Fig. 1

High overlap and correlated quantification of label-free shotgun proteomic data sets from two different laboratories. Venn diagram of overlap between colorectal cancer (CRC) tissue proteomics data sets produced in Amsterdam (AMS) by the Jimenez laboratory and in the USA by TCGA/CPTAC [13] (upper panel) and scatter plot of log2-transformed mean spectral counts for proteins in the overlap (lower panel). The proteome data were generated using different workflows and MS platforms (AMS: 5-band GeLC-MS/MS on a QExactive platform; TCGA/CPTAC: 12-fraction 2D-LC-MS/MS on an LTQ-Orbitrap), while for data analysis the same pipeline was used (MSFG + with ID Picker). The integrated CRC dataset contains 10,701 assembled proteins at 0.54% protein FDR and 0.1% peptide FDR. The result shows high inter-laboratory reproducibility of colorectal cancer proteomes generated for distinct sample sets, a prerequisite for successful meta-analysis and biomarker validation. Black numbers in the Venn diagram indicate annotation with a combined list of 2634 cancer genes/drivers from cancer genomics studies (Additional file 2: Table S2), revealing that 1123 proteins including 150 mutant cancer proteins were identified by both CRC proteomics studies