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

@article{Weisser2013AnAP,
  title={An automated pipeline for high-throughput label-free quantitative proteomics.},
  author={Hendrik Weisser and Sven Nahnsen and Jonas Grossmann and Lars Nilse and Andreas Quandt and Hendrik Brauer and Marc Sturm and Erhan Kenar and Oliver Kohlbacher and Ruedi Aebersold and Lars Malmstr{\"o}m},
  journal={Journal of proteome research},
  year={2013},
  volume={12 4},
  pages={1628-44}
}
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… CONTINUE READING
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