The advantage of laser-capture microdissection over whole tissue analysis in proteomic profiling studies

Research output: Contribution to journalArticle


Laser-capture microdissection (LCM) offers a reliable cell population enrichment tool and has been successfully coupled to MS analysis. Despite this, most proteomic studies employ whole tissue lysate (WTL) analysis in the discovery of disease biomarkers and in profiling analyses. Furthermore, the influence of tissue heterogeneity in WTL analysis, nor its impact in biomarker discovery studies have been completely elucidated. In order to address this, we compared previously obtained high resolution MS data from a cohort of 38 breast cancer tissues, of which both LCM enriched tumor epithelial cells and WTL samples were analyzed. Label-free quantification (LFQ) analysis through MaxQuant software showed a significantly higher number of identified and quantified proteins in LCM enriched samples (3404) compared to WTLs (2837). Furthermore, WTL samples displayed a higher amount of missing data compared to LCM both at peptide and protein levels (p-value < 0.001). 2D analysis on co-expressed proteins revealed discrepant expression of immune system and lipid metabolisms related proteins between LCM and WTL samples. We hereby show that LCM better dissected the biology of breast tumor epithelial cells, possibly due to lower interference from surrounding tissues and highly abundant proteins. All data have been deposited in the ProteomeXchange with the dataset identifier PXD002381 (


  • Tommaso De Marchi
  • Rene B H Braakman
  • Christoph Stingl
  • Martijn M van Duijn
  • Marcel Smid
  • John A. Foekens
  • Theo M. Luider
  • John W. M. Martens
  • Arzu Umar
External organisations
  • Erasmus University Medical Center
Research areas and keywords


  • Biomarkers, Tumor, Breast Neoplasms, Estrogen Receptor alpha, Female, Humans, Laser Capture Microdissection, Proteome, Proteomics, Tandem Mass Spectrometry, Treatment Outcome, Comparative Study, Journal Article, Research Support, Non-U.S. Gov't
Original languageEnglish
Pages (from-to)1474-85
Issue number10
Publication statusPublished - 2016 May
Publication categoryResearch
Externally publishedYes