#ClassiCOL
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archaeoalex.bsky.social
Delightful to see an important new Denisovan site and artefacts recognised. Even more pleasing personally to see that #ClassiCOL was used! Keep your eyes peeled for the new ClassiCOL 2, live on GitHub and with a brand new publication in the coming days. github.com/EngelsI/Clas...
September 14, 2026 at 5:37 PM
archaeoalex.bsky.social
Thanks Matthew! We’re really happy this is finally out there #openaccess! Ian and I are giving a tutorial in the @paastacommunity.bsky.social for the latest ClassiCOL version soon, with new optimisations for minimal computing power and speedy analysis - check it out on github.com/EngelsI/Clas...
March 16, 2025 at 10:43 AM
paastacommunity.bsky.social
Our next #PAASTACommunity seminar series is coming up on *Wed 02 April at 16:00 CET* with @archaeoalex.bsky.social presenting a tutorial on ClassiCOL!
March 20, 2025 at 1:39 PM
paastacommunity.bsky.social
In case anyone missed @archaeoalex.bsky.social's talk on using the ClassiCOL tool, it's now live on our YouTube channel! : youtu.be/CA36dn_zKfs?...
June 9, 2025 at 3:46 PM
matthewcollins.bsky.social
5/9 Most impressive is the tool's ability to identify taxonomic mixtures in samples like coprolites, contaminated specimens, and to suggest taxonomies not represented in sequence databases (including extinct taxa). #archaeology
Overview of the ClassiCOL pipeline. (A) Schematic of the ClassiCOL algorithm workflow starting from a search engine output file. The numbers represented in the table are randomly chosen to highlight the possible difference between two taxonomic branches. (B). Schematic overview of peptide reuse from independent mutations after the speciation event, which are important for classification over different taxonomic levels. The peptides represented in the scheme are true peptides, from different spectra, that were found in the goat reference data set from Rüther et al. (8) (C). Visual representation of the collagen-species bicluster. The cluster is zoomed in at the Pecora family level on a sample from Rangifer tarandus (RMC42); the lighter the color in the heatmap, the greater the coverage for that collagen sequence. The y-axis represents the species taxonomic tree, the x-axis represents the homology between collagen sequences, colored by relatedness. (D). Output sunburst plot of the Rangifer tarandus sample, where higher scores represent higher likelihood that the named taxon approximates the sample content. All ambiguity is retained in the final output, whether originating from the isoBLAST approach or directly from the search engine results. Overview of the ClassiCOL outcome scenarios. This schematic (created with Xmind) shows all potential outcome scenarios of the ClassiCOL algorithm in the form of a decision tree. (i) Depicts the scenario of the identification of a single species, which can be the true species or the most closely related species in the database, (ii) shows how to interpret an outcome specific to a higher taxonomic level than the species level, and (iii) visualizes how to infer a physical and/or a genetic mixture from the ClassiCOL output files. We have included “coprolite” and “bag dust” as real-life examples of physical sample mixtures analyzed with ClassiCOL.
March 16, 2025 at 9:08 AM
matthewcollins.bsky.social
2/9 The authors present two novel algorithms: isoBLAST and ClassiCOL, which embrace peptide ambiguity rather than trying to eliminate it - a conceptual shift in palaeoproteomics. #teammasspec
March 16, 2025 at 9:08 AM
matthewcollins.bsky.social
4/9 ClassiCOL then resolves this ambiguity through an anti-Occam's razor approach, following the taxonomic tree and discarding branches that don't contribute unique peptides, until reaching maximum specificity. #archaeology
Demonstration of taxonomic uncertainties from a ZooMS/MS output file. (A). Unipept (36) sunburst view on Mascot result of Homo sapiens reference sample of Rüther et al. (8) showing uniqueness of peptide stretches on different taxonomic levels (Figure S1). Sunburst plot is colored via phylogenetic relatedness. (B). Histogram showing the percentage amino acid distribution between the human reference proteome (UP000005640), collected from Uniprot (red) and solely collagen sequences extracted from the same human proteome from Uniprot (blue). (C). Demonstrative overview of Homo sapiens collagen peptides, alongside the top results with similar Mascot scoring. Due to an isobaric switch the protein of origin and species of origin can change. Unfortunately, intensity prediction and the accompanying MS2PIP (63) score does not always change either, compromising this second-pass solution to further filter the peptide results.
March 16, 2025 at 9:08 AM
biorxiv-bioinfo.bsky.social
ClassiCOL: LC-MS/MS analysis for ancient species Classification via Collagen peptide ambiguation https://www.biorxiv.org/content/10.1101/2024.10.01.616034v1
ClassiCOL: LC-MS/MS analysis for ancient species Classification via Collagen peptide ambiguation https://www.biorxiv.org/content/10.1101/2024.10.01.616034v1
LC-MS/MS extends on the MALDI-TOF ZooMS approach by providing fragmentation spectra for each peptide
www.biorxiv.org
October 2, 2024 at 11:47 PM
portaljogada10.bsky.social
Apesar de indicar erros para o revés no clássicol, lateral adota discurso de paciência com o começo de trabalho de Luis Castro
#Grêmio #CampeonatoGaúcho #CampeonatoGaúchode2026 #Gauchão2026 #GreNal #luiscastro #MarcosRocha
Marcos Rocha justifica derrota no Gre-Nal: “Superados na vontade”
Apesar de indicar erros para o revés no Gre-Nal, lateral adota discurso de paciência com o começo de trabalho de Luis Castro
jogada10.com.br
January 26, 2026 at 12:40 PM
biorxivpreprint.bsky.social
ClassiCOL: LC-MS/MS analysis for ancient species Classification via Collagen peptide ambiguation https://www.biorxiv.org/content/10.1101/2024.10.01.616034v1
ClassiCOL: LC-MS/MS analysis for ancient species Classification via Collagen peptide ambiguation https://www.biorxiv.org/content/10.1101/2024.10.01.616034v1
LC-MS/MS extends on the MALDI-TOF ZooMS approach by providing fragmentation spectra for each peptide
www.biorxiv.org
October 2, 2024 at 11:47 PM