A deeper look at carrier proteome effects for single-cell proteomics
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A deeper look at carrier proteome effects for single-cell proteomics. / Ye, Zilu; Batth, Tanveer S.; Rüther, Patrick; Olsen, Jesper V.
In: Communications Biology , Vol. 5, 150, 2022.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - A deeper look at carrier proteome effects for single-cell proteomics
AU - Ye, Zilu
AU - Batth, Tanveer S.
AU - Rüther, Patrick
AU - Olsen, Jesper V.
N1 - Publisher Copyright: © 2022, The Author(s).
PY - 2022
Y1 - 2022
N2 - 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.
AB - 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.
U2 - 10.1038/s42003-022-03095-4
DO - 10.1038/s42003-022-03095-4
M3 - Journal article
C2 - 35194133
AN - SCOPUS:85125155023
VL - 5
JO - Communications Biology
JF - Communications Biology
SN - 2399-3642
M1 - 150
ER -
ID: 300772814