Mass Spectrometric Detected Cancer Proteins as Resources for Cancer Research

Area of Science:

• Proteomics
• Cancer Biology
• Bioinformatics

Background:

• Mass spectrometry (MS) data for cancer proteins is fragmented across studies.
• This fragmentation hinders protein detection benchmarking and retrieval.
• A unified resource is needed for comprehensive cancer proteomics analysis.

Purpose of the Study:

• To create an integrated database of MS-detected cancer proteins.
• To harmonize and standardize proteomics data from diverse cancer sources.
• To facilitate benchmarking and analysis of cancer-associated proteins.

Main Methods:

• Assembled data from 27 large-scale cancer proteomics sources (cohorts, cell lines, PDX models).
• Harmonized protein identifications to UniProtKB-Swiss-Prot (release 2025_01).
• Integrated data under FDR control to create a unified catalog.

Main Results:

• Generated a unified catalog of 15,964 MS-supported human proteins.
• Identified 525 proteins newly supported by MS evidence in the integrated cancer context.
• Highlighted immune, barrier, chromatin, and genome regulatory pathways for newly identified proteins.

Conclusions:

• The Mass Spectrometric Detected Cancer Proteins (MSCP) resource provides a unified, provenance-aware catalog for cancer proteomics.
• MSCP enables cohort- and model-specific querying and evidence aggregation.
• This resource facilitates standardized comparisons, assay planning, and translational cancer research.