In silico fragment ions

Demirev et al. reported the identification of proteins and their source microorganism Bacillus atrophaeus and Bacillus cereus) using a MALDI-TOF-TOF-MS/ MS and top-down proteomic identification with software developed in-house. The software compares the m/z of MS/MS fragment ions to the m/z of in silico fragment ions (a, b, y, and loss of NH3 or H2O) derived from bacterial protein sequences having the same MW as the protein biomarker. A P-value algorithm was also developed to score/rank identifications based on a number of parameters including the number of MS/MS in silico matches [17],... 

The multisequence FASTA file was uploaded to the GPMAW software (version 8.01a5) and processed to produce individual text files containing in silico fragment ions for each protein sequence. The header line of each text file shows the ExPASy accession nunaber, the protein name. 

All the in silico fragment ion files were then batch uploaded to their respective database in the USDA software. 

Figure 25.7 is a GUI image of ranked identifications for a non-residue-specific in silico fragment ion comparison. The top identification of both algorithms is identical, and the lower-ranked identifications have scores that are significantly different from that of the top-ranked identification. 

Batch process PASTA file GPMAW Output text files containing in silico fragment ions of each sequence... 

FIGURE 25.8 GUI image of the Compare Graphs function of the top-ranked identification. MS/MS spectra (Rgure 25.5) and the bar code-like spectra of the top in sUico identification (bottom). A scrollable sidebar displays the MS/MS fragment ions and their matched in silico fragment ions. 

Average m/z of In Silico Fragment Ions and MS/MS Data Processing... 

Recently, significant progress has been made in the development of software for the prediction of drug metabolites and the automated identification of metabolite peaks from the complex mixtures. The next step, automated assignment of biotransformations and fragment ions, will be a major focus for scientists involved in drug metabolism studies. In addition, the attempts will be made in the development of in silico tools to predict the rate of metabolism and drug metabolism enzymes involved in the metabolism. 

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