0000000000349106

AUTHOR

Brendan Maclean

showing 2 related works from this author

A multicenter study benchmarks software tools for label-free proteome quantification

2016

The consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from SWATH-MS (sequential window acquisition of all theoretical fragment ion spectra), a method that uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test datasets from hybrid proteome samples of defined quantitative composition acquired on two different MS instrument…

0301 basic medicineInternationalityProteomeComputer sciencemedia_common.quotation_subjectSoftware toolQuantitative proteomicsBiomedical EngineeringBioengineeringcomputer.software_genreBioinformaticsSensitivity and SpecificityApplied Microbiology and BiotechnologyArticleMass Spectrometry03 medical and health sciencesSoftwareQuality (business)media_commonLabel freeStaining and Labeling030102 biochemistry & molecular biologybusiness.industryReproducibility of ResultsBenchmarkingComputingMethodologies_PATTERNRECOGNITION030104 developmental biologyMulticenter studyProteomeBenchmark (computing)Molecular MedicineData miningbusinesscomputerAlgorithmsSoftwareBiotechnologyNature Biotechnology
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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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