Dataset Information

Towards a species search engine: KISSE offers a rigorous statistical framework for bone collagen tandem mass spectrometry data

ABSTRACT: 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.

INSTRUMENT(S):

ORGANISM(S): Ziphius Cavirostris Balaena Mysticetus Phoca Vitulina Eschrichtius Robustus Ursus Arctos (brown Bear) (grizzly Bear) Physeter Falco Peregrinus Hydrodamalis Gigas Cygnus Cygnus Rangifer Tarandus (reindeer) (cervus Tarandus) Mirounga Leonina Ursus Maritimus (polar Bear) (thalarctos Maritimus) Halichoerus Grypus

SUBMITTER: Hassan Gharibi

LAB HEAD: Roman A. Zubarev

PROVIDER: PXD060919 | Pride | 2025-11-10

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20180516_ETciD_HCD_SUB03_PolarBear1_Rep1.raw	Raw
	20180516_ETciD_HCD_SUB03_PolarBear1_Rep2.raw	Raw
	20180516_ETciD_HCD_SUB03_PolarBear1_Rep3.raw	Raw
	20180516_ETciD_HCD_SUB04_PolarBear2_Rep1.raw	Raw
	20180516_ETciD_HCD_SUB04_PolarBear2_Rep2.raw	Raw

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Publications

Toward a Species Search Engine: KISSE Offers a Rigorous Statistical Framework for Bone Collagen Tandem Mass Spectrometry Data.

Gharibi Hassan H Saei Amir Ata AA Chernobrovkin Alexey L AL Lundstrom Susanna L SL Lyu Hezheng H Meng Zhaowei Z Vegvari Akos A Gaetani Massimilliano M Zubarev Roman A RA

Advanced science (Weinheim, Baden-Wurttemberg, Germany) 20250811 40

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, a first approximation of the species search engine (SSE) is introduced. SSE named ...[more]

PMID: 40787835

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Project description:Groupers (Epinephelidae) are ecologically, commercially, and culturally important predatory fishes throughout their global distribution range in tropical, subtropical and occasionally temperate regions. They are key species for modern and ancient fisheries in the Mediterranean which have been heavily overfished in the past century leading to smaller catch sizes, lower CPUE, and decreased biomass. There are four species of grouper native to the Mediterranean within the Epinephelus genus.The abundance and distribution of grouper species prior to the 20th century in the Mediterranean remains poorly known. Using peptide mass fingerprinting, also known as Zooarchaeology by Mass Spectrometry (ZooMS), we investigated if ZooMS is a viable method for identifying intra-genus grouper bones to species level. Due to the lack of publicly available genomic sequences and for validation of ZooMS markers, we reconstructed collagen type I amino acid sequences using LC-MS/MS for four Epinephelus spp. Adequate variation between collagen sequences enabled the production of the best supported phylogenetic tree for Mediterranean Epinephelus spp. to date. We identified 23 previously undescribed ZooMS biomarkers capable of distinguishing groupers to the species level. Our novel biomarkers were applied to a case study of 23 grouper/comber fish bones from the Middle to Late Holocene archaeological site of Kinet Höyük, located along the coast of Iskenderun Bay, Turkey. ZooMS markers enabled species level identification of 19 bones with 18 identified as Epinephelus aeneus and 1 identified as Epinephelus marginatus. Combining ZooMS identifications with catch size reconstructions has revealed that E. aeneus is capable of growing ca. 30 cm larger than previously reported. This abundance and dominance of E. aeneus locally at Kinet Höyük is consistent with E. aeneus being the most prevalent grouper species in Iskenderun Bay today, testifying to several millennia of this species local population persistence despite fishing pressure, habitat degradation, and climatic changes.