.

MSRC Bioinformatics

MSRC Bioinformatics Core Data

Name Publication Description
Mouse liver homogenate
4/26/2011
ScanRanker: Ma et al The files in directory were generated from a whole mouse liver protein extract obtained from adult CD1 mice in Vanderbilt University Mass Spectrometry Research Center. Proteins were reduced with DTT and alkylated with iodoacetamide prior to digestion with sequencing grade Trypsin. Four replicate LC-MS/MS runs were performed on a Bruker Esquire HCT ultra ion trap. Funding from U24 CA126479 supported this collection.
Mouse spinophilin immunoprecipitations
10/24/2008
Novel spinophilin-associated proteins: Baucum et al In each of the LC-MS/MS experiments, an antibody (from goat, mouse, or rabbit) was used to immunoprecipitate spinophilin from either mouse or rat striatum, with IgG or knockout controls. The proteins were separated by SDS-PAGE, reduced with DTT, alkylated with iodoacetamide, and digested by trypsin. The resulting peptides were separated by RPLC en route to a Thermo LTQ for data-dependent tandem mass spectrometry. Grant support from NIH MH63232, NS044282, MH65215, NS061537, CA126218, AHA 0815090E and a Hobbs Discovery grant contributed support to mass spectrometry on this project.
Human embryonic kidney APPL1 pulldowns
10/6/2008
APPL1 phosphorylation sites: Gant-Branum et al FLAG-GFP-APPL1 was pulled down from Human embryonic kidney (HEK) cells. The protein was separated into three equal aliquots and digested by trypsin, chymotrypsin, and Glu C proteases, respectively. The Proteomics Core of the MSRC collected MS/MS data from both LTQ and Orbitrap mass spectrometers for these samples. This work was supported by the Vanderbilt University College of Arts and Sciences, the Vanderbilt Institute for Chemical Biology, the American Society for Mass Spectrometry (Research Award), and NIH grants MH071674 and T32CA78136.
Human depleted serum
10/6/2008
IDPicker 2.0: Ma et al The files in directory were generated from depleted human serum processed by Lisa Zimmerman of the Ayers Institute at Vanderbilt University. Proteins were reduced and alkylated using iodoacetamide. Peptides were produced through trypsin digestion, and the three hour RPLC separations (including a two hour shallow gradient) were conducted on an LTQ Orbitrap at the Ayers Institute. Eight centroided tandem mass spectra were collected following each profile MS scan. Collection of these data was supported by U24 CA126479.
Human depleted plasma
6/17/2008
IDPicker 2.0: Ma et al Penelope Drake collected human plasma for the NCI CPTAC Biospecimen Working Group at University of California, San Francisco. Birgit Schilling and Bradford Gibson at The Buck Institute for Age Research depleted the 14 most abundant proteins from these samples, reduced and alkylated disulfide bridges with iodoacetamide, digested with trypsin, and conducted LC-MS/MS on an Applied Biosystems QSTAR-Elite. These WIFF and SCAN files represent the original instrument captures from this instrument. The Tabb Laboratory converted these data to mzXML format (included in a separate directory). These data were collected via funding from NCI CPTAC: U24 CA0126477.
Human DLD1 lysate
5/28/2008
IDPicker 2.0: Ma et al The files in directory were generated from human colon adenocarcinoma cells (DLD-1 cell line) by Patrick Halvey of the Ayers Institute at Vanderbilt University. Proteins were reduced and alkylated using iodoacetamide. Peptides were produced through trypsin digestion, and the 90-minute RPLC separations (including a one hour shallow gradient) were conducted on an LTQ-XL at the Ayers Institute. Five centroided tandem mass spectra were collected following each MS scan. Collection of these data was supported by U24 CA126479.
Yeast whole cell extracts
1/9/2008
Network-assisted protein identification: Li et al The files in directory were generated from the NCI CPTAC yeast lysate reference material. Trypsin digests were produced by Lisa Zimmerman of Vanderbilt. Reduction and alkylation included the use of iodoacetamide for blocking cysteines, and the three hour RPLC separations (including a two hour shallow gradient) were conducted on an LTQ-XL Orbitrap at the Vanderbilt Mass Spectrometry Research Center. Eight centroided tandem mass spectra were collected following each profile MS scan. Collection of these data was supported by U24 CA126479.
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.
SCX vs IEF of human RKO cells
6/1/07
Evaluation of SCX vs IEF: Slebos et al These datasets were generated from the human colorectal carcinoma cell line RKO and from a primary rectal adenocarcinoma for method development (Slebos et al. J Prot. Res., Oct 2008; 7: 5286-5294). The main comparison in the paper was between strong cation exchange (SCX) and isoelectric Focusing (IEF) as a first dimension for peptide separation. These data were generated on an LTQ-Orbitrap using 10ug and 100ug quantities of RKO protein lysate. To study peptide and protein coverage by either SCX or IEF, 9 replicate runs were conducted using 50ug quantities of the primary carcinoma specimen. The study was supported by the National Cancer Institute Clinical Proteomic Technologies Assessment for Cancer program through National Institutes of Health Grant 1U24CA126479.
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.

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