PXD055927-1

PXD055927 is an original dataset announced via ProteomeXchange.

Title	Benchmarking of quantitative proteomics workflows for Limited proteolysis mass spectrometry
Description	Limited proteolysis coupled with mass spectrometry (LiP-MS) has emerged as a powerful technique for detecting protein structural changes and drug-protein interactions on a proteome-wide scale. However, there is no consensus on the best quantitative proteomics workflow for analyzing LiP-MS data. In this study, we comprehensively benchmarked two major quantification approaches—data-independent acquisition (DIA) and tandem mass tag (TMT) isobaric labeling—in combination with LiP-MS, using a drug-target deconvolution assay as a model system. Our results show that while TMT labeling enabled the quantification of more peptides and proteins with lower coefficients of variation (CVs), DIA-MS exhibited greater accuracy in identifying true drug targets and stronger dose-response correlation in protein targets peptides. Additionally, we evaluated the performance of freely available (FragPipe) versus commercial (Spectronaut) software tools for DIA-MS analysis, revealing that the choice between precision (FragPipe) and sensitivity (Spectronaut) largely depends on the specific experimental context. Our findings underscore the importance of selecting the appropriate LiP-MS quantification strategy based on the study objectives. This work provides valuable guidelines for researchers in structural proteomics and drug discovery, and highlights how advancements in mass spectrometry instrumentation, such as the Astral mass spectrometer, may further improve sensitivity and protein sequence coverage, potentially reducing the need for TMT labeling.
HostingRepository	PRIDE
AnnounceDate	2025-03-31
AnnouncementXML	Submission_2025-03-31_10:40:14.869.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tomas Koudelka
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-16 23:01:34	ID requested
⏵ 1	2025-03-31 10:40:15	announced

10.1016/J.MCPRO.2025.100945;

submitter keyword: DIA, TMT,Limited Proteolysis, Staurosporine

Ilaria Piazza
contact affiliation	Max Delbrück Center for Molecular Medicine Robert-Rössle-Straße 10 13125 Berlin, Germany.
contact email	Ilaria.Piazza@mdc-berlin.de
lab head
Tomas Koudelka
contact affiliation	Max Delbrück Center for Molecular Medicine
contact email	t.koudelka82@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD055927
     1. Label: PRIDE project
     2. Name: Benchmarking of quantitative proteomics workflows for Limited proteolysis mass spectrometry