Description

This track hub contains the peptides that were identified by Clinical Proteomic Tumor Analysis Consortium (CPTAC) in their deep mass spectrometry based characterization of the proteome content of breast, colorectal and ovarian cancer biospecimens that were initially sequenced by The Cancer Genome Atlas. Please, address questions to info@fenyolab.org.

Global proteome measurements were performed on all tumor types to provide quantitative information on protein concentrations. For breast and ovarian tumors, quantitative measurements were also done on the phosphoproteome to provide more detailed information on cell signaling.

Display Conventions and Configuration

The tracks are colored according to the cancer awareness ribbon colors: all cancers - lavender, colorectal - brown, breast - pink, and ovarian - teal. The quantitative information shown is the spectral count of the peptide.

Methods

Frozen tumor pieces were obtained from TCGA and cryopulverized. Proteins were reduced, alkylated and subjected to trypsin digestion. Peptides separated using an off-line high pH (7.5 or 10) reversed-phase chromatography followed by low pH reversed-phase chromatography in-line with Thermo Fisher Q-Exactive (breast and ovarian tumors) or Orbitrap Velos (colorectal tumors) mass spectrometers. For the colorectal tumors, the quantitation was done using label-free quantitation (spectral counting and area under the curve). 4-plex iTRAQ labeling was used for the ovarian and breast tumors: 3 tumor samples and internal control was mixed and analyzed together. For breast and ovarian tumors the sample were split between global proteomics analysis and phosphoproteomic analysis. For the phosphoproteomic analysis, phosphopeptides were enriched using immobilized metal affinity chromatography (IMAC).

Peptides were identified and quantified by the CPTAC Common Data Analysis Pipeline (CDAP) which uses a set of open-source tools including MS-GF+ for identification, ProMS for precursor peak area calculations, and PhosphoRS for localization of modifications (see parameters settings and software versions). The peptides are mapped onto the human genome (hg19) using PGx.

Credits

The data was generated by the CPTAC Consortium, and hubs were created by the Fenyo Lab (info@fenyolab.org) at NYU School of Medicine. This work was supported by National Cancer Institute (NCI) CPTAC awards U24CA159988, U24CA160019, U24CA160034, U24CA160035, U24CA160036 and by CPTAC contract 13XS068 from Leidos Biomedical Research, Inc.

Data Release Policy

All data is freely available to the public, subject to the data use guidelines.

References

Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC; NCI CPTAC, Proteogenomic characterization of human colon and rectal cancer, Nature 513(2014) 382-387.