PXD061551

PXD061551 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	MS-based amyloidosis typing in FFPE tissue samples
Description	Amyloidoses are characterized by the pathological deposition of non-degradable misfolded protein fibrils. Precise identification of the fibril-forming protein is crucial for prognosis and correct therapeutic intervention. Here, we present a reproduceable method for amyloid typing using relative quantification to enhance the accuracy and reliability of proteomic amyloid typing. In this study, we analyzed 62 FFPE tissue samples (+4 replicates of one tissue sample using different set-ups), using liquid chromatography-tandem mass spectrometry and employed internal normalization of iBAQ values of amyloid-related proteins relative to serum amyloid-P component (APCS) for amyloidosis typing. This method demonstrated robust performance across multiple LC-MS/MS platforms, as well as for samples with low amounts of amyloid, and achieved complete concordance with IHC typed amyloidosis cases. More importantly, it resolved several unclear amyloid cases with inconclusive staining results. Finally, we established machine learning approach (XGBoost) achieving 94% accuracy by using ~160 amyloid-related proteins as input variables.
HostingRepository	MassIVE
AnnounceDate	2025-09-22
AnnouncementXML	Submission_2025-09-22_05:49:49.404.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Eyyub Bag
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	Acetyl; Carbamidomethyl; Oxidation; Met-loss
Instrument	Q Exactive Plus; Q Exactive HF; LTQ Velos; timsTOF; Orbitrap Fusion

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-06 15:36:00	ID requested
⏵ 1	2025-09-22 05:49:49	announced

Publication List

no publication

no publication

Keyword List

submitter keyword: Amyloidosis, Mass Spectrometry, FFPE-proteomics, DatasetType:Proteomics

submitter keyword: Amyloidosis, Mass Spectrometry, FFPE-proteomics, DatasetType:Proteomics

Contact List

Prof. Dr. Stephan Singer
contact affiliation	Department of Pathology and Neuropathology, University Hospital Tuebingen
contact email	stephan.singer@med.uni-tuebingen.de
lab head
Eyyub Bag
contact affiliation	Tuebingen University Hospital
contact email	eyyub.bag@med.uni-tuebingen.de
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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MassIVE dataset URI

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://massive-ftp.ucsd.edu/v09/MSV000097248/