This data was uploaded on 01/15/2014 in conjunction with a manuscript entitled "The generating function approach for peptide identification in spectral networks" that was accepted to the RECOMB 2014 conference.

Decompress all of the *.tar.gz files to access the raw data. The specs_ms_Rep2_CID.mgf file contains all clustered MS/MS spectra used in the RECOMB paper.

*.RAW - All unfiltered spectra from the following study (high/low CID/ETD decision tree MS/MS from multiple enzymes+SCX fractions of a whole yeast cell lysate). Only CID scans from the 2nd technical replicate were extracted for results reported in the RECOMB paper.

Swaney DL, Wenger CD, Coon JJ (2010) Value of using multiple proteases for large-scale mass spectrometry-based proteomics. J. Proteome Res. 9:1323–1329.

specs_ms_Rep2_CID.mgf - All CID MS/MS scans from the 2nd technical replicate that were clustered by MSCluster (all spectra used in the RECOMB paper)