PEAKS Tips Page

This part of the support page will grow with new tips and tricks that will be posted each month. Our user group is invited to post their tips and strategies used with PEAKS to be shared with the rest of the community. Please submit your tips for posting by clicking: Submit Tip.

Setting error tolerances rule of thumb

ET with hybrid mass spectrometers

Data processing expectation

Bad sequence or poor instrument calibration indicator

Setting error tolerances is mainly dependent on 2 things; our instrument and your data quality. In PEAKS, in the Tools/PEAKS protein ID window, a user selects the type of mass spectrometer that they generated the data with. The message in blue indicate the suggested error tolerance typical for the instrument. This is only a suggestion, you know your instrument better than anyone.
As mentioned the other dependency of appropriate error tolerance setting is the quality of the data. This is more tricky. The best way to determine the data specific tolerance is to use data that is typical of your data quality and the proteins/peptide present in the sample data are known. Play with the error tolerance setting until the best results are found.

For PEAKS sake don't do it. PEAKS uses all the data, noise and all in the analysis. Use PEAKS "Centroid and deconvote for analysis" tool build into our software. Having no preprocessing done before PEAKS gets the data will make the result that PEAKS return that much better. Processing non-preprocessed data maybe slower compared to processed.

hybrid mass spectrometers are typically set to handle MS runs and MS/MS differently. For example, an LTQFT will process the precusor at a higher mass accuracy then the tandem sample. In the Tools, PEAKS protein ID window it is a good practise to set the "Parent mass error tolerance" and the "Fragment mass error tolerance" separately based on the type of hybrid instrument that you have. Using the LTQFT example set the Parent mass error tolerance to 0.01da (FT setting) and set the Fragment mass error tolerance between 0.3 and 0.5 (ion trap setting).

If you are using PEAKS 3.0 then expect 10 seconds per spectrum and if using 3.1 then expect 3-4 second per spectrum on average. PEAKS 3.0 would then give 360 spectra analyzed per hour and 3.1, 900 spectra per hour.

If the error plot in the "ion table frame" of the "spectrum main processing window" is skewed, this suggests that the mass spectrometer is miscalibrated or the sequence is bad. If all the spectrum form a particular trial are slanted in the same way by roughly the same ammount this could be a poor instrument calibration indicator. PEAKS compensates for this in its analysis. Similiarly, if only one or two of the plots have a skew, it is probible that that particular sequence is bad.

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De Novo Sequencing Protein ID PTM Seq. Tag Search Raw Data Tech Support Request Prices Try PEAKS Our Research User Comments	Superior de novo sequencing and protein ID Software PEAKS PEAKS Tips Page This part of the support page will grow with new tips and tricks that will be posted each month. Our user group is invited to post their tips and strategies used with PEAKS to be shared with the rest of the community. Please submit your tips for posting by clicking: Submit Tip. PEAKS Tips Setting error tolerances rule of thumb Preprocessing data ET with hybrid mass spectrometers Data processing expectation Bad sequence or poor instrument calibration indicator Setting error tolerances rule of thumb Setting error tolerances is mainly dependent on 2 things; our instrument and your data quality. In PEAKS, in the Tools/PEAKS protein ID window, a user selects the type of mass spectrometer that they generated the data with. The message in blue indicate the suggested error tolerance typical for the instrument. This is only a suggestion, you know your instrument better than anyone. As mentioned the other dependency of appropriate error tolerance setting is the quality of the data. This is more tricky. The best way to determine the data specific tolerance is to use data that is typical of your data quality and the proteins/peptide present in the sample data are known. Play with the error tolerance setting until the best results are found. Preprocessing Data For PEAKS sake don't do it. PEAKS uses all the data, noise and all in the analysis. Use PEAKS "Centroid and deconvote for analysis" tool build into our software. Having no preprocessing done before PEAKS gets the data will make the result that PEAKS return that much better. Processing non-preprocessed data maybe slower compared to processed. Error tolerances for hybrid mass spectrometers hybrid mass spectrometers are typically set to handle MS runs and MS/MS differently. For example, an LTQFT will process the precusor at a higher mass accuracy then the tandem sample. In the Tools, PEAKS protein ID window it is a good practise to set the "Parent mass error tolerance" and the "Fragment mass error tolerance" separately based on the type of hybrid instrument that you have. Using the LTQFT example set the Parent mass error tolerance to 0.01da (FT setting) and set the Fragment mass error tolerance between 0.3 and 0.5 (ion trap setting). Data processing expectation If you are using PEAKS 3.0 then expect 10 seconds per spectrum and if using 3.1 then expect 3-4 second per spectrum on average. PEAKS 3.0 would then give 360 spectra analyzed per hour and 3.1, 900 spectra per hour. Bad sequence or poor instrument calibration indicator If the error plot in the "ion table frame" of the "spectrum main processing window" is skewed, this suggests that the mass spectrometer is miscalibrated or the sequence is bad. If all the spectrum form a particular trial are slanted in the same way by roughly the same ammount this could be a poor instrument calibration indicator. PEAKS compensates for this in its analysis. Similiarly, if only one or two of the plots have a skew, it is probible that that particular sequence is bad.