Addressing the Protease Bias in Quantitative Proteomics

Woessmann, JakobKTH,Science for Life Laboratory, SciLifeLab,Proteinvetenskap (författare)

QC 20230524
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.

MEDICIN OCH HÄLSOVETENSKAP Medicinska och farmaceutiska grundvetenskaper Cell- och molekylärbiologi hsv//swe
MEDICAL AND HEALTH SCIENCES Basic Medicine Cell and Molecular Biology hsv//eng
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

Kotol, DavidKTH,Science for Life Laboratory, SciLifeLab,Proteinvetenskap(Swepub:kth)u1yd1hdh (författare)
Hober, Andreas,1992-KTH,Proteinvetenskap,Science for Life Laboratory, SciLifeLab(Swepub:kth)u15bkxsl (författare)
Uhlén, MathiasKTH,Science for Life Laboratory, SciLifeLab,Proteinvetenskap(Swepub:kth)u1dulvmw (författare)
Edfors, FredrikKTH,Proteinvetenskap,Science for Life Laboratory, SciLifeLab(Swepub:kth)u149ml0e (författare)
KTHScience for Life Laboratory, SciLifeLab (creator_code:org_t)

Ingår i:Journal of Proteome Research: American Chemical Society (ACS)21:10, s. 2526-25341535-38931535-3907

Av författaren/redakt...: Woessmann, Jakob; Kotol, David; Hober, Andreas, ...; Uhlén, Mathias; Edfors, Fredrik

Om ämnet

MEDICIN OCH HÄLSOVETENSKAP: MEDICIN OCH HÄLS ...; och Medicinska och f ...; och Cell och molekyl ...

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