The Peak Erazor is a small program for the pre-analysis, calibration and filtering of your mass list prior to peptide mass search (PMS) or protein digest analysis.
The following functions can be performed with PeakErazor:
- Filtering. By comparing with an internal list of known contaminants (typically tryptic autolytic peptides and keratin derived peptides) you can easily in a two-click procedure eliminate these impurities and thus get a higher precision in the following analysis. The filtering is based on a list of impurities that may be modified by the user.
- Calibration. The most common way of calibrating a mass spectrum is to select two known peaks (typically tryptic autodigest fragments) and then perform a two-point calibration. However, by using PeakErazor you can quickly perform a mulit-point calibration on all recognized peaks (trypsin, keratin and other contaminants). This can in favorable cases increase your precision by a factor of two.
Furthermore, in order to obtain the highest precision you need in most cases to manually inspect and correct the mass assigment of your mass spectrum. If you for some reason have to re-calibrate the spectrum, these assignments will be lost and you will have to do the analysis all over.
In cases where you cannot find any ‘contaminant’ peaks on which to calibrate, you can switch to mass defect mode, in order to calibrate without calibrants, just the peptide masses.
- Contamination detection. By using the built-in database you can detect system specific contaminants after you have recoreded a few hundred mass spectra. These can then easily be added to the contamination list.
- Peptide coverage. When analyzing a known protein you can, in combination with GPMAW, generate a peptide mass list, which you can use for internal calibration.
- Precision check. Using the built-in graph and ppm-list, you can check the presicion of your data and use this in combination with your final results to verify an identification or to determine the actual precision of your data.
- Background subtraction. From a limited number of spectra you can extract background peaks (e.g. experiment specific contaminants) for more precise analysis. An alternative use is to identify unique peaks when working with isoforms.
The PeakErazor program works through a four-tabbed dialog
- Peak list: This is the page where you paste in your peak list, compare it to the background list (the Erazor list) and performs the multipoint calibration.
- Erazor list: The list of background/contamination peaks (e.g. tryptic autodigest and keratin peptide masses).
- Background: Based on a list of samples, you can quickly extract contanimating (repeating) mass values. Can also be used for inserting a peptide list (e.g. copied from GPMAW) to be used for calibration.
- Evaluation: Whenever you paste a (calibrated) peak list onto the clipboard, the list is copied to a file on disk (just the date and the peak list, no additional information). This enables you (after a few hundred spectra) to re-calibrate your Erazor list and include contamination mass values particular to your system.
In addition to the tabbed window there is an essential graph window, showing the relationship between the deviation (in ppm) and the peptide mass value of recognized contaminants. Alternatively the graph shows the deviation of the mass defect for all peptide mass values. The graph is turned on and off through the graph button.