Benchmarking common quantification strategies for large-scale phosphoproteomics

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Benchmarking common quantification strategies for large-scale phosphoproteomics. / Hogrebe, Alexander; von Stechow, Louise; Bekker-Jensen, Dorte B.; Weinert, Brian T.; Kelstrup, Christian D.; Olsen, Jesper V.

In: Nature Communications, Vol. 9, No. 1, 1045, 2018, p. 1-13.

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

Harvard

Hogrebe, A, von Stechow, L, Bekker-Jensen, DB, Weinert, BT, Kelstrup, CD & Olsen, JV 2018, 'Benchmarking common quantification strategies for large-scale phosphoproteomics', Nature Communications, vol. 9, no. 1, 1045, pp. 1-13. https://doi.org/10.1038/s41467-018-03309-6

APA

Hogrebe, A., von Stechow, L., Bekker-Jensen, D. B., Weinert, B. T., Kelstrup, C. D., & Olsen, J. V. (2018). Benchmarking common quantification strategies for large-scale phosphoproteomics. Nature Communications, 9(1), 1-13. [1045]. https://doi.org/10.1038/s41467-018-03309-6

Vancouver

Hogrebe A, von Stechow L, Bekker-Jensen DB, Weinert BT, Kelstrup CD, Olsen JV. Benchmarking common quantification strategies for large-scale phosphoproteomics. Nature Communications. 2018;9(1):1-13. 1045. https://doi.org/10.1038/s41467-018-03309-6

Author

Hogrebe, Alexander ; von Stechow, Louise ; Bekker-Jensen, Dorte B. ; Weinert, Brian T. ; Kelstrup, Christian D. ; Olsen, Jesper V. / Benchmarking common quantification strategies for large-scale phosphoproteomics. In: Nature Communications. 2018 ; Vol. 9, No. 1. pp. 1-13.

Bibtex

@article{a99cb98d79f24f3588443e8f7d5700b0,
title = "Benchmarking common quantification strategies for large-scale phosphoproteomics",
abstract = "Comprehensive mass spectrometry (MS)-based proteomics is now feasible, but reproducible quantification remains challenging, especially for post-translational modifications such as phosphorylation. Here, we compare the most popular quantification techniques for global phosphoproteomics: label-free quantification (LFQ), stable isotope labeling by amino acids in cell culture (SILAC) and MS2- and MS3-measured tandem mass tags (TMT). In a mixed species comparison with fixed phosphopeptide ratios, we find LFQ and SILAC to be the most accurate techniques. MS2-based TMT yields the highest precision but lowest accuracy due to ratio compression, which MS3-based TMT can partly rescue. However, MS2-based TMT outperforms MS3-based TMT when analyzing phosphoproteome changes in the DNA damage response, since its higher precision and larger identification numbers allow detection of a greater number of significantly regulated phosphopeptides. Finally, we utilize the TMT multiplexing capabilities to develop an algorithm for determining phosphorylation site stoichiometry, showing that such applications benefit from the high accuracy of MS3-based TMT.",
author = "Alexander Hogrebe and {von Stechow}, Louise and Bekker-Jensen, {Dorte B.} and Weinert, {Brian T.} and Kelstrup, {Christian D.} and Olsen, {Jesper V.}",
year = "2018",
doi = "10.1038/s41467-018-03309-6",
language = "English",
volume = "9",
pages = "1--13",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "nature publishing group",
number = "1",

}

RIS

TY - JOUR

T1 - Benchmarking common quantification strategies for large-scale phosphoproteomics

AU - Hogrebe, Alexander

AU - von Stechow, Louise

AU - Bekker-Jensen, Dorte B.

AU - Weinert, Brian T.

AU - Kelstrup, Christian D.

AU - Olsen, Jesper V.

PY - 2018

Y1 - 2018

N2 - Comprehensive mass spectrometry (MS)-based proteomics is now feasible, but reproducible quantification remains challenging, especially for post-translational modifications such as phosphorylation. Here, we compare the most popular quantification techniques for global phosphoproteomics: label-free quantification (LFQ), stable isotope labeling by amino acids in cell culture (SILAC) and MS2- and MS3-measured tandem mass tags (TMT). In a mixed species comparison with fixed phosphopeptide ratios, we find LFQ and SILAC to be the most accurate techniques. MS2-based TMT yields the highest precision but lowest accuracy due to ratio compression, which MS3-based TMT can partly rescue. However, MS2-based TMT outperforms MS3-based TMT when analyzing phosphoproteome changes in the DNA damage response, since its higher precision and larger identification numbers allow detection of a greater number of significantly regulated phosphopeptides. Finally, we utilize the TMT multiplexing capabilities to develop an algorithm for determining phosphorylation site stoichiometry, showing that such applications benefit from the high accuracy of MS3-based TMT.

AB - Comprehensive mass spectrometry (MS)-based proteomics is now feasible, but reproducible quantification remains challenging, especially for post-translational modifications such as phosphorylation. Here, we compare the most popular quantification techniques for global phosphoproteomics: label-free quantification (LFQ), stable isotope labeling by amino acids in cell culture (SILAC) and MS2- and MS3-measured tandem mass tags (TMT). In a mixed species comparison with fixed phosphopeptide ratios, we find LFQ and SILAC to be the most accurate techniques. MS2-based TMT yields the highest precision but lowest accuracy due to ratio compression, which MS3-based TMT can partly rescue. However, MS2-based TMT outperforms MS3-based TMT when analyzing phosphoproteome changes in the DNA damage response, since its higher precision and larger identification numbers allow detection of a greater number of significantly regulated phosphopeptides. Finally, we utilize the TMT multiplexing capabilities to develop an algorithm for determining phosphorylation site stoichiometry, showing that such applications benefit from the high accuracy of MS3-based TMT.

U2 - 10.1038/s41467-018-03309-6

DO - 10.1038/s41467-018-03309-6

M3 - Journal article

C2 - 29535314

VL - 9

SP - 1

EP - 13

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

IS - 1

M1 - 1045

ER -

ID: 194518468