MRM screening/biomarker discovery with linear ion trap MS: a library of human cancer-specific peptides

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dc.contributor.authorYang, Xuen
dc.contributor.authorLazar, Iuliana M.en
dc.contributor.departmentBiological Sciencesen
dc.contributor.departmentFralin Life Sciences Instituteen
dc.date.accessioned2016-08-09T02:44:22Zen
dc.date.available2016-08-09T02:44:22Zen
dc.date.issued2009-03-27en
dc.description.abstractBackground The discovery of novel protein biomarkers is essential in the clinical setting to enable early disease diagnosis and increase survivability rates. To facilitate differential expression analysis and biomarker discovery, a variety of tandem mass spectrometry (MS/MS)-based protein profiling techniques have been developed. For achieving sensitive detection and accurate quantitation, targeted MS screening approaches, such as multiple reaction monitoring (MRM), have been implemented. Methods MCF-7 breast cancer protein cellular extracts were analyzed by 2D-strong cation exchange (SCX)/reversed phase liquid chromatography (RPLC) separations interfaced to linear ion trap MS detection. MS data were interpreted with the Sequest-based Bioworks software (Thermo Electron). In-house developed Perl-scripts were used to calculate the spectral counts and the representative fragment ions for each peptide. Results In this work, we report on the generation of a library of 9,677 peptides (p < 0.001), representing ~1,572 proteins from human breast cancer cells, that can be used for MRM/MS-based biomarker screening studies. For each protein, the library provides the number and sequence of detectable peptides, the charge state, the spectral count, the molecular weight, the parameters that characterize the quality of the tandem mass spectrum (p-value, DeltaM, Xcorr, DeltaCn, Sp, no. of matching a, b, y ions in the spectrum), the retention time, and the top 10 most intense product ions that correspond to a given peptide. Only proteins identified by at least two spectral counts are listed. The experimental distribution of protein frequencies, as a function of molecular weight, closely matched the theoretical distribution of proteins in the human proteome, as provided in the SwissProt database. The amino acid sequence coverage of the identified proteins ranged from 0.04% to 98.3%. The highest-abundance proteins in the cellular extract had a molecular weight (MW)<50,000. Conclusion Preliminary experiments have demonstrated that putative biomarkers, that are not detectable by conventional data dependent MS acquisition methods in complex un-fractionated samples, can be reliable identified with the information provided in this library. Based on the spectral count, the quality of a tandem mass spectrum and the m/z values for a parent peptide and its most abundant daughter ions, MRM conditions can be selected to enable the detection of target peptides and proteins.en
dc.description.sponsorshipNCS: R21CA126669en
dc.description.sponsorshipNational Cancer Instituteen
dc.description.versionPublished versionen
dc.format.extent? - ? (11) page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifier.citationBMC Cancer. 2009 Mar 27;9(1):96en
dc.identifier.doihttps://doi.org/10.1186/1471-2407-9-96en
dc.identifier.issn1471-2407en
dc.identifier.urihttp://hdl.handle.net/10919/72124en
dc.identifier.volume9en
dc.language.isoenen
dc.publisherBiomed Centralen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000265612200001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderXu Yang et al.; licensee BioMed Central Ltd.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectOncologyen
dc.subjectMONITORING MASS-SPECTROMETRYen
dc.subjectBREAST-CANCERen
dc.subjectABSOLUTE QUANTIFICATIONen
dc.subjectQUANTITATIVE PROTEOMICSen
dc.subjectLIQUID-CHROMATOGRAPHYen
dc.subjectBIOMARKER DISCOVERYen
dc.subjectSHOTGUN PROTEOMICSen
dc.subjectHUMAN PLASMAen
dc.subjectPROTEINen
dc.subjectEXPRESSIONen
dc.titleMRM screening/biomarker discovery with linear ion trap MS: a library of human cancer-specific peptidesen
dc.title.serialBMC Canceren
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Faculty of Health Sciencesen
pubs.organisational-group/Virginia Tech/Scienceen
pubs.organisational-group/Virginia Tech/Science/Biological Sciencesen
pubs.organisational-group/Virginia Tech/Science/COS T&R Facultyen

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