Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra

By John D. Venable, M. Dong, J. Wohlschlegel, A. Dillin, John R. Yates III. Nature Methods, 2004

750 citations recorded by the source corpus.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/bb42fdc02774abdf2991e0246ce58f97dd946cfa

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Citations in the corpus

IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs (2020, background): “A mixture model (Equation (3)) is built using type 1 and −1 ions, and the expectation-maximization (EM) algorithm is used to fit the model and subsequently calculate the posterior probability.”
DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics (2015, methodology): “Recent improvements in MS instrumentation have enabled alternative workflows to DDA, namely, DIA methods 4,6,8–14 , diA-umpire: comprehensive computational framework for data-independent acquisition proteomics Chih-Chiang Tsou 1,2 , Dmitry Avtonomov 2 , Brett Larsen 3 , Monika Tucholska 3 ,…”
The Skyline Ecosystem: Informatics for Quantitative Mass Spectrometry Proteomics (2017, methodology): “(A detailed review of DIA methodology can be found elsewhere (Chapman, Goodlett, and Masselon 2014; Bilbao et al. 2015), including peptide-centric approaches to DIA (Ting et al. 2015).)”
Less label, more free: Approaches in label‐free quantitative mass spectrometry (2011, methodology): “There may be a bias in this type of data for co-eluting peptides towards omitting the lower abundant peptides from MS/MS [68].”
Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis* (2012, methodology): “DIA acquisition using consecutive swaths is not novel per se (18, 20).”
Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial (2018, positive): “Since the first implementations of DIA in the early 2000s (Masselon et al , 2000; Purvine et al , 2003; Venable et al , 2004), numerous improvements in terms of data acquisition speed, mass accuracy and resolution have taken place on the instrument side.”