Evidence map›Paper›PMID 40787835›Full record

ArticleAdvanced science (Weinheim, Baden-Wurttemberg, Germany)2025

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

Hassan Gharibi, Amir Ata Saei, Alexey L Chernobrovkin, Susanna L Lundstrom, Hezheng Lyu, Zhaowei Meng, Akos Vegvari, Massimilliano Gaetani, Roman A Zubarev

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Advanced science (Weinheim, Baden-Wurttemberg, Germany), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Hassan GharibiDivision of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17177, Sweden.ORCID https://orcid.org/0000-0002-3072-4929
Amir Ata SaeiDepartment of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden.ORCID https://orcid.org/0000-0002-2639-6328
Alexey L ChernobrovkinPelago Bioscience, Solna, 171 65, Sweden.
Susanna L LundstromDivision of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17177, Sweden.
Hezheng LyuDivision of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17177, Sweden.ORCID https://orcid.org/0009-0008-7995-6473
Zhaowei MengDivision of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17177, Sweden.ORCID https://orcid.org/0000-0002-7721-2795
Akos VegvariDivision of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17177, Sweden.ORCID https://orcid.org/0000-0002-1287-0906
Massimilliano GaetaniDivision of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17177, Sweden.ORCID https://orcid.org/0000-0001-5610-0797
Roman A ZubarevDivision of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17177, Sweden.ORCID https://orcid.org/0000-0001-9839-2089

Funding

Vetenskapsrådet 2017-04303Vetenskapsrådet 2021-05223
6 · The paper itself

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, a first approximation of the species search engine (SSE) is introduced. 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. The advantages and limitations of the proposed approach, and the possibility of extending it to other tissues is discussed.

Indexed as

Bone and BonesCollagenProteomicsSearch EngineTandem Mass SpectrometryAnimalsHumansSpecies SpecificityCollagencollagen sequencesLC‐MS/MSproteomicsspecies Identification

Identifiers

PMID40787835
PMCPMC12561455

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.