Detection of co-eluted peptides using database search methods

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dc.contributor.authorAlves, Gelio
dc.contributor.authorOgurtsov, Aleksey Y
dc.contributor.authorKwok, Siwei
dc.contributor.authorWu, Wells W
dc.contributor.authorWang, Guanghui
dc.contributor.authorShen, Rong-Fong
dc.contributor.authorYu, Yi-Kuo
dc.date.accessioned2021-12-06T15:42:13Z
dc.date.available2021-12-06T15:42:13Z
dc.date.issued2008-07-02
dc.description.abstractCurrent experimental techniques, especially those applying liquid chromatography mass spectrometry, have made high-throughput proteomic studies possible. The increase in throughput however also raises concerns on the accuracy of identification or quantification. Most experimental procedures select in a given MS scan only a few relatively most intense parent ions, each to be fragmented (MS2) separately, and most other minor co-eluted peptides that have similar chromatographic retention times are ignored and their information lost. We have computationally investigated the possibility of enhancing the information retrieval during a given LC/MS experiment by selecting the two or three most intense parent ions for simultaneous fragmentation. A set of spectra is created via superimposing a number of MS2 spectra, each can be identified by all search methods tested with high confidence, to mimick the spectra of co-eluted peptides. The generated convoluted spectra were used to evaluate the capability of several database search methods – SEQUEST, Mascot, X!Tandem, OMSSA, and RAId_DbS – in identifying true peptides from superimposed spectra of co-eluted peptides. We show that using these simulated spectra, all the database search methods will gain eventually in the number of true peptides identified by using the compound spectra of co-eluted peptides. Reviewed by Vlad Petyuk (nominated by Arcady Mushegian), King Jordan and Shamil Sunyaev. For the full reviews, please go to the Reviewers' comments section.en_US
dc.description.urihttps://doi.org/10.1186/1745-6150-3-27
dc.identifierhttps://doi.org/10.13016/hxtl-1zu9
dc.identifier.citationAlves, G., Ogurtsov, A.Y., Kwok, S. et al. Detection of co-eluted peptides using database search methods. Biol Direct 3, 27 (2008).en_US
dc.identifier.urihttp://hdl.handle.net/1903/28194
dc.language.isoen_USen_US
dc.publisherSpringer Natureen_US
dc.relation.isAvailableAtCollege of Computer, Mathematical & Natural Sciencesen_us
dc.relation.isAvailableAtMathematicsen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us
dc.subjectReceiver Operating Characteristicen_US
dc.subjectReceiver Operating Characteristic Curveen_US
dc.subjectComplex Protein Mixtureen_US
dc.subjectCompound Spectrumen_US
dc.subjectTheoretical Fragmenten_US
dc.titleDetection of co-eluted peptides using database search methodsen_US
dc.typeArticleen_US

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