple item record

dc.contributor.authorSchenk, Susannen_US
dc.contributor.authorSchoenhals, Gary J.en_US
dc.contributor.authorDe Souza, Gustavo A.en_US
dc.contributor.authorMann, Matthiasen_US
dc.date.accessioned2013-10-31T12:57:45Z
dc.date.available2013-10-31T12:57:45Z
dc.date.issued2008-09-15eng
dc.PublishedBMC Medical Genomics 1:41eng
dc.identifier.issn1755-8794
dc.identifier.urihttps://hdl.handle.net/1956/7464
dc.description.abstractBackground: The immense diagnostic potential of human plasma has prompted great interest and effort in cataloging its contents, exemplified by the Human Proteome Organization (HUPO) Plasma Proteome Project (PPP) pilot project. Due to challenges in obtaining a reliable blood plasma protein list, HUPO later re-analysed their own original dataset with a more stringent statistical treatment that resulted in a much reduced list of high confidence (at least 95%) proteins compared with their original findings. In order to facilitate the discovery of novel biomarkers in the future and to realize the full diagnostic potential of blood plasma, we feel that there is still a need for an ultra-high confidence reference list (at least 99% confidence) of blood plasma proteins. Methods: To address the complexity and dynamic protein concentration range of the plasma proteome, we employed a linear ion-trap-Fourier transform (LTQ-FT) and a linear ion trap-Orbitrap (LTQ-Orbitrap) for mass spectrometry (MS) analysis. Both instruments allow the measurement of peptide masses in the low ppm range. Furthermore, we employed a statistical score that allows database peptide identification searching using the products of two consecutive stages of tandem mass spectrometry (MS3). The combination of MS3 with very high mass accuracy in the parent peptide allows peptide identification with orders of magnitude more confidence than that typically achieved. Results: Herein we established a high confidence set of 697 blood plasma proteins and achieved a high 'average sequence coverage' of more than 14 peptides per protein and a median of 6 peptides per protein. All proteins annotated as belonging to the immunoglobulin family as well as all hypothetical proteins whose peptides completely matched immunoglobulin sequences were excluded from this protein list. We also compared the results of using two high-end MS instruments as well as the use of various peptide and protein separation approaches. Furthermore, we characterized the plasma proteins using cellular localization information, as well as comparing our list of proteins to data from other sources, including the HUPO PPP dataset. Conclusion: Superior instrumentation combined with rigorous validation criteria gave rise to a set of 697 plasma proteins in which we have very high confidence, demonstrated by an exceptionally low false peptide identification rate of 0.29%.en_US
dc.language.isoengeng
dc.publisherBioMed Centraleng
dc.rightsAttribution CC BYeng
dc.rights.urihttp://creativecommons.org/licenses/by/2.0/eng
dc.titleA high confidence, manually validated human blood plasma protein reference seten_US
dc.typePeer reviewed
dc.typeJournal article
dc.date.updated2013-08-28T17:02:50Z
dc.description.versionpublishedVersionen_US
dc.rights.holderCopyright 2008 Schenk et al; licensee BioMed Central Ltd.
dc.rights.holderSusann Schenk et al.; licensee BioMed Central Ltd.
dc.source.articlenumber41
dc.identifier.doihttps://doi.org/10.1186/1755-8794-1-41
dc.source.journalBMC Medical Genomics
dc.source.401


Files in this item

Thumbnail
Thumbnail
Thumbnail
Thumbnail

This item appears in the following Collection(s)

Show simple item record

Attribution CC BY
Except where otherwise noted, this item's license is described as Attribution CC BY