Proteomic Protocols for Differential Protein Expression Analyses

Research output: Contribution to book/anthology/report/proceedingBook chapterResearchpeer-review

Protocols are described for preparation of various types of samples for differential protein expression proteomics using nano liquid chromatography-tandem mass spectrometry (nLCMS/MS). Fresh frozen tissue, formalin-fixed paraffin-embedded (FFPE) tissue, cells, pull-downs, immunoprecipitations, and plasma or serum can be processed. For transplantation studies, it should be noted that samples must be comparable; thus, similar cells or organ systems from the same species can be compared when only a minority of the proteins change expression levels. For xenotransplantation studies, caution should be taken, as different species possess proteins with differences in primary structure. The sample preparation technique is based on spin filter devices using sodium deoxycholate (SDC) as detergent for extraction of proteins. The detergent is removed using phase extraction with ethyl acetate, and samples can be used for label-free quantification (LFQ) analysis or peptides can be labeled with tandem mass tags (TMT).

Original languageEnglish
Title of host publicationXenotransplantation : Methods and Protocols
EditorsChristina Costa
Number of pages12
PublisherHumana Press
Publication year2020
ISBN (print)978-1-0716-0254-6
ISBN (Electronic)978-1-0716-0255-3
Publication statusPublished - 2020
SeriesMethods in Molecular Biology

    Research areas

  • Cells, Differential protein expression analysis, FFPE, Label-free quantification, Plasma, Proteomics, Pull-downs, Serum, Spin filter device-based preparation, TMT labeling, Tissue, nLC-MS/MS

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