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Identification and sequencing analysis of intact proteins via collision‐induced dissociation and quadrupole time‐of‐flight mass spectrometry
Author(s) -
NemethCawley Jennifer F.,
Rouse Jason C.
Publication year - 2002
Publication title -
journal of mass spectrometry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.475
H-Index - 121
eISSN - 1096-9888
pISSN - 1076-5174
DOI - 10.1002/jms.281
Subject(s) - chemistry , mass spectrometry , chromatography , quadrupole time of flight , collision induced dissociation , top down proteomics , protein mass spectrometry , peptide mass fingerprinting , peptide , dissociation (chemistry) , isobaric labeling , database search engine , bottom up proteomics , time of flight mass spectrometry , tandem mass spectrometry , ion , analytical chemistry (journal) , proteomics , biochemistry , search engine , ionization , organic chemistry , information retrieval , computer science , gene
Identifying unknown proteins has become a central focal point for proteomic and biopharmaceutical development laboratories. Our laboratory investigated using quadrupole time‐of‐flight mass spectrometry (Qq/TOFMS) for the analysis of intact proteins for the purpose of identifying unknowns while limiting the number of sample‐handling steps between protein extraction and identification. Eight standard proteins, both unmodified and disulfide‐bonded and ranging in mass from 5 to 66 kDa, were analyzed using nanoelectrospray and collision‐induced dissociation to generate peptide sequence tags. An MS analysis, followed by MS/MS analyses on two to five individual protein charge states, were obtained to make an identification. Peptide sequence tags were extracted from the MS/MS data and used, in conjunction with molecular mass and source origin, to obtain protein identifications using the web‐based search engine ProteinInfo ( www.proteometrics.com ). All of the proteins were unambiguously identified from the input data, after which, all of the major product ions were identified for structural information. In most cases, N‐ and/or C‐terminal ions, and also stretches of consecutive product ions from the protein interior, were observed. This method was applied to the analysis and identification of an unknown detected via reversed‐phase high‐performance liquid chromatography. Copyright © 2002 John Wiley & Sons, Ltd.