A pipeline for differential proteomics in unsequenced species

Şule Yılmaz, Bjorn Victor, Niels Hulstaert, Elien Vandermarliere, Harald Barsnes, Sven Degroeve, Surya Gupta, Adriaan Sticker, Sarah Gabriël, Pierre Dorny, Magnus Palmblad, Lennart Martens

    Research output: Contribution to journalA1: Web of Science-articlepeer-review


    Shotgun proteomics experiments often take the form of a differential analysis, where two or more samples are compared against each other. The objective is to identify proteins that are either unique to a specific sample or a set of samples (qualitative differential proteomics), or that are significantly differentially expressed in one or more samples (quantitative differential proteomics). However, the success depends on the availability of a reliable protein sequence database for each sample. To perform such an analysis in the absence of a database, we here propose a novel, generic pipeline comprising an adapted spectral similarity score derived from database search algorithms that compares samples at the spectrum level to detect unique spectra. We applied our pipeline to compare two parasitic tapeworms: Taenia solium and Taenia hydatigena, of which only the former poses a threat to humans. Furthermore, because the genome of T. solium recently became available, we were able to prove the effectiveness and reliability of our pipeline a posteriori.

    Original languageEnglish
    JournalJournal of Proteome Research
    Issue number6
    Pages (from-to)1963-1970
    Number of pages8
    Publication statusPublished - 2016


    • Journal Article


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