Albert Tian Chen

Hi, I unfortunately have not tested any of this on Lumos data. You may have better luck asking on the official MaxQuant Google group: https://groups.google.com/g/maxquant-list

Hi Devender, I'm not part of the MaxQuant team - just made this guide to help others. The official help forum is on Google Groups here: https://groups.google.com/g/maxquant-list

Hi, I never had a problem with using the modifications file on linux. Could it be a spelling/capitalization error? i.e., `Phospho (K)` instead of `Phospho (k)`? I would also make...

Can you check if the CPU is running when it's stuck at "preparing searches"? I've had a few runs where it seems stuck at this step but it's actually still...

Hi, Thanks for the detailed info. I haven't run into that issue before, but I suspect it's Mac OSX specific. Note that MacOS is Unix-based, not Linux based, and while...

Hi, Thanks for the update. I haven't run into this error before, and I don't have any experience with Singularity (the shell script outputs in this repo are designed for...

Have you confirmed that mono is working? You can test it with `mono --version`. What MaxQuant version are you using?

That's great! You should let the MaxQuant developers know about this discrepancy with the later version: [https://groups.google.com/forum/#!forum/maxquant-list](https://groups.google.com/forum/#!forum/maxquant-list)

How many files are you processing? It's my anecdotal experience that the FDR calculation can be memory-heavy so maybe you are running out of RAM. You can also check the...

In your output folder for your run (MaxQuant calls this the "combined" folder), go into `combined/proc` and look for a file named `Applying_FDR 11.error.txt` (or something like that). Inside that...