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.
Our pipeline uses the freely available SearchGUI, PeptideShaker, and DBToolKit tools, and reuses code from the open source compomics-utilities library. The probability-derived similarity scoring function to compare experimental MS/MS spectra was developed as both a stand-alone module and a GUI version in Java, and its source code and executables are available at https://github.com/compomics/spectrum_similarity.
See also: http://www.bign2n.ugent.be/tools.
A Pipeline for Differential Proteomics in Unsequenced Species. Yilmaz, Sule; Victor, Bjorn; Hulstaert, Niels; Vandermarliere, Elien; Barsnes, Harald; Degroeve, Sven; Gupta, Surya; Sticker, Adriaan; Gabriel, Sarah; Dorny, Pierre; Palmblad, Magnus; Martens, Lennart. JOURNAL OF PROTEOME RESEARCH, 15 (6):1963-1970; 10.1021/acs.jproteome.6b00140 JUN 2016