MS/MS Shotgun Proteomics Data Repository

Notes

This website provides raw/processed data files from (LC/)LC-MS/MS experiments, information on experimental procedures, data collection and post-processing.

• Experimentation followed our standard protocols (as specified under "General information") unless stated otherwise.
• All files are gzipped for storage space reasons.
• Other experimental details are provided in the respective manuscripts/publications. This website does NOT have information on the purpose/further outcomes of the experiments for which the MS/MS data was collected. This website purely publishes the MS/MS raw data.
• For some datasets, result files are available (formats see below). For details on these calculations, please refer to the respective publications and websites (see Links below). If you are interested in result files for any of the raw data files, please contact me directly (cvogel at mail utexas edu).
• Most of the data provided here has been collected on a Thermo LTQ OrbiTrap Classic; some data is from an older Thermo DecaPlus LCQ.
• For each sample, several injections (RAW files) are available, usually labeled with small letters. They are combined during the post-processing via Peptide/ProteinProphet. An injection is chosen to participate in the combined results if it correlates considerably with other injections. In other words, amongst several technical replicates (injections), we chose the consistent replicates, and ignore the outliers.

General information

• Protocol for tryptic digest of protein mixture prior to MS/MS experiment - The protocol includes CYS modification which is specified in the parameter files below. Some older experiments do not use CYS modification which is indicated in the text.
• Parameter files for typical MS/MS experiment on LTQ-Orbitrap
  • Yeast, LTQ Orbitrap, incl. CYS modification
  • Human, LTQ Orbitrap, incl. CYS modification
  • E. coli, LCQ, no CYS modification
  • E. coli, LTQ Orbitrap, no CYS modification
• Formats for raw and post-processed data:
  • .RAW data is the Thermo MS/MS output format, readable with Bioworks/Sequest
  • .SRF or .DTA is the output of the SEQUEST database search
  • .XML formats are used by Peptide/ProteinProphet
  • 0.05.PROTLST is the ProteinProphet output file parsed for 5% FDR (see below)
  • .BIGPARSE or .APEX or .ZSCORE is the output of the APEX post-processing (see below)
• Protocol for APEX calculations - estimates of protein concentrations and differential expression, including Perl scripts to create above-mentioned files and Oi-values to create APEX estimates
• Fasta files used in SEQUEST searches:
  • E.coli K12
  • Pseudomonas aeruginosa PA01
  • Yeast - SGD April 2006
  • Human - ENSEMBL 44.36f, longest transcript only
  • Human - ENSEMBL 49.36f, longest transcript only
  • Mouse - ENSEMBL 49.37f, longest transcript only
  • Rice - japonica 5.0, longest transcript only

Data

Other links

• APEX Protocol - supplementary website to the published Nature Protocol (Vogel, Marcotte, 2008) based on the method published in Lu/Vogel/Wang (Nature Biotechnology, 2007)
• APEX Quantitative Proteomics Tool - developed by John Braisted and colleagues at the J. Craig Venter Insitute, Rockville, MD.
• Open Proteomics Database - MS/MS database initiated by John Prince/Edward Marcotte (Nature Biotechnology 2004)
• PeptideProphet, ProteinProphet - as part of the Transproteomic Pipeline software for mass spectrometry data analysis
• Peptide Detectability Predictor - for LC/MS Ion Traps
• Thermo LTQ Orbitrap
• Thermo Bioworks/Sequest

Please do not hesitate to contact me for any additional questions.