timsTOF HT Improves Protein Identification and Quantitative Reproducibility for Deep Unbiased Plasma Protein Biomarker Discovery
Dijana Vitko, Wan-Fang Chou, Sara Nouri Golmaei, Joon‐Yong Lee, Chinmay Belthangady, John E. Blume, Jessica K. Chan, Guillermo Flores-Campuzano, Yuntao Hu, Manway Liu, Mark A. Marispini, Megan Mora, Saividya Ramaswamy, Purva Ranjan, Preston Williams, Robert J.X. Zawada, Philip Ma, Bruce E. Wilcox
Abstract
High Resolution Image Download MS PowerPoint Slide Mass spectrometry (MS) is a valuable tool for plasma proteome profiling and disease biomarker discovery. However, wide-ranging plasma protein concentrations, along with technical and biological variabilities, present significant challenges for deep and reproducible protein quantitation. Here, we evaluated the qualitative and quantitative performance of timsTOF HT and timsTOF Pro 2 mass spectrometers for analysis of neat (unfractionated) and Proteograph-processed plasma across a wide range of peptide loading masses and liquid chromatography (LC) gradients. We observed up to a 76% increase in total plasma peptide precursors identified and a >2-fold boost in quantifiable plasma peptide precursors (CV < 20%) with timsTOF HT compared to Pro 2. In an exploratory analysis of 20 late-stage lung cancer and 20 control plasma samples, which were expected to exhibit distinct proteomes, an approximate 50% increase in total and statistically significant plasma peptide precursors ( q < 0.05) was observed with timsTOF HT compared to Pro 2. Our data demonstrate the superior performance of timsTOF HT for identifying and quantifying differences between biologically diverse samples, allowing for improved disease biomarker discovery in large cohort studies. Moreover, researchers can leverage data sets from this study to optimize their liquid chromatography–mass spectrometry (LC–MS) workflows for plasma protein profiling and biomarker discovery. (ProteomeXchange identifier: PXD047854 and PXD047839).