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Addressing the Protease Bias in Quantitative Proteomics
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- Woessmann, Jakob (author)
- KTH,Science for Life Laboratory, SciLifeLab,Proteinvetenskap
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- Kotol, David (author)
- KTH,Science for Life Laboratory, SciLifeLab,Proteinvetenskap
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- Hober, Andreas, 1992- (author)
- KTH,Proteinvetenskap,Science for Life Laboratory, SciLifeLab
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- (creator_code:org_t)
- 2022-08-31
- 2022
- English.
- In: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 21:10, s. 2526-2534
- Journal article (peer-reviewed)
Abstract
Subject headings
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- Protein quantification strategies using multiple proteases have been shown to deliver poor interprotease accuracy in label-free mass spectrometry experiments. By utilizing six different proteases with different cleavage sites, this study explores the protease bias and its effect on accuracy and precision by using recombinant protein standards. We established 557 SRM assays, using a recombinant protein standard resource, toward 10 proteins in human plasma and determined their concentration with multiple proteases. The quantified peptides of these plasma proteins spanned 3 orders of magnitude (0.02-70 μM). In total, 60 peptides were used for absolute quantification and the majority of the peptides showed high robustness. The retained reproducibility was achieved by quantifying plasma proteins using spiked stable isotope standard recombinant proteins in a targeted proteomics workflow.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Cell- och molekylärbiologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Cell and Molecular Biology (hsv//eng)
Keyword
- absolute quantification
- multiple proteases
- plasma proteomics
- SRM
- targeted proteomics
- Blood Proteins
- Endopeptidases
- Humans
- Isotope Labeling
- Isotopes
- Peptide Hydrolases
- Peptides
- Proteomics
- Recombinant Proteins
- Reproducibility of Results
- peptide
- plasma protein
- proteinase
- recombinant protein
- stable isotope
- isotope
- peptide hydrolase
- Article
- controlled study
- female
- human
- kernel method
- male
- mass spectrometry
- plasma
- quantitative analysis
- reproducibility
- procedures
Publication and Content Type
- ref (subject category)
- art (subject category)
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