Recalibrating PKL-Files derived from MS-experiments.

As I just heard it often happens that the output of mass spectrometry experiments is shifted by a constant ppm value. That may happen if the room temperature changes (caused by a perverse air conditioner or one of your trainees again leaved the door open), what invalidates the calibration of a TOF instrument. All further analysis will fail or bring wrong scores although you know the m/z values of all peaks should be shifted to the right by 55.2 ppm to get the correct values… Repeating the experiments is often very expensive and of course time consuming, but here is the solution!

With this tool you can shift all m/z values of such an PKL-file. You can decide whether to shift all spectra or just a single one of the file! After shifting the data just save it as new PKL-file, so the original values are not lost.

There is also a small spectrum viewer to visually validate the resulting spectra. In figure 1 you can see a screen shot taken from an example PKL-file.

Figure 2 displays a result of a Mascot search before and after shifting of a spectrum. As you can see all scores increase more or less while the expects decrease, denoting a more secure hit.

It’s written in JAVA to have it OS independent, all you need is a JRE, get it from Java (also free).

For bugs or feature requests just send me a ping and I’ll see what I can do..


Binaries and sourcecode are available from adjustPKL @ GitHub.

git clone

Martin Scharm

stuff. just for the records.

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