PXD060140

PXD060140 is an original dataset announced via ProteomeXchange.

Title	SWAPS: a modular deep-learning empowered peptide identity propagation framework beyond match-between-run
Description	Mass spectrometry (MS)-based proteomics relies heavily on MS/MS (MS2) data, which does not fully exploit the available MS1 information. Traditional peptide identification propagation (PIP) methods, such as Match-Between-Runs (MBR), are limited to similar runs, particularly with the same liquid chromatography (LC) gradients, thus potentially underutilizing available proteomics libraries. We introduce SWAPS, a novel and modular MS1-centric framework incorporating advances in peptide property prediction, extensive proteomics libraries, and deep learning-based post-processing to enable and explore PIP across more diverse experimental conditions and LC gradients. SWAPS substantially enhances precursor identifications, especially in shorter gradients. On the example of 30-, 15-, and 7.5-minute gradients, SWAPS achieves increases of 46.3%, 86.2%, and 112.1% on precursor-level over MS2-based identifications from MaxQuant. Despite the inherent challenges in controlling false discovery rates (FDR) with MS1-based methods, SWAPS demonstrates strong efficacy in deconvoluting MS1 signals, offering powerful discrimination and deeper sequence exploration while maintaining quantitative accuracy. By building on and applying peptide property predictions in practical contexts, SWAPS reveals that current models, while advanced, are still not yet fully comparable to experimental measurements, sparking the need for further research. Additionally, its modular design allows seamless integration of future improvements, positioning SWAPS as a forward-looking tool in proteomics.
HostingRepository	MassIVE
AnnounceDate	2025-02-26
AnnouncementXML	Submission_2025-02-26_02:23:54.038.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Bernhard Kuster
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; scientific name: Three-species mixture HYE;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF HT

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-24 01:41:04	ID requested
⏵ 1	2025-02-26 02:23:54	announced

no publication

submitter keyword: SWAPS, timsTOF, MS1-based, Match-Between-Runs, DatasetType:Proteomics

Bernhard Kuster
contact affiliation	Chair of Proteomics and Bioanalytics, Technical University of Munich
contact email	kuster@tum.de
lab head
Bernhard Kuster
contact affiliation	Chair of Proteomics and Bioanalytics, Technical University of Munich
contact email	proteomics.kusterlab@gmail.com
dataset submitter

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.ucsd.edu/v09/MSV000096926/