Mass spectrometry has become an inseparable part of modern biology. Recording spectra is not a difficult task but its analysis sometimes becomes very painful. In such situations, software that can provide the necessary tools to analyze spectra, assign peaks and search the database is greatly valued.
Bruker Biotools is one such software package: it can do all the above mentioned functions. Additionally, one can carry out de novo sequencing with MS/MS data. The most notable feature that I have used is the Peak Picking option followed by database searching with the assigned peaks. To perform the database search, the software connects to www.matrixscience.com by default; this is where the database search software runs. The search is submitted to the online server and once the results have been retrieved, they can be saved and analyzed later. With the help of "Get Hits", the results can be selectively transferred to the MS spectrum and then saved.
The software supports several types of data files including those obtained from MALDI or a deconvoluted ESI-MS spectrum. Single or multiple files can be opened with one click in separate tabs in the same window. The spectrum can simply be copied and pasted to power point, but the resolution is compromised. Colors for the spectrum and its background, matched and unmatched peaks, etc. can be defined. Moreover, the spectrum can be displayed in various modes that include simple line, cross and point, as well as a combination of these.
There are two algorithms for peak picking. The SNAP method makes use of the signal-to-noise (S/N) ratio and the goodness threshold values. The S/N ratio can be between 2.0 and 4.0. If the value is lowered then the peak picking process takes longer. Another algorithm, Sum Peak Finder, also makes use of the S/N ratio but also takes peak width into the calculation and is much faster than SNAP. The Peak Finder window provides the option of picking peaks according to m/z (mass/charge) range. Once the peak picking process is over, peaks can be manually added or deleted to further refine your search.
De novo sequencing can be done using Biotools. If the MS/MS data is loaded, it is recognized automatically and the required options are activated. b- and y- ions are detected and the software predicts the sequence based on the peaks which are present. The complete instructions for de novo sequencing are given in the manual; however, some practice is required to gain proficiency with this tool. Fortunately, demo data is provided for such practice.
Another useful tool is Mascot Batch Mode for database searching. This is required when several data files need to be submitted for database search. All parameters can be defined prior to start. This tool comes in very handy in high throughput proteomics.
Sequence Editor is an additional useful tool within the Biotools Software. Any result that is retrieved during database analysis can be opened in the Sequence Editor with a single click. Sequence Editor allows further refinement of the spectrum by searching for unmatched peaks in the given sequence using options like post-translational modifications. This should be performed only when the given sequence matches very well. Theoretical digestion is also possible in this case and the peptide masses can be exported to the spectrum for matching. This tool, therefore, is useful in the characterization of known proteins, post-translational modifications, etc.
Overall, this software is very good in quickly assigning the mass spectrum of peptides and searching the database.