Quantitative proteomic analysis of microdissected breast cancer tissues: comparison of label-free and SILAC-based quantification with shotgun, directed, and targeted MS approaches

Research output: Contribution to journalArticle


Quantitative proteomics plays an important role in validation of breast-cancer-related biomarkers. In this study, we systematically compared the performance of label-free quantification (LFQ) and SILAC with shotgun and directed methods for quantifying breast-cancer-related markers in microdissected tissues. We show that LFQ leads to slightly higher coefficient of variation (CV) for protein quantification (median CV = 16.3%) than SILAC quantification (median CV = 13.7%) (P < 0.0001), but LFQ method enables ∼60% more protein quantification and is also more reproducible (∼20% more proteins were quantified in all replicate samples). Furthermore, we describe a method to accurately quantify multiple proteins within one pathway, that is, "focal adhesion pathway", in trace amounts of breast cancer tissues using a SILAC-based SRM assay. Using this SILAC-based SRM assay, we precisely quantified five "focal adhesion" proteins with good quantitative precision (CV range: 2.4-5.9%) in replicate whole tissue lysate samples and replicate microdissected samples (CV range: 5.8-16.1%). Our results show that in microdissected breast cancer tissues LFQ in combination with shotgun proteomics performed the best overall and is therefore suitable for both biomarker discovery and validation in these types of specimens. The SILAC-based SRM method can be used for the development of clinically relevant protein assays in tumor biopsies.


  • Ning Qing Liu
  • Lennard J M Dekker
  • Christoph Stingl
  • Coşkun Güzel
  • Tommaso De Marchi
  • John W. M. Martens
  • John A. Foekens
  • Theo M. Luider
  • Arzu Umar
External organisations
  • Erasmus University Medical Center
Research areas and keywords


  • Amino Acid Sequence, Biomarkers, Tumor, Breast Neoplasms, Cell Adhesion Molecules, Cell Line, Tumor, Female, Focal Adhesions, Humans, Isotope Labeling, Laser Capture Microdissection, Molecular Sequence Data, Proteome, Proteomics, Reference Standards, Reproducibility of Results, Tandem Mass Spectrometry, Comparative Study, Journal Article, Research Support, Non-U.S. Gov't
Original languageEnglish
Pages (from-to)4627-41
JournalJournal of Proteome Research
Issue number10
Publication statusPublished - 2013 Oct 4
Publication categoryResearch
Externally publishedYes