title: An automated pipeline for high-throughput label-free quantitative proteomics.
abstract: We present a computational pipeline for the quantification of peptides and proteins in label-free LC-MS/MS data sets. 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 on the basis of two small data sets 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 heterogeneous data set of 58 LC-MS/MS runs.
authors: Department of Biology, Institute of Molecular Systems Biology, ETH Zürich , 8093 Zürich, Switzerland.
authors: Hendrik
authors: H
authors: Weisser
authors: Sven
authors: S
authors: Nahnsen
authors: Jonas
authors: J
authors: Grossmann
authors: Lars
authors: L
authors: Nilse
authors: Andreas
authors: A
authors: Quandt
authors: Hendrik
authors: H
authors: Brauer
authors: Marc
authors: M
authors: Sturm
authors: Erhan
authors: E
authors: Kenar
authors: Oliver
authors: O
authors: Kohlbacher
authors: Ruedi
authors: R
authors: Aebersold
authors: Lars
authors: L
authors: Malmström
mesh_terms: D000465:Algorithms; D001331:Automation; D002853:Chromatography, Liquid / Q000379:methods; D057166:High-Throughput Screening Assays / Q000379:methods; D006801:Humans; D007921:Leptospira interrogans; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D013297:Streptococcus pyogenes; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D011506:Proteins