Extending the Coverage of Lys-C/Trypsin-Based Bottom-up Proteomics by Cysteine S-Aminoethylation

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

Standard

Extending the Coverage of Lys-C/Trypsin-Based Bottom-up Proteomics by Cysteine S-Aminoethylation. / Tomioka, Ryota; Tomioka, Ayana; Ogata, Kosuke; Chan, Hsin Ju; Chen, Li Yu; Guzman, Ulises H.; Xuan, Yue; Olsen, Jesper V.; Chen, Yu Ju; Ishihama, Yasushi.

In: Journal of the American Society for Mass Spectrometry, Vol. 35, No. 2, 2024, p. 386-396.

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

Harvard

Tomioka, R, Tomioka, A, Ogata, K, Chan, HJ, Chen, LY, Guzman, UH, Xuan, Y, Olsen, JV, Chen, YJ & Ishihama, Y 2024, 'Extending the Coverage of Lys-C/Trypsin-Based Bottom-up Proteomics by Cysteine S-Aminoethylation', Journal of the American Society for Mass Spectrometry, vol. 35, no. 2, pp. 386-396. https://doi.org/10.1021/jasms.3c00448

APA

Tomioka, R., Tomioka, A., Ogata, K., Chan, H. J., Chen, L. Y., Guzman, U. H., Xuan, Y., Olsen, J. V., Chen, Y. J., & Ishihama, Y. (2024). Extending the Coverage of Lys-C/Trypsin-Based Bottom-up Proteomics by Cysteine S-Aminoethylation. Journal of the American Society for Mass Spectrometry, 35(2), 386-396. https://doi.org/10.1021/jasms.3c00448

Vancouver

Tomioka R, Tomioka A, Ogata K, Chan HJ, Chen LY, Guzman UH et al. Extending the Coverage of Lys-C/Trypsin-Based Bottom-up Proteomics by Cysteine S-Aminoethylation. Journal of the American Society for Mass Spectrometry. 2024;35(2):386-396. https://doi.org/10.1021/jasms.3c00448

Author

Tomioka, Ryota ; Tomioka, Ayana ; Ogata, Kosuke ; Chan, Hsin Ju ; Chen, Li Yu ; Guzman, Ulises H. ; Xuan, Yue ; Olsen, Jesper V. ; Chen, Yu Ju ; Ishihama, Yasushi. / Extending the Coverage of Lys-C/Trypsin-Based Bottom-up Proteomics by Cysteine S-Aminoethylation. In: Journal of the American Society for Mass Spectrometry. 2024 ; Vol. 35, No. 2. pp. 386-396.

Bibtex

@article{277365a041e346d683fe6d555b781474,
title = "Extending the Coverage of Lys-C/Trypsin-Based Bottom-up Proteomics by Cysteine S-Aminoethylation",
abstract = "To improve the coverage in bottom-up proteomics, S-aminoethylation of cysteine residues (AE-Cys) was carried out with 2-bromoethylamine, followed by cleavage with lysyl endopeptidase (Lys-C) or Lys-C/trypsin. A model study with bovine serum albumin showed that the C-terminal side of AE-Cys was successfully cleaved by Lys-C. The frequency of side reactions at amino acids other than Cys was less than that in the case of carbamidomethylation of Cys with iodoacetamide. Proteomic analysis of A549 cell extracts in the data-dependent acquisition mode after AE-Cys modification afforded a greater number of identified protein groups, especially membrane proteins. In addition, label-free quantification of proteins in mouse nonsmall cell lung cancer (NSCLC) tissue in the data-independent acquisition mode after AE-Cys modification showed improved NSCLC pathway coverage and greater reproducibility. Furthermore, the AE-Cys method could identify an epidermal growth factor receptor peptide containing the T790 M mutation site, a well-established lung-cancer-related mutation site that has evaded conventional bottom-up methods. Finally, AE-Cys was found to fully mimic Lys in terms of collision-induced dissociation fragmentation, ion mobility separation, and cleavage by Lys-C/trypsin, except for sulfoxide formation during sample preparation.",
keywords = "bottom-up proteomics, cysteine S-aminoethylation, membrane proteomics, T790 M EGFR",
author = "Ryota Tomioka and Ayana Tomioka and Kosuke Ogata and Chan, {Hsin Ju} and Chen, {Li Yu} and Guzman, {Ulises H.} and Yue Xuan and Olsen, {Jesper V.} and Chen, {Yu Ju} and Yasushi Ishihama",
note = "Publisher Copyright: {\textcopyright} 2024 American Society for Mass Spectrometry. Published by American Chemical Society. All rights reserved.",
year = "2024",
doi = "10.1021/jasms.3c00448",
language = "English",
volume = "35",
pages = "386--396",
journal = "Journal of The American Society for Mass Spectrometry",
issn = "1044-0305",
publisher = "Springer Nature",
number = "2",

}

RIS

TY - JOUR

T1 - Extending the Coverage of Lys-C/Trypsin-Based Bottom-up Proteomics by Cysteine S-Aminoethylation

AU - Tomioka, Ryota

AU - Tomioka, Ayana

AU - Ogata, Kosuke

AU - Chan, Hsin Ju

AU - Chen, Li Yu

AU - Guzman, Ulises H.

AU - Xuan, Yue

AU - Olsen, Jesper V.

AU - Chen, Yu Ju

AU - Ishihama, Yasushi

N1 - Publisher Copyright: © 2024 American Society for Mass Spectrometry. Published by American Chemical Society. All rights reserved.

PY - 2024

Y1 - 2024

N2 - To improve the coverage in bottom-up proteomics, S-aminoethylation of cysteine residues (AE-Cys) was carried out with 2-bromoethylamine, followed by cleavage with lysyl endopeptidase (Lys-C) or Lys-C/trypsin. A model study with bovine serum albumin showed that the C-terminal side of AE-Cys was successfully cleaved by Lys-C. The frequency of side reactions at amino acids other than Cys was less than that in the case of carbamidomethylation of Cys with iodoacetamide. Proteomic analysis of A549 cell extracts in the data-dependent acquisition mode after AE-Cys modification afforded a greater number of identified protein groups, especially membrane proteins. In addition, label-free quantification of proteins in mouse nonsmall cell lung cancer (NSCLC) tissue in the data-independent acquisition mode after AE-Cys modification showed improved NSCLC pathway coverage and greater reproducibility. Furthermore, the AE-Cys method could identify an epidermal growth factor receptor peptide containing the T790 M mutation site, a well-established lung-cancer-related mutation site that has evaded conventional bottom-up methods. Finally, AE-Cys was found to fully mimic Lys in terms of collision-induced dissociation fragmentation, ion mobility separation, and cleavage by Lys-C/trypsin, except for sulfoxide formation during sample preparation.

AB - To improve the coverage in bottom-up proteomics, S-aminoethylation of cysteine residues (AE-Cys) was carried out with 2-bromoethylamine, followed by cleavage with lysyl endopeptidase (Lys-C) or Lys-C/trypsin. A model study with bovine serum albumin showed that the C-terminal side of AE-Cys was successfully cleaved by Lys-C. The frequency of side reactions at amino acids other than Cys was less than that in the case of carbamidomethylation of Cys with iodoacetamide. Proteomic analysis of A549 cell extracts in the data-dependent acquisition mode after AE-Cys modification afforded a greater number of identified protein groups, especially membrane proteins. In addition, label-free quantification of proteins in mouse nonsmall cell lung cancer (NSCLC) tissue in the data-independent acquisition mode after AE-Cys modification showed improved NSCLC pathway coverage and greater reproducibility. Furthermore, the AE-Cys method could identify an epidermal growth factor receptor peptide containing the T790 M mutation site, a well-established lung-cancer-related mutation site that has evaded conventional bottom-up methods. Finally, AE-Cys was found to fully mimic Lys in terms of collision-induced dissociation fragmentation, ion mobility separation, and cleavage by Lys-C/trypsin, except for sulfoxide formation during sample preparation.

KW - bottom-up proteomics

KW - cysteine S-aminoethylation

KW - membrane proteomics

KW - T790 M EGFR

U2 - 10.1021/jasms.3c00448

DO - 10.1021/jasms.3c00448

M3 - Journal article

C2 - 38287222

AN - SCOPUS:85184516841

VL - 35

SP - 386

EP - 396

JO - Journal of The American Society for Mass Spectrometry

JF - Journal of The American Society for Mass Spectrometry

SN - 1044-0305

IS - 2

ER -

ID: 383398544