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ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC-MS/MS Experiments
Choi, Meena; Eren-Doğu, Zeynep Filiz; Colangelo, Christopher; Cottrell, John; Hoopmann, Michael R.; Kapp, Eugene A.; Vitek, Olga (Amer Chemical Soc, 2017)Detection of differentially abundant proteins in label-free quantitative shotgun liquid chromatography tandem mass spectrometry (LC-MS/MS) experiments requires a series of computational steps that identify and quantify ... -
MSstatsQC 2.0: R/Bioconductor Package for Statistical Quality Control of Mass Spectrometry-Based Proteomics Experiments
Doğu, Eralp; Taheri, Sara Mohammad; Olivella, Roger; Marty, Florian; Lienert, Ian; Reiter, Lukas; Vitek, Olga (Amer Chemical Soc, 2019)MSstatsQC is an R/Bioconductor package for statistical monitoring of longitudinal system suitability and quality control in mass spectrometry-based proteomics. MSstatsQC was initially designed for targeted selected reaction ... -
MSstatsQC: Longitudinal System Suitability Monitoring and Quality Control for Targeted Proteomic Experiments
Doğu, Eralp; Mohammad-Taheri, Sara; Abbatiello, Susan E.; Bereman, Michael S.; MacLean, Brendan; Schilling, Birgit; Vitek, Olga (Amer Soc Biochemistry Molecular Biology Inc, 2017)Selected Reaction Monitoring (SRM) is a powerful tool for targeted detection and quantification of peptides in complex matrices. An important objective of SRM is to obtain peptide quantifications that are (1) suitable for ...
