enonimos

@huiyinc The PSM tables between v17 and v18 are identical, and the behavior I observed is the same between v17 and v18, so this does appear to be a TMT-Integrator...

Hi Huiyin, Here is a link to a zip archive that has the files you requested. https://www.dropbox.com/s/39s9mojtr2fdio3/TMT%20Integrator%20MS1%20vs%20MS2%20files.zip?dl=0 The two PSM files are the same dataset analyzed by TMT Integrator with...

Hi Huiyin, Yes that's correct, I sent the PSM tables for v18 because the issue I saw isn't one that appeared after the update, it occurs in both v17 and...

Hi Huiyin, I see, the global MS1 minimum makes sense. I agree if this value were to be written into the RefInt columns, then that would avoid confusion. Thanks, Todd

Hi Alexey and Fengchao, Thank you for the clarification and comparison to TMT-I. This strategy makes sense to me and I would support its inclusion as feature in IonQuant. Regarding...

Hi Fengchao, Thank you for the link, I missed that section. Unfortunately, I am interested in phospho LFQ, so the threshold peak filter will not be a long term solution...

Thanks Fengchao, one last question. Do you know yet if this module will produce mzml encoded files with similarly large size as msconvert? And therefore having 64GB+ RAM will be...

Ok that's great. Also, you have probably considered this, but another future workaround for phosphoLFQ with PASEF could be if there was a way to filter peaks in mzml generation...

Ok I see, so even though I didn't get any errors, I shouldn't trust that the recalibrated data is accurate from mzml?

I have followed up on the suggestion to disable mass recalibration for analyzing PASEF mzml and I used a computer that has 144GB of RAM. I made it farther through...