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Proteomic Data Sets and Software

Name Publication Description
Proteogenomic analysis reveals unanticipated adaptations of colorectal tumor cells to deficiencies in DNA mismatch repair Cancer Research, Halvey et al​ The files in this download correspond to "Proteogenomic analysis reveals unanticipated adaptations of colorectal tumor cells to deficiencies in DNA mismatch repair. Halvey PJ, Wang X, Wang J, Bhat AA, Dhawan P, Li M, Zhang B, Liebler DC, Slebos RJ". The article was published in Cancer Research (PMID: 24247723)
Shotgun Proteomics Data Sets of Formalin Fixed Paraffin Embedded (FFPE) Colon Tissues Molecular & Cellular Proteomics: Sprung RW et al. The files in this download were generated from frozen and formalin-fixed-paraffin-embedded (FFPE) colon tissues. Samples are prepared for shotgun proteomic analysis following the methods described in Sprung et al, Molecular Cellular Proteomics, 2009 Aug;8(8):1988-98.

The 1, 3, 5 and 10 year data are from clinically fixed samples that spent different lengths of time in a warehouse. The 1, 2 and 4 day fixation data are from samples we fixed in the lab for different lengths of time. The 0 day fixation sample is an unfixed control. The samples were subjected to either a multi-dimensional shotgun analysis consisting of IEF separations or straight LC-MS/MS analysis. Each sample was analyzed in replicates on a Thermo LTQ mass spectrometer. Please cite the publication if you utilize this dataset in any form of public discourse (publications, talks, etc.)

Data collection was supported by U24 CA126479, P50 CA95103, and by a generous gift from the Jim Ayers Foundation. Sprung acknowledges support from Canary Foundation and American Cancer Society Early Detection postdoctoral fellowship.
Supporting Tool Suite Production Proteomics: Ma et al This archive contains the BUS (backup utility service), ScanSifter (file format converter), FileCollector (batch file manager), and other tools for managing data within a biotechnology facility. Utilities are presented in both binary and source code. Documentation for the Proteomics Support Tool Suite is available here. This work was supported by the National Cancer Institute through the Clinical Proteomic Technology Assessment for Cancer (CPTAC) program U24 CA126470 to Daniel C. Liebler and R01 CA126218 to David L. Tabb.
Yeast lysates from LTQ Velos
(4/26/2011)
ScanRanker: Ma et al The files in directory were generated utilizing the CPTAC Yeast Performance Standard that was digested with trypsin in Rapigest10. Two microliter portions of peptide mixture were analyzed using a Velos ion trap mass spectrometer (Thermo, San Jose, CA) equipped with an Eksigent 1D Plus NanoLC pump and Eksigent NanoLC-AS1 autosampler (Eksigent, Dublin, CA). The MS/MS spectra were collected using data-dependent scanning in which one full MS spectrum was followed by four MS-MS spectra. MS/MS spectra were recorded using dynamic exclusion of previously analyzed precursors for 60 s with a repeat count of 1 and a repeat duration of 1. A total of five replicate LC-MS/MS experiments were performed and 192,330 MS/MS spectra were collected. Collection of these data was supported by NIH grant U24 CA126479.
OrbiTrap head and neck cancer comparative proteomics data set for Vanderbilt QuasiTel manuscript
(9/7/2010)
Journal of Proteome Research: Li et al The files in this download correspond to "Comparative Shotgun Proteomics Using Spectral Count Data and Quasi-Likelihood Modeling," by Ming Li, William Gray, Haixia Zhang, Christine H. Chung, Dean Billheimer, Wendell G. Yarbrough, Daniel C. Liebler, Yu Shyr, and Robbert J.C. Slebos. The article was published in the Journal of Proteome Research (2010) 9: 4295-4305.

Both "normal" and "cancer" samples pooled together tissues from twenty different individuals. The "normal" samples represent tonsil epithelia obtained from pediatric tonsillectomies. The "cancer" samples represent macrodissected oral carcinomas from Stage I-III. Tissues were subjected to protein purification, reduction and alkylation with iodoacetamide, and digestion with trypsin. The resulting peptides were separated in four replicate IEF strips for each of the two pools. The IEF strips were then cut to twenty fractions, with each being subjected to LC-MS/MS on a Thermo Orbitrap, where precursors were measured in the Orbitrap while fragments were measured in the LTQ mass analyzer.

Data collection was supported by U24 CA126479 and by a generous gift from the Jim Ayers Foundation. Tissue collection was supported by gifts from the Barry Baker Foundation and Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation .
Depletion of Abundant Plasma Proteins and Limitations of Plasma Proteomics
(8/10/2010)
Journal of Proteome Research: Tu et al The files in this download correspond to "Depletion of Abundant Plasma Proteins and Limitations of Plasma Proteomics" by Chengjian Tu, Paul A. Rudnick, Misti Y. Martinez, Kristin L. Cheek, Stephen E. Stein, Robbert J.C. Slebos, and Daniel C. Liebler. The article was published in the Journal of Proteome Research (2010) 9: 4982-4991.

The paper evaluates the impact of Agilent MARS 7 and MARS 14 depletion columns on plasma samples destined for discovery proteomics analysis. All analyses were carried out on an LTQ XL, where alkylation was handled through the use of iodoacetamide and digestion was carried out by trypsin.

DatasetA in this collection represents LC-MS/MS analyses of flow-through and bound fractions from three columns of each of these two types. DatasetB, containing the bulk of the data, includes the LC-MS/MS results for replicate LC-MS/MS experiments for MARS 7, MARS 14, and crude plasma preparations performed on IEF-separated fractions. In the final part of file names, "B14" would indicate that the file is the 14th IEF fraction of 20 for the 'B' process replicate. DatasetC, in contrast to the others, represents LC-MS/MS analyses of mixtures of RKO cell line lysates with different proportions of plasma as indicated.

Data collection was supported by U24 CA126479 and by a generous gift from the Jim Ayers Foundation.
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 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.
SCX vs IEF of human RKO cells (6/1/2007) 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.