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Getting the software

This software is included in the current TPP distribution.

In a nutshell

StPeter is a module within the trans-proteomic pipeline to perform label-free quantification on shotgun MS/MS spectra.

More detail

StPeter performs protein-level quantification of mass spectrometry data using MS/MS data. The primary unit of quantification is the Spectral Index, which is an extension of spectral counting that integrates fragment ion peak intensity. The protein quantities are normalized by protein length and total spectral index abundance across the entire sample. An additional features computes the distributed Normalized Spectral Index (dSIn), which includes the use of degenerate peptide spectrum matches through distribution weighted by novel PSM contribution to the proteins.


We provide two tutorials that replicate the analyses performed in the publication

StPeter Tutorial 1

StPeter Tutorial 2


  • Michael Hoopmann
  • Jason Winget


StPeter: Seamless Label-Free Quantification with the Trans-Proteomic Pipeline MR Hoopmann, JM Winget, L Mendoza, RL Moritz - Journal of proteome research, 2018

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