Joshua Charkow

Thank you for pointing this out and sorry for not getting back sooner. I think in this case visualising the signal the default parameters may not be appropriate. Changing the...

> I think the problem could be that there are no values > 199 at all so LM may move the RT outside the range without getting penalized (error doesn't...

From the test case it looks like the results are in general improving since the "quality" metrics increases in all examples. Because of this I'm leaning towards the second option....

I don't know if I have appropriate data but I do have openswath chromatograms that I could run it on

Hi Braudi, Many of the columns that you mentioned that are only in the .tsv file are in the .osw file but they are named differently. Most of the transition...

A lot of the information from the .osw file is excluded from the .tsv file exported by pyprophet in order to reduce the size of the .tsv file. To address...

> Thank you for taking care of my requested inquiries, it would be really awesome if the missing data from the OpenSwath TSV file are now also found in the...

In general, the values in FEATURE_MS2 and FEATURE_MS1 are an amalgamation of the values of all the transitions in FEATURE_TRANSITION or FEATURE_PRECURSOR respectively. The total area intensity refers to the...

No problem! Unfortunately, current documentation for OpenSwath is lacking and this is something that we are actively working on. For the time being here are some resources which may be...

> Hi @jcharkow, I just wanted to ask when I can expect the patch? Best regards Sorry for the delay have been busy with other things but patch should be...