Alexey Nesvizhskii

I think Dan wrote a tutorial on that part. If not, Dan – we should put something together, see below From: MNTsnowman ***@***.***> Sent: Saturday, November 13, 2021 2:20 PM...

You are using an old version of the tools Version info: FragPipe version 16.0 MSFragger version 3.3 Philosopher version 4.0.0 (build 1626989421) Please upgrade to the latest FragPipe 17.1 and...

Stephan, You can control MBR, and allow MBR between runs from two experiments only with setting ‘top MBR runs’ to 1 ( in your case, since you only have 2...

Hi Stephan What are other scenarios where such an option of defining parameter groups and doing LFQ separately for each set is useful, in your experience? But we will discuss...

@jd690764 any update on this issue? Do you still have the problem with philosopher output ?

The log looks OK I noticed that you assigned files to different experiments. With Open search, one would typically not assigned files to experiments Can you try with just 1...

Ok. But I am not sure what causes the error though. Can you try with …_c file alone (you have _a, _b, and _c replicates)? I wonder if there is...

Iheremans: For now, please rename the files to get rid of ‘_c’ And what do you want to do? To see the differences in PTMs between two conditions? Then assigned...

Maybe you can contract us directly, and send mzML from FlashDeconv (and without) We can see how the search results look compared to no deconvolution. Best Alexey From: piroman999 ***@***.***>...

Hi Miguel, You would need to discuss with Hui-yin, who is the lead TMT-Integrator developer, if she can add another Index (peptide+modification) to TMT-Integrator. The problem is, do you need...