In-depth proteomic analysis of nonsmall cell lung cancer to discover molecular targets and candidate biomarkers

Takefumi Kikuchi, Mohamed Hassanein, Joseph M. Amann, Qinfeng Liu, Robbert J.C. Slebos, S. M.Jamshedur Rahman, Jacob M. Kaufman, Xueqiong Zhang, Megan D. Hoeksema, Bradford K. Harris, Ming Li, Yu Shyr, Adriana L. Gonzalez, Lisa J. Zimmerman, Daniel C. Liebler, Pierre P. Massion, David P. Carbone

Research output: Contribution to journalArticlepeer-review

69 Citations (Scopus)


Advances in proteomic analysis of human samples are driving critical aspects of biomarker discovery and the identification of molecular pathways involved in disease etiology. Toward that end, in this report we are the first to use a standardized shotgun proteomic analysis method for in-depth tissue protein profiling of the two major subtypes of nonsmall cell lung cancer and normal lung tissues. We identified 3621 proteins from the analysis of pooled human samples of squamous cell carcinoma, adenocarcinoma, and control specimens. In addition to proteins previously shown to be implicated in lung cancer, we have identified new pathways and multiple new differentially expressed proteins of potential interest as therapeutic targets or diagnostic biomarkers, including some that were not identified by transcriptome profiling. Up-regulation of these proteins was confirmed by multiple reaction monitoring mass spectrometry. A subset of these proteins was found to be detectable and differentially present in the peripheral blood of cases and matched controls. Label-free shotgun proteomic analysis allows definition of lung tumor proteomes, identification of biomarker candidates, and potential targets for therapy.

Original languageEnglish
Pages (from-to)916-932
Number of pages17
JournalMolecular and Cellular Proteomics
Issue number10
Publication statusPublished - 2012 Oct

All Science Journal Classification (ASJC) codes

  • Analytical Chemistry
  • Biochemistry
  • Molecular Biology


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