Advanced search
1 file | 2.45 MB Add to list

Simple peptide quantification approach for MS-based proteomics quality control

Teresa Maia (UGent) , An Staes (UGent) , Kim Plasman (UGent) , Jarne Pauwels (UGent) , Katie Boucher (UGent) , Andrea Argentini (UGent) , Lennart Martens (UGent) , Tony Montoye, Kris Gevaert (UGent) and Francis Impens (UGent)
(2020) ACS OMEGA. 5(12). p.6754-6762
Author
Organization
Abstract
Despite its growing popularity and use, bottom-up proteomics remains a complex analytical methodology. Its general workflow consists of three main steps: sample preparation, liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), and computational data analysis. Quality assessment of the different steps and components of this workflow is instrumental to identify technical flaws and avoid loss of precious measurement time and sample material. However, assessment of the extent of sample losses along with the sample preparation protocol, in particular, after proteolytic digestion, is not yet routinely implemented because of the lack of an accurate and straightforward method to quantify peptides. Here, we report on the use of a microfluidic UV/visible spectrophotometer to quantify MS-ready peptides directly in the MS-loading solvent, consuming only 2 mu L of sample. We compared the performance of the microfluidic spectrophotometer with a standard device and determined the optimal sample amount for LC-MS/MS analysis on a Q Exactive HF mass spectrometer using a dilution series of a commercial K562 cell digest. A careful evaluation of selected LC and MS parameters allowed us to define 3 mu g as an optimal peptide amount to be injected into this particular LC-MS/MS system. Finally, using tryptic digests from human HEK293T cells and showing that injecting equal peptide amounts, rather than approximate ones, result in less variable LC-MS/MS and protein quantification data. The obtained quality improvement together with easy implementation of the approach makes it possible to routinely quantify MS-ready peptides as a next step in daily proteomics quality control.
Keywords
LIQUID-CHROMATOGRAPHY, BASIC COMPOUNDS, MASS, PROTEIN, Peptide identification, Proteomics, Peptides and proteins, Chromatography, Ions

Downloads

  • acsomega.0c00080.pdf
    • full text (Published version)
    • |
    • open access
    • |
    • PDF
    • |
    • 2.45 MB

Citation

Please use this url to cite or link to this publication:

MLA
Maia, Teresa, et al. “Simple Peptide Quantification Approach for MS-Based Proteomics Quality Control.” ACS OMEGA, vol. 5, no. 12, 2020, pp. 6754–62, doi:10.1021/acsomega.0c00080.
APA
Maia, T., Staes, A., Plasman, K., Pauwels, J., Boucher, K., Argentini, A., … Impens, F. (2020). Simple peptide quantification approach for MS-based proteomics quality control. ACS OMEGA, 5(12), 6754–6762. https://doi.org/10.1021/acsomega.0c00080
Chicago author-date
Maia, Teresa, An Staes, Kim Plasman, Jarne Pauwels, Katie Boucher, Andrea Argentini, Lennart Martens, Tony Montoye, Kris Gevaert, and Francis Impens. 2020. “Simple Peptide Quantification Approach for MS-Based Proteomics Quality Control.” ACS OMEGA 5 (12): 6754–62. https://doi.org/10.1021/acsomega.0c00080.
Chicago author-date (all authors)
Maia, Teresa, An Staes, Kim Plasman, Jarne Pauwels, Katie Boucher, Andrea Argentini, Lennart Martens, Tony Montoye, Kris Gevaert, and Francis Impens. 2020. “Simple Peptide Quantification Approach for MS-Based Proteomics Quality Control.” ACS OMEGA 5 (12): 6754–6762. doi:10.1021/acsomega.0c00080.
Vancouver
1.
Maia T, Staes A, Plasman K, Pauwels J, Boucher K, Argentini A, et al. Simple peptide quantification approach for MS-based proteomics quality control. ACS OMEGA. 2020;5(12):6754–62.
IEEE
[1]
T. Maia et al., “Simple peptide quantification approach for MS-based proteomics quality control,” ACS OMEGA, vol. 5, no. 12, pp. 6754–6762, 2020.
@article{8671261,
  abstract     = {Despite its growing popularity and use, bottom-up proteomics remains a complex analytical methodology. Its general workflow consists of three main steps: sample preparation, liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), and computational data analysis. Quality assessment of the different steps and components of this workflow is instrumental to identify technical flaws and avoid loss of precious measurement time and sample material. However, assessment of the extent of sample losses along with the sample preparation protocol, in particular, after proteolytic digestion, is not yet routinely implemented because of the lack of an accurate and straightforward method to quantify peptides. Here, we report on the use of a microfluidic UV/visible spectrophotometer to quantify MS-ready peptides directly in the MS-loading solvent, consuming only 2 mu L of sample. We compared the performance of the microfluidic spectrophotometer with a standard device and determined the optimal sample amount for LC-MS/MS analysis on a Q Exactive HF mass spectrometer using a dilution series of a commercial K562 cell digest. A careful evaluation of selected LC and MS parameters allowed us to define 3 mu g as an optimal peptide amount to be injected into this particular LC-MS/MS system. Finally, using tryptic digests from human HEK293T cells and showing that injecting equal peptide amounts, rather than approximate ones, result in less variable LC-MS/MS and protein quantification data. The obtained quality improvement together with easy implementation of the approach makes it possible to routinely quantify MS-ready peptides as a next step in daily proteomics quality control.},
  author       = {Maia, Teresa and Staes, An and Plasman, Kim and Pauwels, Jarne and Boucher, Katie and Argentini, Andrea and Martens, Lennart and Montoye, Tony and Gevaert, Kris and Impens, Francis},
  issn         = {2470-1343},
  journal      = {ACS OMEGA},
  keywords     = {LIQUID-CHROMATOGRAPHY,BASIC COMPOUNDS,MASS,PROTEIN,Peptide identification,Proteomics,Peptides and proteins,Chromatography,Ions},
  language     = {eng},
  number       = {12},
  pages        = {6754--6762},
  title        = {Simple peptide quantification approach for MS-based proteomics quality control},
  url          = {http://dx.doi.org/10.1021/acsomega.0c00080},
  volume       = {5},
  year         = {2020},
}

Altmetric
View in Altmetric
Web of Science
Times cited: