Data processing for fennel protein characterization by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS)
| Autor: | Philippe Schmitt-Kopplin, Diego Centonze, Basem Kanawati, Luigi Macchia, Maria Teresa Melfi, Donatella Nardiello |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Science (General)
Foeniculum Computer applications to medicine. Medical informatics Fennel extract R858-859.7 Peptide Fourier transform ion cyclotron resonance Matlab data processing Custom-made Protein Database Direct-infusion Ft-icr-ms Fennel Proteins In-silico Enzymatic Digestion Matlab Data Processing Peptide Mass Fingerprint 03 medical and health sciences Q1-390 0302 clinical medicine Direct-infusion FT-ICR-MS In-silico enzymatic digestion Fennel proteins Peptide mass fingerprint Peptide-mass fingerprint Data Article 030304 developmental biology chemistry.chemical_classification 0303 health sciences Multidisciplinary Chromatography biology Enzymatic digestion biology.organism_classification chemistry Custom-made protein database Ft icr ms Mass spectrum 030217 neurology & neurosurgery |
| Zdroj: | Data in Brief, Vol 35, Iss, Pp 106960-(2021) Data in Brief Data Brief 35:106960 (2021) |
| ISSN: | 2352-3409 |
| Popis: | An untargeted shot-gun approach is described for the ultra-high-resolution analysis of fennel proteins by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) combined with a home-made Matlab search algorithm. The first step of the proposed bioinformatic strategy was the development of a custom-made fennel protein database, starting from the well-known, on-line available, protein NCBI database, under Foeniculum Vulgare organism, consisting of 231 total proteins. Partial and redundant forms of proteins, repeatedly included in the official NCBI database under different codes, were removed. In the final custom-made database, in addition to the 92 fennel specific non-redundant proteins, 10 proteins belonging to recognized allergenic sources associated with spice-mugwort-allergy syndrome (celery, carrot, parsley, birch, and mugwort) were also included. The second step was the in-silico enzymatic digestion, performed on all the 102 proteins, to obtain a theoretical list of m/z dataset of tryptic peptides. The Matlab processing data was the third and crucial step, necessary to search for in-silico mass calculated peptide sequences in the high resolution ICR mass spectra of the digested fennel extract. The final step was based on database searching in Peptide Mass Fingerprint (PMF) mode by using the matched m/z values as input data. The PMF search results confirmed the presence of 70 proteins (61 fennel specific and 9 allergenic proteins) inside the fennel extract. |
| Databáze: | OpenAIRE |
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