MSstatsTMT Converter Problem

Xiuyuan Chen

unread,

Mar 26, 2024, 11:11:32 AM3/26/24

to MSstats

Hi,

I'm currently using MSstatsTMT (V2.8.0 and V2.1.0) to analyse my TMTpro data, but the function "MaxQtoMSstatsTMTFormat" can't work. That will be grateful if you don't mind providing any suggestions. The error message looks like this:

Error in .mergeAnnotation(input, annotation) :

** Please check the annotation file. The channel name must be matched with that in input data.

I tried to use different formats in the "channel" column, and I also tried to use the output from MaxQuant V2.2.0 and V2.3.1, but none of these worked. Attached link are the examples of my dataset. Thanks!

evidence.txt

proteinGroups.txt

TMTannotation.csv

Mateusz Staniak

unread,

Mar 28, 2024, 11:52:38 AM3/28/24

to MSstats

Hi,

looks like I don't have access to these files on sharepoint. I think I just need to see column names of evidence file and unique values of Channel column in annotation.

Kind regards,

Mateusz

Xiuyuan Chen

unread,

Mar 28, 2024, 3:13:44 PM3/28/24

to MSstats

Hi Mateusz,

So sorry about that, hopefully it can work this time.

Yours sincerely,

Xiuyuan Chen.

evidence.txt

TMTannotation.csv

proteinGroups.txt

Mateusz Staniak

unread,

Mar 28, 2024, 5:59:27 PM3/28/24

to MSstats

Hi,

please try removing the "channel." part of Channel column in annotation.

Kind regards,

Mateusz

Xiuyuan Chen

unread,

Mar 28, 2024, 8:01:52 PM3/28/24

to MSstats

Hi Mateusz,

Sorry but still didn't work. Attached is the annotation file I used. I also tried to remove the "." or start as 0, like "0, 1, 2,..."

Thanks a lot for your patience.

Yours sincerely,

Xiuyuan Chen.

MSstatsTMT_annotation.csv

Xiuyuan Chen

unread,

Mar 16, 2025, 9:23:10 AMMar 16

to MSstats

Hi MSstats team,

Sorry, I still have the same problem, even though I tried multiple versions of MaxQuant, including 2.6.7

Yours sincerely,

Xiuyuan Chen.

Anthony Wu

unread,

Mar 20, 2025, 6:56:14 PMMar 20

to MSstats

Hi,

Can you attach your evidence, protein groups, and annotation file to this thread to help us debug?

Thanks,

Tony

Xiuyuan Chen

unread,

Mar 21, 2025, 2:07:19 AMMar 21

to MSstats

Hi Tony,

Thanks for your response, attached is an example evidence file since the real one is too large.

Hope you have a nice day.

Yours sincerely,

Xiuyuan Chen.

proteinGroups.txt

MSstatsTMT_annotation.csv

evidence_example.txt

Anthony Wu

unread,

Mar 28, 2025, 1:37:46 PMMar 28

to MSstats

Hi,

I took a look and there appears to be an issue with your evidence file. All of the intensities are < 1, which leads MSstatsTMT to filter out all of those PSMs, leading to an error. I don't think having an intensity of < 1 makes sense for all PSMs. Could you check with how you output your processing file (right now it seems you output the intensities to be on a normalized 0-1 scale).

Tony

Xiuyuan Chen

unread,

Apr 9, 2025, 5:54:16 AMApr 9

to MSstats

Hi Tony,

Sorry for the late reply, yes we enable the normalisation function ("ratio to refer to channel") during the MaxQuant search. is there any method to use MSStats while enabling the MaxQuant normalisation?

Hope you have a nice day.

Yours sincerely,

Xiuyuan Chen.

Anthony Wu

unread,

Apr 10, 2025, 10:37:48 AMApr 10

to MSstats

Hi Xiuyuan,

If you use MSstatsTMT, you can disable the normalisation function during the maxQuant search. MSstatsTMT performs normalization already. See this link, specifically noting the "global_norm" and "reference_norm" parameters.