title: A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline.
abstract: The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has produced large proteomics data sets from the mass spectrometric interrogation of tumor samples previously analyzed by The Cancer Genome Atlas (TCGA) program. The availability of the genomic and proteomic data is enabling proteogenomic study for both reference (i.e., contained in major sequence databases) and nonreference markers of cancer. The CPTAC laboratories have focused on colon, breast, and ovarian tissues in the first round of analyses; spectra from these data sets were produced from 2D liquid chromatography-tandem mass spectrometry analyses and represent deep coverage. To reduce the variability introduced by disparate data analysis platforms (e.g., software packages, versions, parameters, sequence databases, etc.), the CPTAC Common Data Analysis Platform (CDAP) was created. The CDAP produces both peptide-spectrum-match (PSM) reports and gene-level reports. The pipeline processes raw mass spectrometry data according to the following: (1) peak-picking and quantitative data extraction, (2) database searching, (3) gene-based protein parsimony, and (4) false-discovery rate-based filtering. The pipeline also produces localization scores for the phosphopeptide enrichment studies using the PhosphoRS program. Quantitative information for each of the data sets is specific to the sample processing, with PSM and protein reports containing the spectrum-level or gene-level ("rolled-up") precursor peak areas and spectral counts for label-free or reporter ion log-ratios for 4plex iTRAQ. The reports are available in simple tab-delimited formats and, for the PSM-reports, in mzIdentML. The goal of the CDAP is to provide standard, uniform reports for all of the CPTAC data to enable comparisons between different samples and cancer types as well as across the major omics fields.
authors: Spectragen Informatics, Bainbridge Island, Washington 98110, United States.|Biomolecular Measurement Division, National Institute of Standards and Technology , Gaithersburg, Maryland 20899, United States.
authors: Paul A
authors: PA
authors: Rudnick
authors: Biomolecular Measurement Division, National Institute of Standards and Technology , Gaithersburg, Maryland 20899, United States.
authors: Sanford P
authors: SP
authors: Markey
authors: Biomolecular Measurement Division, National Institute of Standards and Technology , Gaithersburg, Maryland 20899, United States.
authors: Jeri
authors: J
authors: Roth
authors: Biomolecular Measurement Division, National Institute of Standards and Technology , Gaithersburg, Maryland 20899, United States.
authors: Yuri
authors: Y
authors: Mirokhin
authors: Biomolecular Measurement Division, National Institute of Standards and Technology , Gaithersburg, Maryland 20899, United States.
authors: Xinjian
authors: X
authors: Yan
authors: Biomolecular Measurement Division, National Institute of Standards and Technology , Gaithersburg, Maryland 20899, United States.
authors: Dmitrii V
authors: DV
authors: Tchekhovskoi
authors: Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center , Washington, D.C. 20007, United States.
authors: Nathan J
authors: NJ
authors: Edwards
authors: ESAC, Inc., Rockville, Maryland 20850, United States.
authors: Ratna R
authors: RR
authors: Thangudu
authors: ESAC, Inc., Rockville, Maryland 20850, United States.
authors: Karen A
authors: KA
authors: Ketchum
authors: Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States.
authors: Christopher R
authors: CR
authors: Kinsinger
authors: Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States.
authors: Mehdi
authors: M
authors: Mesri
authors: Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States.
authors: Henry
authors: H
authors: Rodriguez
authors: Biomolecular Measurement Division, National Institute of Standards and Technology , Gaithersburg, Maryland 20899, United States.
authors: Stephen E
authors: SE
authors: Stein
mesh_terms: D014408:Biomarkers, Tumor / Q000378:metabolism; D006801:Humans; D009369:Neoplasms / Q000175:diagnosis* / Q000378:metabolism*; D020543:Proteome / Q000378:metabolism; D040901:Proteomics
chemical_list: D014408:Biomarkers, Tumor; D020543:Proteome
keywords: CPTAC; bioinformatics; cancer; data analysis pipeline; proteomics data resource