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Evaluating linear ion trap incorporation for MS3-based multiplexed single-cell proteomics

ABSTRACT: The project aims to evaluate the use of a linear ion trap to increase the sensitivity of multiplexed single-cell proteomics. Using diluted mouse peptide samples from C10 and Raw, we compared the proteome coverages, data missingness, and quantification performance between linear ion trap and Orbitrap acquisition modes for both MS2 and MS3 based analysis. The optimized RTS-LIT-MS3 method was further applied to the study of macrophage activation at single-cell resolution. Samples were labeled with 16-plex TMT. Data was searched with FragPipe.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Mus Musculus (ncbitaxon:10090)

SUBMITTER: Ying Zhu

PROVIDER: MSV000090178 | MassIVE | Mon Aug 22 14:15:00 BST 2022

REPOSITORIES: MassIVE

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Evaluating Linear Ion Trap for MS3-Based Multiplexed Single-Cell Proteomics.

Park Junho J Yu Fengchao F Fulcher James M JM Williams Sarah M SM Engbrecht Kristin K Moore Ronald J RJ Clair Geremy C GC Petyuk Vladislav V Nesvizhskii Alexey I AI Zhu Ying Y

Analytical chemistry 20230113

There is a growing demand to develop high-throughput and high-sensitivity mass spectrometry methods for single-cell proteomics. The commonly used isobaric labeling-based multiplexed single-cell proteomics approach suffers from distorted protein quantification due to co-isolated interfering ions during MS/MS fragmentation, also known as ratio compression. We reasoned that the use of MS3-based quantification could mitigate ratio compression and provide better quantification. However, previous stud ...[more]

PMID: 36637389

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