Selection of the component programs in the data analysis pipeline was based on the diversity of sample processing and instruments used in the studies. Since both label-free and iTRAQ™ 4plex strategies were used during early “system suitability” (xenograft analysis) evaluation studies, the pipeline was designed to handle both data types as well as data from phosphopeptide and glycopeptide enrichment studies. All laboratories used Thermo Fisher Orbitrap™-based high-resolution mass spectrometers for TCGA samples. In general, the design of the pipeline was based on group consensus by a steering committee of collaborators as well as the availability of tools for the NIST hardware and operating system infrastructure. Details of the pipeline are given below. Importantly, the database file and software versions were not changed throughout the processing of the “system suitability” and TCGA tumor analysis data files. (See Table 1 for a detailed list of software and parameters used.)