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Name	Publication	Description
Canine exocytic vesicles 8/7/2007	FAVS for Naked2 Vesicle Proteomics: Cao et al	These Thermo RAW files represent the proteins found in flow-sorted exocytic vesicles produced from a transfected MDCK (canine) cell line through gradient centrifugation and flowsorting. Proteins were partially run into a gel for cleanup, reduced with DTT, alkylated with iodoacetamide, and digested overnight with trypsin. The resulting peptides were separated both by simple RPLC and by off-line strong cation exchange and subsequent RPLC en route to a Thermo LTQ linear quadrupole ion trap. The vesicle isolation experiment was conducted three times. RAW files in this collection averaged 8428 tandem mass spectra. These data were generated with support from the following NIH grants: CA46413, CA95103, U01 084239, R01 CA126218, U24 CA126479, DK070856.
Yeast whole cell extracts 7/24/2007	DirecTag: Tabb et al	Amy Ham and Kristin Cheek processed these yeast samples at the VUMC Mass Spectrometry Research Center Proteomics Core. Whole cell extracts of S. cerevisiae were reduced and alkylated by DTT and IAA, digested with trypsin, and subjected to 184-minute RPLC separations en route to a Thermo LTQ Orbitrap tandem mass spectrometer. The instrument was set to capture profile MS scans in the Orbitrap and centroid MS/MS scans in the LTQ. These eight RAW files average just over 13,000 tandem mass spectra each. These data were generated under NIH/NCI 1 U24 CA126479.
Human Serum A2M pulldowns 9/16/2006	Prostate Cancer Biomarker Discovery: Burgess et al	Serum samples were collected from six patients with advanced metastatic prostate cancer and six matched patients without evidence of malignancy. Alpha 2 macroglobulin-containing protein complexes were immunoprecipitated and separated by molecular weight in 10% SDS-polyacrylamide gels. Each lane was sliced into into regions and subjected to in-gel digestion. Peptides from each gel region of each patient were subjected to a 95 minute RPLC separation. As peptides eluted in nanospray, the ions were directed to the inlet of a Thermo LTQ tandem mass spectrometer. This work was supported by the Ingram Charitable Trust and National Institutes of Health Grants T32 CA009592, R01 CA126218, ES00267 and CA68485.
Mouse phosphopeptides 7/29/2006	Oncogenic Src and phosphotyrosine: Luo et al	These files contain spectra for phosphopeptides from "Nontransformed" and "Src-transformed" mouse fibroblast cell lines. Chymotrypsin and trypsin were each used for digestion. Two different antibodies were used for purifying phosphotyrosine peptides from the cell lysates. The total set encompasses thirty-six Thermo RAW files, each representing an RPLC of the phos-Tyr peptides. Proteins were reduced with DTT and alkylated with iodoacetamide. These files were produced in one of two different Thermo LTQ instruments at the Vanderbilt Mass Spectrometry Research Center. Each RAW contains approximately 10,000 tandem mass spectra. Each MS was followed by five MS/MS scans, with the exception that an MS/MS/MS scan was captured when the presence of a -98 or -80 Da neutral loss was detected in a MS/MS scan. These experiments were supported by NIH grants GM49882, CA106424, U54 RR020839, 2P50 CA95103, and CA68485.
Yeast whole cell extracts 7/21/2006	Proteomic Parsimony: Zhang et al	Dr. Andrew Link taught the LC-MS/MS section at the 2006 CSHL Proteomic course in July of 2006. Four different groups of students each conducted a MudPIT experiment from a common sample of a S. cerevisiae whole cell lysate. The sample was reduced and alkylated with DTT and IAA prior to trypsin digestion. Each MudPIT included six SCX fractions, each analyzed by a 90 min RPLC separations. Each replicate, produced on a Thermo LTQ, contained approximately 40,600 ms/ms. The CSHL Proteomics course was supported by Grant Number 2T15 CA098595 from the National Cancer Institute.
Sigma49 6/14/2006	MyriMatch: Tabb et al Proteomic Parsimony: Zhang et al	In the Mass Spectrometry Research Center at Vanderbilt University, Amy Ham and Kristin Cheek electrophoresed a mixture of 49 human proteins from Sigma Aldrich (St. Louis, MO) into a short 10% SDS-PAGE gel for cleanup. They reduced and alkylated with iodoacetamide and digested proteins in-gel with trypsin. Three replicate RPLC/MS/MS analyses were produced in a Thermo LTQ instrument (San Jose, CA), yielding approximately 10,900 tandem mass spectra each. This sample represents a pre-production version of the Sigma-Aldrich "Universal Proteomics Standard."
Human gastric vesicles 5/26/2006	Immunoisolated gastric parietal tubuolovesicles: Lapierre et al	Human stomachs from eight transplant patients were used to prepare samples of gastric parietal vesicles. In these data, six of these samples were analyzed by RPLC MS/MS on a Thermo Fisher LTQ instrument for shotgun protein identification. Each set of runs includes both experimental and control runs from SDS and CHAPS elutions. Nine different sets of runs were produced overall from the six samples, for a total of 36 RAW files. Each file contains approximately 10,000 tandem mass spectra. This work was supported by NIH Grants DK-070856, DK-48370, DK-43405, DK-34092, DK-43138, and DK64371.
Yeast Mot1p pulldowns 1/28/2006	Mot1p protein-protein associations: Arnett et al	Mot1p was immunoprecipitated from S. cerevisiae strains YPH252, DPY107, W303, Z1318, YDA106, and YDA136. Each pull-down was reduced with DTT and alkylated with iodoacetamide. A trypsin digest of each was subjected to MudPit analysis, employing triphasic RP/SCX/RP columns. The eluate was electrosprayed at 0.3 microliters a minute into a Thermo LCQ Deca XP Plus tandem mass spectrometer. The files average 2840 ms/ms scans each. This work was supported by NIH grants GM52461, GM64779, HL68744, ES11993, CA098131, and CA126218 as well as NIAID contract number HHSN266200400079C/N01-AI-40079.