PXD015901-1

Global proteome and phosphoproteome data have been acquired for 105 TCGA breast cancer samples using iTRAQ (isobaric Tags for Relative and Absolute Quantification) protein quantification methods. Samples were selected from each of the 4 breast tumor subtypes (Luminal A, Luminal B, Basal-like, HER2-enriched) described in the publication, Comprehensive molecular portraits of human breast tumors (Cancer Genome Atlas Network, Nature 2012).

Three TCGA samples and 1 common internal reference control sample are included in each iTRAQ experiment, consisting of 25 proteome and 13 phosphoproteome files. The internal reference is comprised of a mixture of 40 TCGA samples (of the 105 breast cancer samples) with equal representation of the 4 breast subtypes. Three of the TCGA samples have been assayed in duplicate for quality control purposes.

05TCGA_AO-A12D-01A_AN-A04A-01A_BH-A0AV-01A_Proteome_BI iTRAQ proteome data were acquired twice, before (20130310) and after (20130416) maintenance of the Q Exactive MS system. The "20130416" dataset was used in the final publication (see here).

Global proteome and phosphoproteome data were acquired for three normal breast samples in Experiment 37. Samples "263d3f-I", "blcdb9-I", and "c4155b-C" are normal breast tissue samples that were measured in the iTRAQ-114, -115, and -116 channels, respectively. All normal samples were compared to the internal reference sample in the iTRAQ-117 channel (see CPTAC, TCGA Breast Cancer iTRAQ Sample Mapping file below).

Information on the complete TCGA Breast invasive carcinoma cohort (BRCA) can be found here.
Genomic data for the 105 TCGA samples used in the CPTAC Proteome study can be downloaded from here.

• Dataset imported into MassIVE from https://cptac-data-portal.georgetown.edu/cptac/s/S015 on 10/15/18
• Dataset source: https://pdc.esacinc.com/pdc/browse/filters/study_name:...