PXD060919

PXD060919 is an original dataset announced via ProteomeXchange.

Title	Towards a species search engine: KISSE offers a rigorous statistical framework for bone collagen tandem mass spectrometry data
Description	DNA and bone collagen are two key sources of resilient molecular markers used to identify species from their remains. Collagen is more stable than DNA, and thus it is preferred for ancient and degraded samples. Current mass spectrometry-based collagen sequencing approaches are empirical and lack a rigorous statistical framework. Based on the well-developed approaches to protein identification in shotgun proteomics, we introduce a first approximation of the species search engine (SSE). Our SSE named KISSE is based on a species-specific library of collagenous peptides that uses both peptide sequences and their relative abundances. The developed statistical model can identify the species and the probability of correct identification, as well as determine the likelihood of the analyzed species not being in the library. We discuss the advantages and limitations of the proposed approach and the possibility of extending it to other tissues.
HostingRepository	PRIDE
AnnounceDate	2025-11-10
AnnouncementXML	Submission_2025-11-09_17:02:26.386.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hassan Gharibi
SpeciesList	scientific name: Ursus maritimus (Polar bear) (Thalarctos maritimus); NCBI TaxID: NEWT:29073; scientific name: Ursus arctos (Brown bear) (Grizzly bear); NCBI TaxID: NEWT:9644; scientific name: Falco peregrinus; NCBI TaxID: NEWT:8954; scientific name: Rangifer tarandus (Reindeer) (Cervus tarandus); NCBI TaxID: NEWT:9870; scientific name: Hydrodamalis gigas; NCBI TaxID: NEWT:63631; scientific name: Phoca vitulina; NCBI TaxID: NEWT:9720; scientific name: Physeter; NCBI TaxID: NEWT:9753; scientific name: Mirounga leonina; NCBI TaxID: NEWT:9715; scientific name: Cygnus cygnus; NCBI TaxID: NEWT:219595; scientific name: Halichoerus grypus; NCBI TaxID: NEWT:9711; scientific name: Eschrichtius robustus; NCBI TaxID: NEWT:9764; scientific name: Balaena mysticetus; NCBI TaxID: NEWT:27602; scientific name: Ziphius cavirostris; NCBI TaxID: NEWT:9760;
ModificationList	monohydroxylated residue; deamidated residue
Instrument	Orbitrap Fusion Lumos; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-18 06:53:59	ID requested
⏵ 1	2025-11-09 17:02:27	announced

10.1002/advs.202503963;

Gharibi H, Saei AA, Chernobrovkin AL, Lundstrom SL, Lyu H, Meng Z, Vegvari A, Gaetani M, Zubarev RA, Toward a Species Search Engine: KISSE Offers a Rigorous Statistical Framework for Bone Collagen Tandem Mass Spectrometry Data. Adv Sci (Weinh), 12(40):e03963(2025) [pubmed]

submitter keyword: Collagen,LC-MS/MS, Species Identification

Roman A. Zubarev
contact affiliation	Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
contact email	roman.zubarev@ki.se
lab head
Hassan Gharibi
contact affiliation	Chemical Proteomics Unit, Department of Medical Biochemistry and Biophysics, Karolinska Institutet
contact email	hassan.gharibi@ki.se
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/2025/11/PXD060919

PRIDE project URI

• PRIDE
  1. PXD060919
     1. Label: PRIDE project
     2. Name: Towards a species search engine: KISSE offers a rigorous statistical framework for bone collagen tandem mass spectrometry data