This file has been generated by searching the raw mzXML file of the ProteomeXchange PXD000001 data set against the erwinia_carotovora.fasta using the MSGF+ search engine: java -jar ~/bin/MSGFPlus.20140630/MSGFPlus.jar -s TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML -d erwinia_carotovora.fasta -inst 1 -protocol 2
In this TMT 6-plex experiment, four exogenous proteins were spiked into an equimolar Erwinia carotovora lysate with varying proportions in each channel of quantitation; yeast enolase (ENO) at 10:5:2.5:1:2.5:10, bovine serum albumin (BSA) at 1:2.5:5:10:5:1, rabbit glycogen phosphorylase (PHO) at 2:2:2:2:1:1 and bovin cytochrome C (CYT) at 1:1:1:1:1:2. Proteins were then digested, differentially labelled with TMT reagents, fractionated by reverse phase nanoflow UPLC (nanoACQUITY, Waters), and analysed on an LTQ Orbitrap Velos mass spectrometer (Thermo Scientific). Files in multiple format will be used to illustrate the input/output capabilities that are available to the proteomics audience. The companion package provides dedicated functions to directly download the data.
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