small molecule integration filtering

small molecule integration filtering sufyan pandor  2021-02-11

For a large scale screening experiment (ion mobility 6560) i want to be able to have skyline firstly not integrate a peak if the mass accuracy is outside a specified range and secondly not integrate a peak if an M+1 M+2 is missing and not co-eluting or better yet not at the correct ratio from the theoretical fit

Is any of this possible to get through hundreds of data files/compounds?


Nick Shulman responded:  2021-02-11
One way that you could do this is by using the Document Grid.

After Skyline has extracted chromatograms and chosen peaks, you can look at the results in the document grid.
You can create a report which has the columns that you are interested in filtering on: "Mass Error PPM" and "Isotope Dot Product".

It sounds like you want to remove all the peaks where the Mass error is above a certain number, or the isotope dot product is below a different number. The Document Grid does not allow you to do "OR" filters, but you can certainly remove all the peaks that you need to in two separate steps.

Once you have the Document Grid displaying all of the rows for the peaks that you want to remove, you can select all the rows and use the "Actions" dropdown at the top of the Document Grid and choose "Remove Precursor Peaks".

If you want to learn more about the Document Grid, you should take a look at the Custom Reports tutorial:

-- Nick