Mass-spectrometry analysis of histone post-translational modifications in pathology tissue using the PAT-H-MS approach

Roberta Noberini; Giancarlo Pruneri; Saverio Minucci; Tiziana Bonaldi

doi:10.1016/j.dib.2016.02.028

Mass-spectrometry analysis of histone post-translational modifications in pathology tissue using the PAT-H-MS approach

Data Brief. 2016 Feb 16:7:188-94. doi: 10.1016/j.dib.2016.02.028. eCollection 2016 Jun.

Authors

Roberta Noberini¹, Giancarlo Pruneri², Saverio Minucci³, Tiziana Bonaldi⁴

Affiliations

¹ Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Via Adamello 16, 20139 Milan, Italy.
² School of Medicine, University of Milan, 20122 Milan, Italy; Biobank for Translational Medicine Unit, Department of Pathology, European Institute of Oncology, Via Ripamonti 435, 20141 Milan, Italy.
³ Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy; Drug Development Program, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy; Department of Bioscience, University of Milan, 20133 Milan, Italy.
⁴ Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.

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.

Keywords: Biomarker; Breast cancer; Epigenetics; Formalin-fixed paraffin embedded tissues; Histone posttranslational modifications; Mass spectrometry; Proteomics.