Journal
ANALYTICAL CHEMISTRY
Volume 93, Issue 41, Pages 13791-13799Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.analchem.1c02349
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Funding
- NIH [R01CA233800, R21CA247671, U24 DK116204]
- Mark Foundation for Cancer Research
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PRM-LIVE is a Python-based acquisition engine designed to address the sporadic chromatographic drift issue encountered during PRM analysis on the timsTOF Pro. By using iRT peptides as standards, reproducible detection and quantification of 1857 tryptic peptides was successfully achieved.
Parallel reaction monitoring (PRM) has emerged as a popular approach for targeted protein quantification. With high ion utilization efficiency and first-in-class acquisition speed, the timsTOF Pro provides a powerful platform for PRM analysis. However, sporadic chromatographic drift in peptide retention time represents a fundamental limitation for the reproducible multiplexing of targets across PRM acquisitions. Here, we present PRMLIVE, an extensible, Python-based acquisition engine for the timsTOF Pro, which dynamically adjusts detection windows for reproducible target scheduling. In this initial implementation, we used iRT peptides as retention time standards and demonstrated reproducible detection and quantification of 1857 tryptic peptides from the cell lysate in a 60 min PRM-LIVE acquisition. As an application in functional proteomics, we use PRM-LIVE in an activity-based protein profiling platform to assess binding selectivity of small-molecule inhibitors against 220 endogenous human kinases.
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