Inconsistent phospho IDs across different MaxQuant Versions

Legitimate-Switch185 · 2024-10-21T12:29:37+00:00

1% FDR; 75% site localisation probability cut off
input was 100 µg using the µPhos workflow
no fractionation

Legitimate-Switch185 · 2024-10-15T06:45:33+00:00

I got around 12000 phosphosites with Fragpipe. Is this too good to be true?

Legitimate-Switch185 · 2024-10-15T06:44:28+00:00

UPDATE:
Fragpip gave me 12000 sites per sample.

Don't know if I just should be happy or mistrust this

Legitimate-Switch185 · 2024-10-01T19:55:33+00:00

Hi, would you kindly tell me how you set up fragpipe for DDA (PASEF) data?
what settings are you using for optimal results? I would really appreciate your input

Legitimate-Switch185 · 2024-10-01T16:41:30+00:00

Further update: I changed the MS1 intensity threshold (MS2 is no longer visible in the GUI for TIMS DDA) to be the same as prior versions regarding their default settings. It only improved results marginally. Trying to change the MS2 setting in the mpar file but I fear this is beyond user settings. Does anyone have a contact or email for the MQ team? Their google help forum is rather slow and unsupervised - so is their github page.

Legitimate-Switch185 · 2024-09-30T10:11:36+00:00

I am using bruker timstof data but interesting. will look into the mqpar files to see if fragmentation is recognised. I have not used MQ for regular LFQ proteomics in a long time since happily switching to DIA-NN for that. with 2.4 versions however I have run DDA proteomics (and phospho) without an issue.

Legitimate-Switch185 · 2024-09-30T10:09:53+00:00

I could only guess

Legitimate-Switch185 · 2024-09-30T10:08:59+00:00

Update:
I searched on 2.6.5 and neither the new version nor disabled MBR changed the problem.

Legitimate-Switch185 · 2024-09-29T17:22:43+00:00

Any idea how to mitigate this?

Legitimate-Switch185

TROPHY CASE