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Title: Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data

In mass spectrometry-based bottom-up proteomics, data-independent acquisition (DIA) is an emerging technique due to its comprehensive and unbiased sampling of precursor ions. However, current DIA methods use wide precursor isolation windows, resulting in co- fragmentation and complex mixture spectra. Thus, conventional database searching tools that identify peptides by interpreting individual MS/MS spectra are inherently limited in analyzing DIA data. Here we discuss an alternative approach, peptide-centric analysis, which tests directly for the presence and absence of query peptides. We discuss how peptide-centric analysis resolves some limitations of traditional spectrum-centric analysis, and we outline the benefits of peptide-centric analysis in general.
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Publication Date:
OSTI Identifier:
Report Number(s):
Journal ID: ISSN 1535-9476; 48148; 48680; 400412000
DOE Contract Number:
Resource Type:
Journal Article
Resource Relation:
Journal Name: Molecular and Cellular Proteomics; Journal Volume: 14
American Society for Biochemistry and Molecular Biology
Research Org:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org:
Country of Publication:
United States
Bioinformatics; Mass Spectrometry; SWATH-MS; Tandem MassSpectrometry; Target identification; MS/MS data analysis; analyte-centric analysis; data-independent acquisition; peptide-centric analysis; Environmental Molecular Sciences Laboratory