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An automated pipeline for high-throughput label-free quantitative proteomics.

Citation Weisser, Hendrik; Nahnsen, Sven; Grossmann, Jonas; Nilse, Lars; Quandt, Andreas; Brauer, Hendrik; Sturm, Marc; Kenar, Erhan; Kohlbacher, Oliver; Aebersold, Ruedi; Malmstrom, Lars; An automated pipeline for high-throughput label-free quantitative proteomics. J Proteome Res (2013), -: Epub ahead of print.
Abstract We present a computational pipeline for the quantification of peptides and proteins in label-free LC-MS/MS datasets. The pipeline is composed of tools from the OpenMS software framework and is applicable to the processing of large experiments (50+ samples). We describe several enhancements that we have introduced to OpenMS to realize the implementation of this pipeline. They include new algorithms for centroiding of raw data, for feature detection, for the alignment of multiple related measurements, and a new tool for the calculation of peptide and protein abundances. Where possible, we compare the performance of the new algorithms to that of their established counterparts in OpenMS. We validate the pipeline based on two small datasets that provide ground truths for the quantification. There, we also compare our results to those of MaxQuant and Progenesis LC-MS -- two popular alternatives for the analysis of label-free data. We then show how our software can be applied to a large heterogenous dataset of 58 LC-MS/MS runs.
Synopsis We describe a protocol for label-free quantification of shotgun data using OpenMS.
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