An Automated Pipeline for High-Throughput Label-Free Quantitative Proteomics

作者:Weisser Hendrik; Nahnsen Sven; Grossmann Jonas; Nilse Lars; Quandt Andreas; Brauer Hendrik; Sturm Marc; Kenar Erhan; Kohlbacher Oliver; Aebersold Ruedi; Malinstroemt Lars
来源:Journal of Proteome Research, 2013, 12(4): 1628-1644.
DOI:10.1021/pr300992u

摘要

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.

  • 出版日期2013-4
  • 单位上海生物信息技术研究中心