MS/MS Shotgun Proteomics Data Repository
Christine Vogel
Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, MBB 3.210, Austin, TX 78712
Email: cvogel at mail utexas edu
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 is to 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; some data is from an older Thermo DecaPlus LCQ.
- For each sample, several injections (RAW files) are available.
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
- 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
- .BIGPARSE or .APEX or .ZSCORE is the output of the APEX post-processing
- Protocol for APEX calculations
- estimates of protein concentrations and differential expression
- Fasta files used in SEQUEST searches:
Data
Data_01 - Human - Orbitrap - Musashi-1 overexpression in T293 cells
Abreu et al, J Biol Chem. 2009
Data_02 - Yeast - Orbitrap - Wild-type grown in rich medium (YPD), harvested in log-phase
Ramakrishnan et al,
Bioinformatics, 2009
Ramakrishnan et al. Under review
This dataset is part of what we consider a 'gold-standard' of protein expression in wild-type yeast, grown to log-phase in rich medium (YPD).
Data_03 - E. coli - Orbitrap - Wild-type grown in minimal medium (M9), harvested in log-phase
Ramakrishnan et al,
Bioinformatics, 2009
Ramakrishnan et al. Under review
Data_04 - Yeast - LCQ - Polysomal fraction (sucrose gradient)
Ramakrishnan et al,
Bioinformatics, 2009
Ramakrishnan et al. Under review
Data_05 - Human - Orbitrap - Daoy medulloblastoma wildtype, cell lysate
Ramakrishnan et al,
Bioinformatics, 2009
Ramakrishnan et al. Under review
Galante et al, RNA Biology, 2009 (in press)
Data_06 - Human - LCQ - Daoy medulloblastoma wildtype, cell lysate
Ramakrishnan et al,
Bioinformatics, 2009
Ramakrishnan et al. Under review
Data_07 - Human - Orbitrap - T293 embryonic kidney cells, overexpressing GFP, cell lysate and pellet
Ramakrishnan et al. Under review
Data_08 - Human - Orbitrap - U251 gliolastoma, GFP transfected, cell lysate and pellet
Galante et al, RNA Biology, 2009 (in press)
Other links
Please do not hesitate to contact me for any additional questions.
C. Vogel, cvogel at mail utexas edu
May 2009