PXD064794

PXD064794 is an original dataset announced via ProteomeXchange.

Title	IsoBayes: a Bayesian approach for single-isoform proteomics inference
Description	The dataset in this Proteome Exchange entry are specific to the WTC11 benchmarking samples described in the "IsoBayes" publication (Bollon et al.) Motivation: Studying protein isoforms is an essential step in biomedical research; at present, the main approach for analyzing proteins is via bottom-up mass spectrometry proteomics, which return peptide identifications, that are indirectly used to infer the presence of protein isoforms. However, the detection and quantification processes are noisy; in particular, peptides may be erroneously detected, and most peptides, known as shared peptides, are associated to multiple protein isoforms. As a consequence, studying individual protein isoforms is challenging, and inferred protein results are often abstracted to the gene-level or to groups of protein isoforms. Results: Here, we introduce IsoBayes, a novel statistical method to perform inference at the isoform level. Our method enhances the information available, by integrating mass spectrometry proteomics and transcriptomics data in a Bayesian probabilistic framework. To account for the uncertainty in the measurement process, we propose a two-layer latent variable approach: first, we sample if a peptide has been correctly detected (or, alternatively filter peptides); second, we allocate the abundance of such selected peptides across the protein(s) they are compatible with. This enables us, starting from peptide-level data, to recover protein-level data; in particular, we: i) infer the presence/absence of each protein isoform (via a posterior probability), ii) estimate its abundance (and credible interval), and iii) target isoforms where transcript and protein relative abundances significantly differ. We benchmarked our approach in simulations, and in two multi-protease real datasets: our method displays good sensitivity and specificity when detecting protein isoforms, its estimated abundances highly correlate with the ground truth, and can detect changes between protein and transcript relative abundances. Availability and implementation: IsoBayes is freely distributed as a Bioconductor R package, and is accompanied by an example usage vignette.
HostingRepository	PRIDE
AnnounceDate	2025-06-10
AnnouncementXML	Submission_2025-06-10_07:47:49.365.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Erin Jeffery
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-09 15:50:53	ID requested
⏵ 1	2025-06-10 07:47:49	announced

Dataset with its publication pending

submitter keyword: Protein Inference, Orbitrap Eclipse, WTC-11 bottom-up, computational proteomics, DDA

Gloria Sheynkman
contact affiliation	University of Virginia School of Medicine, Department of Molecular Physiology and Biological Physics
contact email	gs9yr@virginia.edu
lab head
Erin Jeffery
contact affiliation	University of Virginia, Department of Molecular Physiology and Biological Physics
contact email	edf4n@virginia.edu
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/PXD064794

PRIDE project URI

• PRIDE
  1. PXD064794
     1. Label: PRIDE project
     2. Name: IsoBayes: a Bayesian approach for single-isoform proteomics inference