Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling

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

Standard

Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling. / Koenig, Claire; Martinez-Val, Ana; Naicker, Previn; Stoychev, Stoyan; Jordaan, Justin; Olsen, Jesper V.

In: STAR Protocols, Vol. 4, No. 3, 102536, 2023.

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

Harvard

Koenig, C, Martinez-Val, A, Naicker, P, Stoychev, S, Jordaan, J & Olsen, JV 2023, 'Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling', STAR Protocols, vol. 4, no. 3, 102536. https://doi.org/10.1016/j.xpro.2023.102536

APA

Koenig, C., Martinez-Val, A., Naicker, P., Stoychev, S., Jordaan, J., & Olsen, J. V. (2023). Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling. STAR Protocols, 4(3), [102536]. https://doi.org/10.1016/j.xpro.2023.102536

Vancouver

Koenig C, Martinez-Val A, Naicker P, Stoychev S, Jordaan J, Olsen JV. Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling. STAR Protocols. 2023;4(3). 102536. https://doi.org/10.1016/j.xpro.2023.102536

Author

Koenig, Claire ; Martinez-Val, Ana ; Naicker, Previn ; Stoychev, Stoyan ; Jordaan, Justin ; Olsen, Jesper V. / Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling. In: STAR Protocols. 2023 ; Vol. 4, No. 3.

Bibtex

@article{d90aaf50840f4d0aa907327c414936fa,
title = "Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling",
abstract = "Tandem mass tags data-dependent acquisition (TMT-DDA) as well as data-independent acquisition-based label-free quantification (LFQ-DIA) have become the leading workflows to achieve deep proteome and phosphoproteome profiles. We present a modular pipeline for TMT-DDA and LFQ-DIA that integrates steps to perform scalable phosphoproteome profiling, including protein lysate extraction, clean-up, digestion, phosphopeptide enrichment, and TMT-labeling. We also detail peptide and/or phosphopeptide fractionation and pre-mass spectrometry desalting and provide researchers guidance on choosing the best workflow based on sample number and input. For complete details on the use and execution of this protocol, please refer to Koenig et al.1 and Mart{\'i}nez-Val et al.2",
keywords = "Mass Spectrometry, Protein Biochemistry, Proteomics",
author = "Claire Koenig and Ana Martinez-Val and Previn Naicker and Stoyan Stoychev and Justin Jordaan and Olsen, {Jesper V.}",
note = "Publisher Copyright: {\textcopyright} 2023 The Authors",
year = "2023",
doi = "10.1016/j.xpro.2023.102536",
language = "English",
volume = "4",
journal = "STAR Protocols",
issn = "2666-1667",
publisher = "Cell Press",
number = "3",

}

RIS

TY - JOUR

T1 - Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling

AU - Koenig, Claire

AU - Martinez-Val, Ana

AU - Naicker, Previn

AU - Stoychev, Stoyan

AU - Jordaan, Justin

AU - Olsen, Jesper V.

N1 - Publisher Copyright: © 2023 The Authors

PY - 2023

Y1 - 2023

N2 - Tandem mass tags data-dependent acquisition (TMT-DDA) as well as data-independent acquisition-based label-free quantification (LFQ-DIA) have become the leading workflows to achieve deep proteome and phosphoproteome profiles. We present a modular pipeline for TMT-DDA and LFQ-DIA that integrates steps to perform scalable phosphoproteome profiling, including protein lysate extraction, clean-up, digestion, phosphopeptide enrichment, and TMT-labeling. We also detail peptide and/or phosphopeptide fractionation and pre-mass spectrometry desalting and provide researchers guidance on choosing the best workflow based on sample number and input. For complete details on the use and execution of this protocol, please refer to Koenig et al.1 and Martínez-Val et al.2

AB - Tandem mass tags data-dependent acquisition (TMT-DDA) as well as data-independent acquisition-based label-free quantification (LFQ-DIA) have become the leading workflows to achieve deep proteome and phosphoproteome profiles. We present a modular pipeline for TMT-DDA and LFQ-DIA that integrates steps to perform scalable phosphoproteome profiling, including protein lysate extraction, clean-up, digestion, phosphopeptide enrichment, and TMT-labeling. We also detail peptide and/or phosphopeptide fractionation and pre-mass spectrometry desalting and provide researchers guidance on choosing the best workflow based on sample number and input. For complete details on the use and execution of this protocol, please refer to Koenig et al.1 and Martínez-Val et al.2

KW - Mass Spectrometry

KW - Protein Biochemistry

KW - Proteomics

U2 - 10.1016/j.xpro.2023.102536

DO - 10.1016/j.xpro.2023.102536

M3 - Journal article

C2 - 37659085

AN - SCOPUS:85169561202

VL - 4

JO - STAR Protocols

JF - STAR Protocols

SN - 2666-1667

IS - 3

M1 - 102536

ER -

ID: 367712319