PXD081190

PXD081190 is an original dataset announced via ProteomeXchange.

Title	Annotation-independent phylogenetic analysis of molecular phenotypes from mass spectrometry data using TreeMS2
Description	Molecular phylogeny is a well-established method for inferring evolutionary relationships from DNA and RNA sequences. Here, we extend this concept beyond genetic information by applying phylogeny-like analysis to proteomic and metabolomic mass spectrometry data, capturing relationships based on the realized molecular phenotype. The resulting phenotype-derived trees can be directly compared with conventional genetic-based trees to identify where molecular phenotypes reflect evolutionary history and where they diverge due to functional adaptation, regulation, or environmental influence. To enable this analysis, we introduce TreeMS2, a computational tool that constructs similarity matrices by directly comparing tandem mass spectra between samples. By bypassing spectrum annotation, TreeMS2 enables rapid, unbiased comparisons to reconstruct biologically meaningful relationships across diverse datasets. In proteomics, phenotype-derived trees recapitulate established taxonomy, with deviations pinpointing sample handling errors. In single-cell proteomics our method distinguishes cell types despite sparse and noisy measurements, and in metabolomics it resolves major biochemical divisions and fine-scale compositional structure. Together, these results establish TreeMS2 as a scalable, annotation-independent framework for deriving molecular relationships from raw mass spectral data. To validate some of our observations, we reprocessed some files that are saved here. Pseudomonas psychrotolerans, Pseudomonas orientalis, and Pseudomonas mandelii were reprocessed because a missampling was expected. These files were searched against the reference proteome of the annotated species and against the proteome of its closest neighbor in the proteomics-based tree, respectively, Ligilactobacillus murinus, Geobacillus stearothermophilus, and Bacillus mojavensis. The Dictyostelium discoideum (D. discoideum) was reprocessed to see whether we would be able to find Escherichia coli (E. coli) in the sample, which was expected as the two were clustered together in the proteomics-based tree and E. coli was the food source on the agar plate D. discoideum was growing on (Carolina item #155996). To investigate whether E. coli was sampled together with Dictyostelium discoideum, a database search was performed on eight D. discoideum fractions against a combined FASTA database containing E. coli and D. discoideum protein sequences.
HostingRepository	PRIDE
AnnounceDate	2026-07-22
AnnouncementXML	Submission_2026-07-22_01:55:33.025.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Charlotte Adams
SpeciesList	scientific name: Dictyostelium discoideum (Slime mold); NCBI TaxID: NEWT:44689; scientific name: Bacillus mojavensis; NCBI TaxID: NEWT:72360; scientific name: Ligilactobacillus murinus; NCBI TaxID: NEWT:1622; scientific name: Geobacillus stearothermophilus; NCBI TaxID: NEWT:1422;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480; Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2026-07-16 07:58:20	ID requested
⏵ 1	2026-07-22 01:55:33	announced

Dataset with its publication pending

submitter keyword: Geobacillus stearothermophilus, Bacillus mojavensis, LC-MSMS, Q Exactive HFX Orbitrap, Orbitrap Exploris 480,Ligilactobacillus murinus, Dictyostelium discoideum

Wout Bittremieux
contact affiliation	Department of Computer Science, University of Antwerp, 2020 Antwerpen, Belgium
contact email	wout.bittremieux@uantwerpen.be
lab head
Charlotte Adams
contact affiliation	University of Antwerp
contact email	charlotte.adams@uantwerpen.be
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/2026/07/PXD081190

PRIDE project URI

• PRIDE
  1. PXD081190
     1. Label: PRIDE project
     2. Name: Annotation-independent phylogenetic analysis of molecular phenotypes from mass spectrometry data using TreeMS2