Novel Proteome Extraction Method Illustrates a Conserved Immunological Signature of MSI-H Colorectal Tumors

Abstract

<jats:p>Using a simple, environment friendly proteome extraction (TOP), we were able to optimize the analysis of clinical samples. Using our TOP method we analyzed a clinical cohort of microsatellite stable (MSS) and unstable (MSI-H) colorectal carcinoma (CRC). We identified a tumor cell specific, STAT1-centered, immune signature expressed by the MSI-H tumor cells. We then showed that long, but not short, exposure to Interferon-γ induces a similar signature in-vitro. We identified 10 different temporal protein expression patterns, classifying the Interferon-γ protein temporal regulation in CRC. Our data sheds light on the changes that tumor cells undergo under long-term immunological pressure in-vivo, the importance of STAT proteins in specific biological scenarios. The data generated could help find novel clinical biomarkers and therapeutic approaches.</jats:p>

SpectiCal: m/z Calibration of MS2 Peptide Spectra Using Known Low Mass Ions

“…In order to test and demonstrate the performance of the tool, the following public ProteomeXchange data sets were downloaded and processed: PXD008369, PXD015162, PXD019252, PXD023650, and PXD028633 . These five data sets were selected as being (1) publicly accessible in the ProteomeXchange repository, (2) conveniently on disk locally already for local reprocessing, (3) from the most commonly used instruments, and (4) relatively small (less than 50 MS runs).…”