Calibration
Re-calibrate your data using internal, external or statistical calibration and linear or quadratic fitting. You can select one of the predefined reference lists or create your own in a build-in editor. In addition, all the matched items such as peptides, fragments or compounds generated by other tool can also be used as your internal standards.
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Peak Picking
Manual peak picking can be very annoying or even impossible for data-rich high-resolution mass spectra. Fortunately, the Peak Picking tool can do the work for you automatically according to specified parameters like signal-to-noise ratio or intensity thresholds. In case you would like to make additional peak picking, there are several tools available to label peaks manually as well. For all the peaks, various parameters can be determined on-the-fly such as charge, baseline intensity, peak width and resolution.
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Deisotoping
Once you have all the peaks labeled use Deisotoping tool to determine peaks charge and remove unwanted isotopes from the final peak list. Not only the mass shift between the isotopes is taken into account but for each peak, its theoretical intensity is also calculated using the averagine formula to resolve possible overlaps.
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Deconvolution
ESI mass spectra typically contain same species in the form of different charge states, which could complicate data interpretation. Using the Deconvolution tool all the multiply-charged species are recalculated into its singly-charged form and group together according to the m/z value and peak width.
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Baseline Correction
Strong baseline distortion poses a common problem of MALDI-TOF mass spectra of proteins and it is essential to handle it correctly. With the Baseline Correction tool you can visually adjust the spectrum baseline and correct your data or just use it within the Peak Picking module.
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Smoothing
Use moving average, Gaussian or Savitzky-Golay smoothing filters to remove signal distortion caused by chemical or electronical noise. These filters can be permanently applied, or just temporarily used prior the peak picking process. You can also check the preview before you modify the data.
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Math Operations
Simple Math Operations are available to average, combine, subtract, normalize or multiply mass spectra. Use this tool for better data comparison or removing signals of a control experiment.
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Crop Data
Use the Crop Data tool to remove unnecessary data from spectrum. In many cases it will significantly reduce storage requirements.
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Batch Processing
If you would like to apply the same processing to multiple documents use the Batch Processing tool, select the documents and hit Apply button. In combination with a possibility to save all the settings as presets, this became a powerful tool for fast data processing.
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