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Export matched RTs and intensities

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Export matched RTs and intensities lincolnh  2025-11-07 10:15
 

Hi Nick,
I'm trying to export a custom report that contains RTs and intensities for all transitions, for all samples. I've included a screenshot of my current report template. I'm confused by the fact that "Interpolated Times" and "Interpolated Intensities" do not contain the same number of points. For example, if I export this report, one of my transitions has 2389 times and 1246 intensities. I've attached a small version of this report as well. I've noticed the same thing when I export "Raw Times" and "Raw Intensities". I'd like to obtain matched pairs of RT, Intensities for each transition. Is this possible?

Also, I'm confused as to what the "Interpolated Number of Points" field is telling me. For the example I mentioned, this number is 406....I can't figure out what this corresponds to.
 
 
Nick Shulman responded:  2025-11-07 14:14
For a particular Transition and a particular Replicate, I would expect that "Interpolated Times" and "Interpolated Intensities" would have the same number of values in them.
Furthermore, all of the transitions for a particular Precursor in a particular Replicate should have the same Interpolated Times as each other, because the purpose of the interpolation is to prepare for peak detection by putting all of the transitions on the same time scale.

In your attached CSV file, which Transition and Replicate are you looking at where you see 2389 times an d1246 intensities?

If you are writing software to analyze this report, you will probably find things easier if you uncheck the "Pivot Replicate Name" checkbox in the Customize Report dialog. Doing that will ensure that each Replicate appears on a different row.
If you are seeing different numbers of intensities and times the most likely cause is that you're not looking at the same Replicate.

-- Nick
 
lincolnh responded:  2025-11-07 14:46
From what I can tell, none of the transition, sample pairs have the same number of times and intensities. For example, here is a code snippet where I explore this:
 
Nick Shulman responded:  2025-11-07 16:36
Here is an Excel spreadsheet where I added columns to count the number of commas for the "Times" and "Intensities" for the first replicate for all of the transitions.
The numbers are always the same.

In your code snippet, I think that "len(rts_test)" is actually the length of the string "rts_test".
If you want the count of values in that string you would have to count the number of commas.
Claude suggested doing the following to convert "rts_test" into a list of numbers:
np.fromstring(rts_test, sep=',')
-- Nick
 
lincolnh responded:  2025-11-10 11:13
Ah that did it! I was expecting ints but the document recorded intensities and RTs as strings. Sorry for the dumb question!
 
lincolnh responded:  2025-11-18 15:00

Perhaps this is another dumb question, but why do the number of interpolated intensities vary between peptides and replicates? This info is given by the "number of points" field. I've noticed this is the case for interpolated and raw intensities. Is there a way to extract the same number of RT, intensity tuples for each peptide, replicate combination? I'm trying to train a machine learning model, which gets tricky when you have inputs of varying lengths.
 
Nick Shulman responded:  2025-11-18 15:51
If you want all of your chromatograms to have the same number of points in them, I would recommend that you interpolate them yourself.
You would start with the "Raw Times" and "Raw Intensities" chromatograms for everything, and decide on the number of points you want, and do linear interpolation for each of those raw chromatograms.

When Skyline is deciding how many points the interpolated chromatogram should have, Skyline tends to choose a number of points that is very similar to the number of points in the raw chromatogram.
In your .raw files, the number of minutes in each run is probably the same, but the number of points in the chromatograms end up being slightly different run to run because the mass spectrometer was acquiring spectra as fast as it could, and that number of spectra just ends up being a different number because of different amounts of time it took to fill the ion traps with the target number of ions based on the actual samples.
-- Nick