yeast-ups1-tal08

Shotgun proteomics using multidimensional liquid chromatography coupled with tandem mass spectrometrywere performed on all biological samples, including universalproteomics standard set (UPS1), the S. cerevisiae Gcn4 affinity-purified complex (Yeast), S. cerevisiaetranscription complexes using the Tal08 minichromosome(Tal08). The RAW files generated from thedifferent LC/MS/MS experiments were converted tomzXML format with the program ReadW. The MS/MSspectra were extracted from the mzXML file using theprogram MzXML2Search and all data was processedusing the SEQUEST software. The UPS1 dataset, developed by Sigma-Aldrichcompany, contains 48 purified human proteins digestedwith trypsin. The SEQUEST search results include17,335 PSMs, among which 8974 PSMs match targetpeptides and 8361 PSMs match decoy peptides. TheYeast dataset contains 6652 proteins and SEQUESToutputs 14,892 PSMs, among which 6703 PSMs matchtarget peptides and 8189 PSMs match decoy peptides.