Abstract
Aberrant histone post-translational modifications (hPTMs) have been implicated with various pathologies, including cancer, and may represent useful epigenetic biomarkers. The data described here provide a mass spectrometry-based quantitative analysis of hPTMs from formalin-fixed paraffin-embedded (FFPE) tissues, from which histones were extracted through the recently developed PAT-H-MS method. First, we analyzed FFPE samples from mouse spleen and liver or human breast cancer up to six years old, together with their corresponding fresh frozen tissue. We then combined the PAT-H-MS approach with a histone-focused version of the super-SILAC strategy-using a mix of histones from four breast cancer cell lines as a spike-in standard- to accurately quantify hPTMs from breast cancer specimens belonging to different subtypes. The data, which are associated with a recent publication (Pathology tissue-quantitative mass spectrometry analysis to profile histone post-translational modification patterns in patient samples (Noberini, 2015) [1]), are deposited at the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD002669.
Highlights
Mass spectrometry raw data and MaxQuant search results Data dependent LC-MS/MS acquired on a Q Exactive instrument (Thermo Fisher Scientific) coupled to a ultra nanoflow high-performance liquid chromatography (HPLC) system (EASY-nLCTM 1000, Thermo Fisher Scientific) MS-RAW files, experimental design and.txt and.apl output files generated by the MaxQuant software Histones were purified from frozen and formalin-fixed and paraffin-embedded (FFPE) mouse and human samples
Data This proteomics dataset comprise LC-MS/MS raw files obtained from bottom-up MS analysis of histone H3 and H4 isolated using different procedures (Fig. 1) from mouse and human tissues, which were either stored as frozen samples or formalin-fixed and paraffin-embedded (FFPE)
The analysis of breast cancer samples was carried out using a super-SILAC mix of heavy-labeled histones from 4 breast cancer cell lines as internal standard
Summary
Mass spectrometry raw data and MaxQuant search results Data dependent LC-MS/MS acquired on a Q Exactive instrument (Thermo Fisher Scientific) coupled to a ultra nanoflow high-performance liquid chromatography (HPLC) system (EASY-nLCTM 1000, Thermo Fisher Scientific) MS-RAW files, experimental design and.txt and.apl output files generated by the MaxQuant software Histones were purified from frozen and FFPE mouse and human samples. Analysis of hPTM marks in FFPE tissue of different origin (mouse spleen and liver and human breast cancer biopsies) and their corresponding fresh-frozen tissues. The data can be used to profile less common PTMs, such as K-ubiquitylation, R-methylation, K-crotonylation, as well as histone H3 variants, among different cancer subtypes. This proteomics dataset comprise LC-MS/MS raw files obtained from bottom-up MS analysis of histone H3 and H4 isolated using different procedures (Fig. 1) from mouse and human tissues, which were either stored as frozen samples or formalin-fixed and paraffin-embedded (FFPE). The analysis of breast cancer samples was carried out using a super-SILAC mix of heavy-labeled histones from 4 breast cancer cell lines as internal standard
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