1
|
Vitko D, Chou WF, Nouri Golmaei S, Lee JY, Belthangady C, Blume J, Chan JK, Flores-Campuzano G, Hu Y, Liu M, Marispini MA, Mora MG, Ramaswamy S, Ranjan P, Williams PB, Zawada RJX, Ma P, Wilcox BE. timsTOF HT Improves Protein Identification and Quantitative Reproducibility for Deep Unbiased Plasma Protein Biomarker Discovery. J Proteome Res 2024; 23:929-938. [PMID: 38225219 PMCID: PMC10913052 DOI: 10.1021/acs.jproteome.3c00646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/17/2024]
Abstract
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 plasma samples (unfractionated) and plasma samples processed using the Proteograph Product Suite (Proteograph) that enables robust deep proteomics sampling prior to mass spectrometry. Samples were evaluated 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. Additionally, approximately 4.5 fold more plasma peptide precursors were detected by both timsTOF HT and timsTOF Pro 2 in the Proteograph analyzed plasma vs neat plasma. In an exploratory analysis of 20 late-stage lung cancer and 20 control plasma samples with the Proteograph, 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).
Collapse
Affiliation(s)
- Dijana Vitko
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Wan-Fang Chou
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Sara Nouri Golmaei
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Joon-Yong Lee
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Chinmay Belthangady
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - John Blume
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Jessica K. Chan
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | | | - Yuntao Hu
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Manway Liu
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Mark A. Marispini
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Megan G. Mora
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Saividya Ramaswamy
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Purva Ranjan
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Preston B. Williams
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Robert J. X. Zawada
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Philip Ma
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Bruce E. Wilcox
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| |
Collapse
|