title: The advantage of laser-capture microdissection over whole tissue analysis in proteomic profiling studies.
abstract: 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 (http://proteomecentral.proteomexchange.org/dataset/PXD002381).
authors.affiliation: Department of Medical Oncology, Erasmus University Medical Center - Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
authors.forename: Tommaso
authors.initials: T
authors.lastname: De Marchi
authors.affiliation: Department of Medical Oncology, Erasmus University Medical Center - Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.|TNO-Rijswijk,  CBRN Protection, Rijswijk, The Netherlands.
authors.forename: Rene B H
authors.initials: RB
authors.lastname: Braakman
authors.affiliation: Department of Neurology, Erasmus University Medical Center Rotterdam, The Netherlands.
authors.forename: Christoph
authors.initials: C
authors.lastname: Stingl
authors.affiliation: Department of Neurology, Erasmus University Medical Center Rotterdam, The Netherlands.
authors.forename: Martijn M
authors.initials: MM
authors.lastname: van Duijn
authors.affiliation: Department of Medical Oncology, Erasmus University Medical Center - Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
authors.forename: Marcel
authors.initials: M
authors.lastname: Smid
authors.affiliation: Department of Medical Oncology, Erasmus University Medical Center - Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
authors.forename: John A
authors.initials: JA
authors.lastname: Foekens
authors.affiliation: Department of Neurology, Erasmus University Medical Center Rotterdam, The Netherlands.
authors.forename: Theo M
authors.initials: TM
authors.lastname: Luider
authors.affiliation: Department of Medical Oncology, Erasmus University Medical Center - Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.|Cancer Genomics, Netherlands.
authors.forename: John W M
authors.initials: JW
authors.lastname: Martens
authors.affiliation: Department of Medical Oncology, Erasmus University Medical Center - Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
authors.forename: Arzu
authors.initials: A
authors.lastname: Umar
mesh_terms: D014408:Biomarkers, Tumor / Q000302:isolation & purification* / Q000378:metabolism; D001943:Breast Neoplasms / Q000378:metabolism* / Q000473:pathology / Q000601:surgery; D047628:Estrogen Receptor alpha / Q000302:isolation & purification / Q000378:metabolism; D005260:Female; D006801:Humans; D061346:Laser Capture Microdissection; D020543:Proteome / Q000302:isolation & purification* / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry; D016896:Treatment Outcome
chemical_list: D014408:Biomarkers, Tumor; C506487:ESR1 protein, human; D047628:Estrogen Receptor alpha; D020543:Proteome
keywords: Bioinformatics; Biomarker; Label-free quantification; Laser-capture microdissection; Orbitrap mass spectrometry; Tissue heterogeneity