PXD055252

PXD055252 is an original dataset announced via ProteomeXchange.

Title	Deep Learning Predicts Peptide Transmission Profiles through FAIMS Directly from Sequence
Description	Peptide ion mobility adds an extra dimension of separation to mass spectrometry-based proteomics. The ability to accurately pre-dict peptide ion mobility would be useful to expedite assay development and to discriminate true answers in database search. There are methods to accurately predict peptide ion mobility through drift tube devices, but methods to predict mobility through high-field asymmetric waveform ion mobility (FAIMS) are underexplored. Here, we successfully model peptide ions’ FAIMS mobility using a multi-label multi-output classification scheme to account for non-normal transmission distributions. We trained two models from over 100,000 human peptide precursors: a random forest and a long-term short-term memory (LSTM) neural network. Both models had different strengths, and the ensemble average of model predictions produced higher F2 score than either model alone. Finally, we explore cases where the models make mistakes, and demonstrate predictive performance of F2=0.66 (AUROC=0.928) on a new test dataset of nearly 40,000 different E. coli peptide ions.
HostingRepository	PRIDE
AnnounceDate	2025-01-17
AnnouncementXML	Submission_2025-01-16_18:23:31.873.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pavel Sinitcyn
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Caenorhabditis elegans; NCBI TaxID: 6239; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	acetylated residue; monohydroxylated residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-27 07:37:33	ID requested
⏵ 1	2025-01-16 18:23:32	announced

10.1101/2024.09.11.612538;

submitter keyword: proteomics,FAIMS

Joshua J.
contact affiliation	Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA Morgridge Institute for Research, Madison, WI, USA National Center for Quantitative Biology of Complex Systems, Madison, WI, USA Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
contact email	jcoon@chem.wisc.edu
lab head
Pavel Sinitcyn
contact affiliation	Utrecht University
contact email	p.sinitcyn@uu.nl
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/2025/01/PXD055252

PRIDE project URI

• PRIDE
  1. PXD055252
     1. Label: PRIDE project
     2. Name: Deep Learning Predicts Peptide Transmission Profiles through FAIMS Directly from Sequence