JinqiuXiao
commented
5 days ago Hi there,
Can you please try it out with the latest MaxQuant 2.6.6.0? We fixed a bug in mass recalibration that could reduce the number of identification in timstof dda data, which was introduced between the MQ 2.4.14 and MQ 2.5.0.0.
We regained proper number of identification with two different dataset that both show reduced identification in post MQ 2.4 version.
Thank you very much for letting us know the issue. Please let us know how it works for your dataset :)
Best, Jinqiu
I completely understand that different iterations of software like MQ can produce different IDs and quant. values to a certain (minimal) extent.
What I am experiencing now however with a phosphoproteomic data set (DDA PASEF, 36 samples, time course experiment with 3 biological replicates sampled in two phases of a bioprocess with 6 time points each time, 2 replicates 26 27 had initially some injection errors so I reran them afterwards on a new column) is a little bit mindblowing.
I have heard that MQ since 2.5 has improved PTM search integration in Andromeda, especially for more low abundant features (I see in benchmark sets a >50% increase in IDs after filtering). Also, based on investigating benchmark sets with 2.4 and 2.6 versions, phosphosite allocation has become a little bit more stringent. Additionally, I know MBR has possibly become more funky based on limited tests with the new versions.
Anyway, and this is the point I cannot explain why is happening, that this 36 sample dataset has (after filtering) in MQ 2.4.10 a biologically sound and comparable number of site IDs across replicates and all samples, while with 2.6.1 and 2.6.4 some samples completely loose IDs (see below). This also happens on phosphopeptide, peptide and protein levels. Initially, I thought it was a problem with MBR and using 2 samples from an independent run, but no, the error persists if I remove those samples. Also, the samples that are getting close to no IDs vary with the MQ version and they also vary if I include the separately run samples (which brings me back to funky MBR). I also found a bug thread on GitHub where a weird taxonomy ID setting did something similar, but no still persisted (see release for 2.6.5, where this error-producing setting was set off by default now). I am currently running a search with MBR completely off but we will see. Additionally, I will do a fragpipe search for this phospho set as well.
Any idea why I am experiencing this with 2.6 versions and not with 2.4?
This also represents protein, peptide and phosphopeptide levels, not exclusively for ST phospho sites!
Additionally I searched on 2.6.5 and neither the new version nor disabled MBR changed the problem
I further played (in the GUI and mqpar file) with adjusting the MS1 and MS2 thresholds to the 2.4.10 releases but to no avail. Also tried other variations of the dataset and tried another dataset but the issue persists. Would really appreciate a comment and help from a MQ person here. Thank you very much!