PXD019719

PXD019719 is an original dataset announced via ProteomeXchange.

Title	Proteomic profiling of soft tissue sarcomas with SWATH mass spectrometry
Description	In this work, we utilise sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) for proteomic profiling of formalin fixed paraffin embedded (FFPE) specimens from a cohort of STS patients (n=36) across four histological subtypes (leiomyosarcoma, synovial sarcoma, undifferentiated pleomorphic sarcoma and dedifferentiated liposarcoma). We quantified 2951 proteins in all cases and show that there is a significant enrichment of gene sets associated with smooth muscle contraction in leiomyosarcoma, RNA splicing regulation in synovial sarcoma and leukocyte activation in undifferentiated pleomorphic sarcoma. We further identified a subgroup of STS cases (independent of histological subtype) that have a distinct expression profile in a panel of 133 proteins, with worse survival outcomes when compared to the rest of the cohort. Our study highlights the value of comprehensive proteomic characterisation as a means to identify histotype-specific STS profiles that describe key biological pathways of clinical and therapeutic relevance; as well as for discovering new prognostic biomarkers in this group of rare and difficult-to-treat diseases.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:21:55.247.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lukas Krasny
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-11 06:21:44	ID requested
1	2021-05-11 07:02:09	announced
2	2021-05-11 22:42:57	announced	2021-05-12: Updated project metadata.
⏵ 3	2024-10-22 05:22:00	announced	2024-10-22: Updated project metadata.

10.1016/j.jprot.2021.104236;

Milighetti M, Krasny L, Lee ATJ, Morani G, Szecsei C, Chen Y, Guljar N, McCarthy F, Wilding CP, Arthur A, Fisher C, Judson I, Thway K, Cheang MCU, Jones RL, Huang PH, Proteomic profiling of soft tissue sarcomas with SWATH mass spectrometry. J Proteomics, 241():104236(2021) [pubmed]

ProteomeXchange project tag: Cancer (B/D-HPP), Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project

submitter keyword: soft tissue sarcoma, DIA-MS,Proteomics, sarcoma, SWATH-MS

Paul Huang
contact affiliation	Molecular and Systems Oncology Laboratory Division of Molecular Pathology The Isntitute of Cancer Research London, United Kingdom
contact email	Paul.Huang@icr.ac.uk
lab head
Lukas Krasny
contact affiliation	The Institute of Cancer Research
contact email	Lukas.Krasny@icr.ac.uk
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/2021/05/PXD019719

PRIDE project URI

• PRIDE
  1. PXD019719
     1. Label: PRIDE project
     2. Name: Proteomic profiling of soft tissue sarcomas with SWATH mass spectrometry