0000000000519405

AUTHOR

Ben C. Collins

0000-0003-0827-3495

showing 2 related works from this author

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics

2016

Nature Methods, 13 (9)

Pluripotent Stem CellsProteomics0301 basic medicineAnalyteStreptococcus pyogenesSoftware toolQuantitative proteomicsProteomic analysisComputational biologyBiologyProteome informaticsProteomicsBioinformaticsBiochemistryArticleMass Spectrometry03 medical and health sciencesSequence Analysis ProteinProtein methodsHumansProtein PrecursorsHuman Induced Pluripotent Stem CellsMolecular BiologyElectronic Data ProcessingReproducibility of ResultsCell BiologyMass spectrometricTargeted proteomics030104 developmental biologyProteolysissense organsPeptidesSequence AlignmentAlgorithmsSoftwareBiotechnologyNature Methods
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Building high-quality assay libraries for targeted analysis of SWATH MS data

2015

Targeted proteomics by selected/multiple reaction monitoring (S/MRM) or, on a larger scale, by SWATH (sequential window acquisition of all theoretical spectra) MS (mass spectrometry) typically relies on spectral reference libraries for peptide identification. Quality and coverage of these libraries are therefore of crucial importance for the performance of the methods. Here we present a detailed protocol that has been successfully used to build high-quality, extensive reference libraries supporting targeted proteomics by SWATH MS. We describe each step of the process, including data acquisition by discovery proteomics, assertion of peptide-spectrum matches (PSMs), generation of consensus sp…

ProteomicsSwath msComputer sciencemedia_common.quotation_subjectComputational biologyBioinformaticsProteomicsGeneral Biochemistry Genetics and Molecular BiologyIdentification (information)Targeted proteomicsPeptide LibraryTandem Mass SpectrometryCombinatorial Chemistry TechniquesQuality (business)media_commonNature Protocols
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