PXD033574

PXD033574 is an original dataset announced via ProteomeXchange.

Title	Addressing the Protease Bias in Quantitative Proteomics
Description	Protein quantification strategies using multiple proteases have been shown to deliver poor inter-protease 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, towards ten proteins in human plasma and determined their concentration with multiple proteases. The quantified peptides of these plasma proteins spanned three 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.
HostingRepository	PanoramaPublic
AnnounceDate	2022-09-02
AnnouncementXML	Submission_2022-09-02_08:55:23.726.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	supported by repository but incomplete data and/or metadata
PrimarySubmitter	Jakob Woessmann
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	Carbamidomethyl; Label:13C(6)15N(2); Label:13C(6)15N(4)
Instrument	TSQ Altis

Revision	Datetime	Status	ChangeLog Entry
0	2022-05-03 22:35:13	ID requested
⏵ 1	2022-09-02 08:55:24	announced

Woessmann J, Kotol D, Hober A, Uhl, é, n M, Edfors F, Addressing the Protease Bias in Quantitative Proteomics. J Proteome Res, 21(10):2526-2534(2022) [pubmed]

submitter keyword: Multiple proteases, SRM, Targeted proteomics, Absolute quantification, Plasma proteomics

Fredrik Edfors
contact affiliation	Science for Life Laboratory, Department of Protein Science (KTH), Stockholm, Sweden
contact email	fredrik.edfors@scilifelab.se
lab head
Jakob Woessmann
contact affiliation	Science for Life Laboratory, Department of Protein Science (KTH), Stockholm, Sweden
contact email	jakob.woessmann@scilifelab.se
dataset submitter

Panorama Public dataset URI