PXD019357

PXD019357 is an original dataset announced via ProteomeXchange.

Title	Activity-based SWATH/DIA proteomic screen enables sensitive differential detection of serine hydrolases from surgically resected OCT-embedded primary lung adenocarcinoma
Description	Lung malignancies are among the leading causes of cancer-related death in the modern world. While the disease is relatively manageable if caught at an early stage, the genomic variability and high level of mutations represent a daunting challenge for diagnosis, staging and prognostic classification. One of the hallmarks of lung cancer is dysregulated activity of serine hydrolases, nevertheless, detection of their activity is challenging because bio specimens are available mostly as OCT-embedded tissues and current limitations of analytical workflows. To address the need for a robust and sensitive activity-based proteomic workflow, we established an ABPP-SWATH/DIA-MS platform and applied it for depletion-dependent differential activity profiling of serine hydrolases on a cohort of lung cancer patient samples. We demonstrated it is compatible with sensitive activity-based studies from OCT-embedded tissues by monitoring over 170 hydrolases across the patient sample cohort identifying over 20 dysregulated hydrolases like PREP, DPPIV and ELANE that have elevated activity in tumours. We confirmed our findings with a fluorescent activity-based probe and activity assays to show that our platform can guide the selection of hydrolases for validation in biochemical assays. Importantly, the method could be applied to reinvestigate the existing collections of lung cancer samples for dysregulated hydrolases and thus improve understanding of molecular biology of cancer and select biomarkers for better disease diagnosis and staging
HostingRepository	PRIDE
AnnounceDate	2025-06-02
AnnouncementXML	Submission_2025-06-01_16:19:29.796.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tatjana Sajic
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2020-05-24 22:51:31	ID requested
⏵ 1	2025-06-01 16:19:30	announced

10.1038/s41467-025-59564-x;

Sajic T, Vizovi, š, ek M, Arni S, Ciuffa R, Mehnert M, Lenglet S, Weder W, Gallart-Ayala H, Ivanisevic J, Buljan M, Thomas A, Hillinger S, Aebersold R, Depletion-dependent activity-based protein profiling using SWATH/DIA-MS detects serine hydrolase lipid remodeling in lung adenocarcinoma progression. Nat Commun, 16(1):4889(2025) [pubmed]

submitter keyword: ABPP,lung adenocarcinoma tissue , SWATH-MS

Prof. Dr. Rudolf Aebersold
contact affiliation	Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland Faculty of Science, University of Zurich, Zurich, Switzerland
contact email	aebersold@imsb.biol.ethz.ch
lab head
Tatjana Sajic
contact affiliation	IMSB, ETH Zurich
contact email	sajic@imsb.biol.ethz.ch
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/06/PXD019357

PRIDE project URI

• PRIDE
  1. PXD019357
     1. Label: PRIDE project
     2. Name: Activity-based SWATH/DIA proteomic screen enables sensitive differential detection of serine hydrolases from surgically resected OCT-embedded primary lung adenocarcinoma