A Highly Sensitive FFPE Tissue Workflow by Coupling the Micro Pillar Array Column) with High Resolution Mass Spectrometry

[Orbitrap_SciLib]

Sarah Trusiak1, Antonius Koller2, Alexander R. Ivanov2,3, Emily I. Chen1
ASMS 2019 Poster
Purpose: This workflow enables comprehensive proteomics analysis of large-scale patient samples with limited starting material. Methods: 50cm PharmaFluidics µPACTM columns were coupled to a Thermo Scientific™ Orbitrap Fusion™ Lumos™ TribridTM mass spectrometer using an Thermo ScientificTM EASY-SprayTM ion source to analyze 10ng to 50ng of protein digests. Results: We found good column to column reproducibility of 50cm µPAC columns for large-scale studies. The setup is capable of delivering >1000 injections of complex samples with 5% CV or less for retention time drift and protein identification. More than 1,500 proteins were detected from 10ng of HeLa Protein Digest Standard. For real sample applications, more than 1,000 proteins were quantified from 5ng of PDX tumor lysates, and more than 1,500 proteins were quantified from 50ng of FFPE tissue lysate. Proteomics analyses from the PDX tumors and FFPE breast cancer tissues demonstrate the feasibility of identifying pathologically relevant biomarkers from limited sample material. More importantly, this limited material workflow is automatable, reproducible, and scalable for large cohort studies.


1Thermo Fisher Scientific Precision Medicine Science Center, Cambridge, MA; 2Northeastern University, Boston, MA, 3Barnett Institute and Dept. of Chem. & Chem. Biology, MA