Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel. / Thielert, Marvin; Itang, Ericka C.M.; Ammar, Constantin; Rosenberger, Florian A.; Bludau, Isabell; Schweizer, Lisa; Nordmann, Thierry M.; Skowronek, Patricia; Wahle, Maria; Zeng, Wen Feng; Zhou, Xie Xuan; Brunner, Andreas David; Richter, Sabrina; Levesque, Mitchell P.; Theis, Fabian J.; Steger, Martin; Mann, Matthias.

In: Molecular Systems Biology, Vol. 19, No. 9, e11503, 2023.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Thielert, M, Itang, ECM, Ammar, C, Rosenberger, FA, Bludau, I, Schweizer, L, Nordmann, TM, Skowronek, P, Wahle, M, Zeng, WF, Zhou, XX, Brunner, AD, Richter, S, Levesque, MP, Theis, FJ, Steger, M & Mann, M 2023, 'Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel', Molecular Systems Biology, vol. 19, no. 9, e11503. https://doi.org/10.15252/msb.202211503

APA

Thielert, M., Itang, E. C. M., Ammar, C., Rosenberger, F. A., Bludau, I., Schweizer, L., Nordmann, T. M., Skowronek, P., Wahle, M., Zeng, W. F., Zhou, X. X., Brunner, A. D., Richter, S., Levesque, M. P., Theis, F. J., Steger, M., & Mann, M. (2023). Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel. Molecular Systems Biology, 19(9), [e11503]. https://doi.org/10.15252/msb.202211503

Vancouver

Thielert M, Itang ECM, Ammar C, Rosenberger FA, Bludau I, Schweizer L et al. Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel. Molecular Systems Biology. 2023;19(9). e11503. https://doi.org/10.15252/msb.202211503

Author

Thielert, Marvin ; Itang, Ericka C.M. ; Ammar, Constantin ; Rosenberger, Florian A. ; Bludau, Isabell ; Schweizer, Lisa ; Nordmann, Thierry M. ; Skowronek, Patricia ; Wahle, Maria ; Zeng, Wen Feng ; Zhou, Xie Xuan ; Brunner, Andreas David ; Richter, Sabrina ; Levesque, Mitchell P. ; Theis, Fabian J. ; Steger, Martin ; Mann, Matthias. / Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel. In: Molecular Systems Biology. 2023 ; Vol. 19, No. 9.

Bibtex

@article{5fe3a36cffb64c07a7896a1022d2917d,
title = "Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel",
abstract = "Single-cell proteomics aims to characterize biological function and heterogeneity at the level of proteins in an unbiased manner. It is currently limited in proteomic depth, throughput, and robustness, which we address here by a streamlined multiplexed workflow using data-independent acquisition (mDIA). We demonstrate automated and complete dimethyl labeling of bulk or single-cell samples, without losing proteomic depth. Lys-N digestion enables five-plex quantification at MS1 and MS2 level. Because the multiplexed channels are quantitatively isolated from each other, mDIA accommodates a reference channel that does not interfere with the target channels. Our algorithm RefQuant takes advantage of this and confidently quantifies twice as many proteins per single cell compared to our previous work (Brunner et al, PMID 35226415), while our workflow currently allows routine analysis of 80 single cells per day. Finally, we combined mDIA with spatial proteomics to increase the throughput of Deep Visual Proteomics seven-fold for microdissection and four-fold for MS analysis. Applying this to primary cutaneous melanoma, we discovered proteomic signatures of cells within distinct tumor microenvironments, showcasing its potential for precision oncology.",
keywords = "DIA, dimethyl labeling, multiplexing, single cells, spatial proteomics",
author = "Marvin Thielert and Itang, {Ericka C.M.} and Constantin Ammar and Rosenberger, {Florian A.} and Isabell Bludau and Lisa Schweizer and Nordmann, {Thierry M.} and Patricia Skowronek and Maria Wahle and Zeng, {Wen Feng} and Zhou, {Xie Xuan} and Brunner, {Andreas David} and Sabrina Richter and Levesque, {Mitchell P.} and Theis, {Fabian J.} and Martin Steger and Matthias Mann",
note = "Publisher Copyright: {\textcopyright} 2023 The Authors. Published under the terms of the CC BY 4.0 license.",
year = "2023",
doi = "10.15252/msb.202211503",
language = "English",
volume = "19",
journal = "Molecular Systems Biology",
issn = "1744-4292",
publisher = "Wiley-Blackwell",
number = "9",

}

RIS

TY - JOUR

T1 - Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel

AU - Thielert, Marvin

AU - Itang, Ericka C.M.

AU - Ammar, Constantin

AU - Rosenberger, Florian A.

AU - Bludau, Isabell

AU - Schweizer, Lisa

AU - Nordmann, Thierry M.

AU - Skowronek, Patricia

AU - Wahle, Maria

AU - Zeng, Wen Feng

AU - Zhou, Xie Xuan

AU - Brunner, Andreas David

AU - Richter, Sabrina

AU - Levesque, Mitchell P.

AU - Theis, Fabian J.

AU - Steger, Martin

AU - Mann, Matthias

N1 - Publisher Copyright: © 2023 The Authors. Published under the terms of the CC BY 4.0 license.

PY - 2023

Y1 - 2023

N2 - Single-cell proteomics aims to characterize biological function and heterogeneity at the level of proteins in an unbiased manner. It is currently limited in proteomic depth, throughput, and robustness, which we address here by a streamlined multiplexed workflow using data-independent acquisition (mDIA). We demonstrate automated and complete dimethyl labeling of bulk or single-cell samples, without losing proteomic depth. Lys-N digestion enables five-plex quantification at MS1 and MS2 level. Because the multiplexed channels are quantitatively isolated from each other, mDIA accommodates a reference channel that does not interfere with the target channels. Our algorithm RefQuant takes advantage of this and confidently quantifies twice as many proteins per single cell compared to our previous work (Brunner et al, PMID 35226415), while our workflow currently allows routine analysis of 80 single cells per day. Finally, we combined mDIA with spatial proteomics to increase the throughput of Deep Visual Proteomics seven-fold for microdissection and four-fold for MS analysis. Applying this to primary cutaneous melanoma, we discovered proteomic signatures of cells within distinct tumor microenvironments, showcasing its potential for precision oncology.

AB - Single-cell proteomics aims to characterize biological function and heterogeneity at the level of proteins in an unbiased manner. It is currently limited in proteomic depth, throughput, and robustness, which we address here by a streamlined multiplexed workflow using data-independent acquisition (mDIA). We demonstrate automated and complete dimethyl labeling of bulk or single-cell samples, without losing proteomic depth. Lys-N digestion enables five-plex quantification at MS1 and MS2 level. Because the multiplexed channels are quantitatively isolated from each other, mDIA accommodates a reference channel that does not interfere with the target channels. Our algorithm RefQuant takes advantage of this and confidently quantifies twice as many proteins per single cell compared to our previous work (Brunner et al, PMID 35226415), while our workflow currently allows routine analysis of 80 single cells per day. Finally, we combined mDIA with spatial proteomics to increase the throughput of Deep Visual Proteomics seven-fold for microdissection and four-fold for MS analysis. Applying this to primary cutaneous melanoma, we discovered proteomic signatures of cells within distinct tumor microenvironments, showcasing its potential for precision oncology.

KW - DIA

KW - dimethyl labeling

KW - multiplexing

KW - single cells

KW - spatial proteomics

U2 - 10.15252/msb.202211503

DO - 10.15252/msb.202211503

M3 - Journal article

C2 - 37602975

AN - SCOPUS:85168570946

VL - 19

JO - Molecular Systems Biology

JF - Molecular Systems Biology

SN - 1744-4292

IS - 9

M1 - e11503

ER -

ID: 364546531