PXD042450

PXD042450 is an original dataset announced via ProteomeXchange.

Title	Assessing the role of trypsin in quantitative plasma- and single-cell proteomics towards clinical application
Description	Mass spectrometry-based bottom-up proteomics is rapidly evolving and routinely applied in large biomedical studies. Proteases are a central component of every bottom-up proteomics experiment, digesting proteins into peptides. Trypsin has been the most widely applied protease in proteomics, due to its characteristics. With ever-larger cohort sizes and possible future clinical application of mass spectrometry-based proteomics, the technical impact of trypsin becomes increasingly relevant. To assess possible biases introduced by trypsin digestion, we evaluated the impact of eight commercially available trypsins in a variety of bottom-up proteomics experiments, and across a range of protease concentrations and storage times. To investigate the universal impact of these technical attributes, we included bulk HeLa-cell lysate, human plasma and single HEK293 cells, which were analyzed over a range of Selected Reaction Monitoring (SRM), Data-Independent Acquisition (DIA), and Data-Dependent Acquisition (DDA) instrument methods on three LC-MS instruments. Quantification methods employed encompassed both label-free approaches and absolute quantification utilizing spike-in heavy-labeled recombinant protein fragment standards. Based on this extensive dataset, we report variations between commercial trypsins, their source, as well as their concentration. Furthermore, we provide suggestions on the handling of trypsin in large scale studies.
HostingRepository	PanoramaPublic
AnnounceDate	2023-08-29
AnnouncementXML	Submission_2023-08-29_11:56:48.132.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; Orbitrap Eclipse; Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-05-23 18:49:17	ID requested
⏵ 1	2023-08-29 11:56:48	announced

Woessmann J, Petrosius V, Ü, resin N, Kotol D, Aragon-Fernandez P, Hober A, Auf dem Keller U, Edfors F, Schoof EM, Assessing the Role of Trypsin in Quantitative Plasma and Single-Cell Proteomics toward Clinical Application. Anal Chem, 95(36):13649-13658(2023) [pubmed]

submitter keyword: Trypsin, bottom-up proteomics, single-cell proteomics, plasma proteomics, absolute quantification, targeted proteomics

Fredrik Edfors
contact affiliation	Science for Life Laboratory, KTH - The Royal Institute of Technology
contact email	fredrik.edfors@scilifelab.se
lab head
Jakob Woessmann
contact affiliation	Science for Life Laboratory, KTH─Royal Institute of Technology
contact email	jakob.woessmann@scilifelab.se
dataset submitter

Panorama Public dataset URI