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MaxQuant and Perseus Bug Reporting
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Maxquant (v2.6.3.0) does not exit "Prepare_crosslink_search" stage #104

Open medardus333 opened 1 month ago

medardus333 commented 1 month ago

Hi,

as the google group does not work for me (it states I have no access) and the contact group admin does also not work, I try it here.

I'm trying to do a crosslink search of TMT labelled samples. I have tried the search with a full FASTA (45,000 protein entries), but MQ was stuck in the "Preparing_crosslink_search" stage. I let MQ (earlier version) run in the background for 3 weeks, but it only filled up my harddrive with more than 1TB of tmpPeptide files.

I tried again with a 50 protein FASTA, where MQ then finished. However, this is not very comprehensive.

For the current experiment, I have cut down the FASTA to around 1,000 protein entries. After starting the search, MaxQuant functions normally until the "Preparing_crosslink_search" stage, where MQ (v.2.6.3.0) again just starts to fill up my harddrive with > 100 GB of tmpPeptide files.

Is there an upper limit for how many proteins can be in the FASTA to have a reasonable MQ run time? Also, during the "Preparing_crosslink_search" stage only a single CPU core gets used.

Best

Florian

WalterViegener commented 1 month ago

Dear Florian, Can you please check your proc folder for .error.txt files? At Combining apl files for crosslink search there should be an message that this is not implemented yet. Anyways, we do not support labelled crosslinking experiments.

medardus333 commented 1 month ago

Hi Walter,

I unfortunately already deleted the whole folder as it was filling up my harddrive completely. Currently repeating with a 150 protein FASTA (70kB), which resulted in 38GB peptides file and MQ is currently joining the temporary modpep mass lists (currently 14h into the "prepare_crosslink_search"). So I would guess anything above a 200 protein FASTA is not feasible to search with MQ using my setup.

As for the labelling, I set the experiment type as "standard" and set TMT label as a fixed n-terminal modification, the lysine as variable (as the cross-link is on lysines). Reporter ion intensities I will integrate using R.

Cheers Florian

WalterViegener commented 3 weeks ago

Dear Florian, You should set as experiment "Reporter MS2" or "Reporter MS3" and can then set your TMT label (NOT as modification). This setting is if you used orbitrap (I guess since you before had used Standard setting) Otherwise please tell me more about your experiment. In case you used TIMS-DDA you can select reporter ions.

As for the crosslinker. We have a tab called Crosslinks (in Group-specific parameters) where you can select your crosslinker. I can help you there if you tell me which crosslinker you used.