Mass spectrometric profiling of tryptic digests of trifluoroethanol extracts from core needle biopsies of breast cancer tissues is a viable sample screening tool for biomarker discovery

Application of classifying limited sampling biopsies by matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) based mass spectral profiling prior to liquid chromatography–tandem mass spectrometry (LC–MS/MS) analysis was studied. The trifluoroethanol (TFE) isolates from core needle biopsies from stage II (nonmetastatic) and stage IV (metastatic) breast tumors were subjected to trypsin digestion and the peptides were profiled on MALDI-ToF. The p value for TFE-based isolation method induced, intra- and inter-day variability (range 0.69–1.00) indicated reproducible protein isolation. MALDI-ToF mass spectrometry profiling of peptides showed five discriminant peaks with fold change > 2 or