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Chromagraphic Analysis¶ In targeted proteomics, such as SRM / MRM / PRM / DIA applications, groups of chromatograms need to be analyzed frequently. OpenMS provides several powerful tools for analysis of chromatograms. Most of them are part of the OpenSWATH suite of tools and are also discussed in the OpenSwath documentation.

In targeted proteomics, such as SRM / MRM / PRM / DIA applications, groups ofchromatograms need to be analyzed frequently. OpenMS provides several powerfultools for analysis of chromatograms. Most of them are part of the OpenSWATHsuite of tools and are also discussed in the OpenSwath documentation.

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Peak Detection¶

Here, we will focus on a simple example where 2 peptides are analyzed. We willneed 2 input files: the chromatogram files that contains the chromatographicraw data (raw SRM traces or extracted ion chromatograms from PRM/DIA data) aswell as the library file used to generated the data which contains informationabout the targeted peptides:

Here we see that for the first group of transitions (tr_gr1), a single peakat retention time 3119 seconds was found. However, for the second group oftransitions, two peaks are found at retention times 3119 seconds and at3055 seconds.

Visualization¶

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Chromagraphica Double Dry Plate Holder

We can confirm the above analysis by visual inspection of the chrom.mzMLfile produced above in the TOPPView software:

However, our output above contains more information than only retention time:

Based on the output above, we can infer that the peak at 3055 seconds islikely the correct peak for tr_gr2 since it has a high library dot product(0.95) while the peak at 3119 seconds is likely incorrect for tr_gr2 sinceits dot product is low (0.75). We also see that a peak at 3119 seconds islikely correct for tr_gr1 since it matches well with the expected libraryintensities and has a high dot product (0.99).

Note: to get an overview over all available scores for a particular MRM feature f, you can use

Smoothing¶

Now you may want to show the chromatograms to your collaborator, but you noticethat most software solutions smooth the chromatograms before display. In orderto provide smooth chromatograms, you can apply a filter using pyOpenMS:

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Which leads to the following smoothed chromatographic traces: