Mass spectrometry applied to bottom-up proteomics: entering the high-throughput era for hypothesis testing
Proteins constitute a key class of molecular components that perform essential biochemical
reactions in living cells. Whether the aim is to extensively characterize a given protein or to …
reactions in living cells. Whether the aim is to extensively characterize a given protein or to …
Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present
Mass-spectrometry-based proteomics is continuing to make major contributions to the
discovery of fundamental biological processes and, more recently, has also developed into …
discovery of fundamental biological processes and, more recently, has also developed into …
Comparison of full-scan, data-dependent, and data-independent acquisition modes in liquid chromatography–mass spectrometry based untargeted metabolomics
Full-scan, data-dependent acquisition (DDA), and data-independent acquisition (DIA) are
the three common data acquisition modes in high resolution mass spectrometry-based …
the three common data acquisition modes in high resolution mass spectrometry-based …
OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data
There are amendments to 10.1038/nbt. 2841 220 volume 32 NumBeR 3 mARCH 2014
NATURE BIoTECHNoloGy as Skyline23 and PeakView (AB SCIEX), can visualize the XIC …
NATURE BIoTECHNoloGy as Skyline23 and PeakView (AB SCIEX), can visualize the XIC …
Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis
Most proteomic studies use liquid chromatography coupled to tandem mass spectrometry to
identify and quantify the peptides generated by the proteolysis of a biological sample …
identify and quantify the peptides generated by the proteolysis of a biological sample …
Andromeda: a peptide search engine integrated into the MaxQuant environment
J Cox, N Neuhauser, A Michalski… - Journal of proteome …, 2011 - ACS Publications
A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in
sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel …
sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel …
Byonic: advanced peptide and protein identification software
M Bern, YJ Kil, C Becker - Current protocols in bioinformatics, 2012 - Wiley Online Library
Byonic is the name of a software package for peptide and protein identification by tandem
mass spectrometry. This software, which has only recently become commercially available …
mass spectrometry. This software, which has only recently become commercially available …
[HTML][HTML] Technical advances in proteomics: new developments in data-independent acquisition
The ultimate aim of proteomics is to fully identify and quantify the entire complement of
proteins and post-translational modifications in biological samples of interest. For the last 15 …
proteins and post-translational modifications in biological samples of interest. For the last 15 …
More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC− MS/MS
Shotgun proteomics entails the identification of as many peptides as possible from complex
mixtures. Here we investigate how many peptides are detectable by high resolution MS in …
mixtures. Here we investigate how many peptides are detectable by high resolution MS in …
Parallel reaction monitoring using quadrupole‐Orbitrap mass spectrometer: principle and applications
A Bourmaud, S Gallien, B Domon - Proteomics, 2016 - Wiley Online Library
Targeted mass spectrometry‐based approaches are nowadays widely used for quantitative
proteomics studies and more recently have been implemented on high resolution/accurate …
proteomics studies and more recently have been implemented on high resolution/accurate …