%0 Journal Article
%T Fast Proteome Identification and Quantification from Data-Dependent Acquisition¨CTandem Mass Spectrometry (DDA MS/MS) Using Free Software Tools
%A Jesse G. Meyer
%J Methods and Protocols | An Open Access Journal from MDPI
%D 2019
%R https://doi.org/10.3390/mps2010008
%X The identification of nearly all proteins in a biological system using data-dependent acquisition (DDA) tandem mass spectrometry has become routine for organisms with relatively small genomes such as bacteria and yeast. Still, the quantification of the identified proteins may be a complex process and often requires multiple different software packages. In this protocol, I describe a flexible strategy for the identification and label-free quantification of proteins from bottom-up proteomics experiments. This method can be used to quantify all the detectable proteins in any DDA dataset collected with high-resolution precursor scans and may be used to quantify proteome remodeling in response to drug treatment or a gene knockout. Notably, the method is statistically rigorous, uses the latest and fastest freely-available software, and the entire protocol can be completed in a few hours with a small number of data files from the analysis of yeast. View Full-Tex
%U https://www.mdpi.com/2409-9279/2/1/8