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arXiv · 1811.11846

Fast Proteome Identification and Quantification from Data-Dependent Acquisition - Tandem Mass Spectrometry using Free Software Tools

Jesse G. Meyer
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Abstract

Identification of nearly all proteins in a system using data-dependent acquisition (DDA) mass spectrometry has become routine for simple organisms, such as bacteria and yeast. Still, quantification of the identified proteins may be a complex process and require multiple different software packages. This protocol describes 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. This protocol may be used to quantify proteome remodeling in response to a drug treatment or a gene knockout. Notably, the method uses the latest and fastest freely-available software, and the entire protocol can be completed in a few hours with data from organisms with relatively small genomes, such as yeast or bacteria.

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BibTeXRIS

Jesse G. Meyer. 2018-11-28. Fast Proteome Identification and Quantification from Data-Dependent Acquisition - Tandem Mass Spectrometry using Free Software Tools. https://doi.org/10.3390/mps2010008

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