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A deeper look at carrier proteome effects for single-cell proteomics.

ABSTRACT: Multiplexing approaches using tandem mass tags with a carrier proteome to boost sensitivity have advanced single cell proteomics by mass spectrometry (SCoPE-MS). Here, we probe the carrier proteome effects in single cell proteomics with mixed species TMTpro-labeled samples. We demonstrate that carrier proteomes, while increasing overall identifications, dictate which proteins are identified. We show that quantitative precision and signal intensity are limited at high carrier levels, hindering the recognition of regulated proteins. Guidelines for optimized mass spectrometry acquisition parameters and best practices for fold-change or protein copy number-based comparisons are provided.

SUBMITTER: Ye Z

PROVIDER: S-EPMC8863851 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature

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A deeper look at carrier proteome effects for single-cell proteomics.

Ye Zilu Z Batth Tanveer S TS Rüther Patrick P Olsen Jesper V JV

Communications biology 20220222 1

Multiplexing approaches using tandem mass tags with a carrier proteome to boost sensitivity have advanced single cell proteomics by mass spectrometry (SCoPE-MS). Here, we probe the carrier proteome effects in single cell proteomics with mixed species TMTpro-labeled samples. We demonstrate that carrier proteomes, while increasing overall identifications, dictate which proteins are identified. We show that quantitative precision and signal intensity are limited at high carrier levels, hindering th ...[more]

PMID: 35194133

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