An Integrated Workflow for Global, Glyco-, and Phospho-proteomic Analysis of Tumor Tissues

Yangying Zhou, Tung Shing Mamie Lih, Ganglong Yang, Shao Yung Chen, Lijun Chen, Daniel W. Chan, Hui Zhang, Qing Kay Li

Research output: Contribution to journalArticle

Abstract

Recently, the rapid development and application of mass spectrometry (MS)-based technologies have markedly improved the comprehensive proteomic characterization of global proteome and protein post-translational modifications (PTMs). However, the current conventional approach for global proteomic analysis is often carried out separately from PTM analysis. In our study, we developed an integrated workflow for multiplex analysis of global, glyco-, and phospho-proteomics using breast cancer patient-derived xenograft (PDX) tumor samples. Our approach included the following steps: trypsin-digested tumor samples were enriched for phosphopeptides through immobilized metal ion affinity chromatography (IMAC), followed by enrichment of glycopeptides through mixed anion exchange (MAX) method, and then the flow-through peptides were analyzed for global proteomics. Our workflow demonstrated an increased identification of peptides and associated proteins in global proteome, as compared to those using the peptides without PTM depletion. In addition to global proteome, the workflow identified phosphopeptides and glycopeptides from the PTM enrichment. We also found a subset of glycans with unique distribution profiles in the IMAC flow-through, as compared to those enriched directly using the MAX method. Our integrated workflow provided an effective platform for simultaneous global proteomic and PTM analysis of biospecimens.

Original languageEnglish (US)
Pages (from-to)1842-1849
Number of pages8
JournalAnalytical chemistry
Volume92
Issue number2
DOIs
StatePublished - Jan 21 2020

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ASJC Scopus subject areas

  • Analytical Chemistry

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