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biodavidjm / artMS

Analytical R Tools for Mass Spectrometry

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question about User defined PTM

hemingwang opened this issue · comments

commented

Hi,
When I run the artMS, I want to use my modification. But I found it has mistake.
my artMS version is 1.8.3
my config file is:
data:
modifications: PTM:STY:ph
my R code is:
artmsQuantification(yaml_config_file = "my_config.yaml")

the R console is:

artmsQuantification(yaml_config_file = "my_config.yaml")
The PTM name used in the evidence file, and the third position in PTM:STY:PH must be all lowercase characters
Error in artmsQualityControlEvidenceBasic(evidence_file = config$files$evidence, :
Error: unexpected format for specifying a user-defined modification typePTM:STY:PH

I am looking forward to your reply.

commented

Hi @hemingwang ,

this should be an easy fix. As the error is indicating, you just need to replace PTM:STY:PH by PTM:STY:ph ("ph" must be lower case, same as MaxQuant.

However, as explained in the vignette, that's the "general" form. For phosphorylation is one of the 3 main PTMs most frequently PTMs so they have their own "shortcut". So you can directly use PH, i.e., in the configuration file:

modifications: PH

Please, give it a try and let us know how it goes.

Thanks!

commented

Thank you help me in patience!
At the beginning, I want to use my defined PTM(ad). So I write PTM:STY:ad in the config file. The console result is "I used the AD". So I feel puzzled.
Then I write PTM:STY:ph in the config file. It is the same wrong.
But I write PH in the config file is no wrong.

Best wishes!

commented

Not sure I fully understand what the problem was. Not sure what PTM:STY:ad is. Would you mind clarifying? And PTM:STY:ph should have worked (I cannot reproduce the error, on our side, PTM:STY:ph works perfectly.

How did you install artMS? what type of posttranslational modification did you search in MaxQuant? phosphorylation? (I don't know what "AD" is). It would help us a lot if you could provide the exact error that you get when you run a configuration file with "PTM:STY:ph". Would you mind sharing?

Thanks!

commented

Closing the issue. Please, don't hesitate to re-open it if you have anything else to add