MassIVE MSV000090178

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

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Description

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. [doi:10.25345/C5FQ9Q91D] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Multiplexed single cell proteomics ; Linear ion trap ; RTS-MS3 ; nanoPOTS

Contact

Principal Investigators:
(in alphabetical order) 		Ying Zhu, Pacific Northwest National Laboratory, United States
Submitting User: alchemistmatt

Publications

Park J, Yu F, Fulcher JM, Williams SM, Engbrecht K, Moore RJ, Clair GC, Petyuk V, Nesvizhskii AI, Zhu Y.
Evaluating Linear Ion Trap for MS3-Based Multiplexed Single-Cell Proteomics.
Anal Chem. Epub 2023 Jan 13.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

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Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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