OpenMS

An open-source framework for mass spectrometry and TOPP – The OpenMS Proteomics Pipeline

MetaProSIP

MetaProSIP

MetaProSIP: automated inference of elemental fluxes in microbial communities

Download sample data and TOPPAS workflows:
MetaProSIP sample data
Please note that experimental data (mzML files) have already been picked to reduce the size of the file.

Example output and quality control report for 15N mix dataset (replicate a, 1:3):
MetaProSIP quality control report

Download Win64 installer:
Win64 installer
Note that MetaProSIP requires R installed and accessible via the path environment variable.
Additionally, following R libraries need to be installed:
gplots
fpc
clValid

Raw files:
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000382.

Publications:
@article{sachsenberg2014metaprosip,
title={MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics},
author={Sachsenberg, Timo and Herbst, Florian-Alexander and Taubert, Martin and Kermer, Ren{\’e} and Jehmlich, Nico and von Bergen, Martin and Seifert, Jana and Kohlbacher, Oliver},
journal={Journal of proteome research},
year={2014},
publisher={ACS Publications}
}
FAQ:

  • I get an “Error: Process returned with non 0 status.“ “Error: File not found (the file ‘C:/Users/USER/AppData/Local/Temp/cluster_result_15NMix_1_3_a_picked_yD9N.dat’ could not be found)“.
    Make sure that a suitable R version (32 bit) and the R packages are installed and add the directory to you PATH environment variable.