An untargeted shot-gun approach is described for the ultra- high-resolution analysis of fennel proteins by Fourier trans- form 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 de- velopment of a custom-made fennel protein database, start- ing from the well-known, on-line available, protein NCBI database, under Foeniculum Vulgare organism, consisting of 231 total proteins. Partial and redundant forms of pro- teins, repeatedly included in the official NCBI database un- der 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 al- lergenic sources associated with spice-mugwort-allergy syn- drome (celery, carrot, parsley, birch, and mugwort) were also included. The second step was the in-silico enzymatic diges- tion, performed on all the 102 proteins, to obtain a theoreti- cal list of m/z dataset of tryptic peptides. The Matlab process- ing 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 val- ues as input data. The PMF search results confirmed the pres- ence of 70 proteins (61 fennel specific and 9 allergenic pro- teins) inside the fennel extract.
Data processing for fennel protein characterization by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS)
Maria Teresa Melfi;Diego Centonze;Donatella Nardiello
2021-01-01
Abstract
An untargeted shot-gun approach is described for the ultra- high-resolution analysis of fennel proteins by Fourier trans- form 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 de- velopment of a custom-made fennel protein database, start- ing from the well-known, on-line available, protein NCBI database, under Foeniculum Vulgare organism, consisting of 231 total proteins. Partial and redundant forms of pro- teins, repeatedly included in the official NCBI database un- der 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 al- lergenic sources associated with spice-mugwort-allergy syn- drome (celery, carrot, parsley, birch, and mugwort) were also included. The second step was the in-silico enzymatic diges- tion, performed on all the 102 proteins, to obtain a theoreti- cal list of m/z dataset of tryptic peptides. The Matlab process- ing 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 val- ues as input data. The PMF search results confirmed the pres- ence of 70 proteins (61 fennel specific and 9 allergenic pro- teins) inside the fennel extract.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
