Problem about user-defined modification type

[Wang-Xuejun]

Hi, I would like to add a new modification: biotinylation in artMS. I changed the modification name Biotinylation to biotinylation(lowercase) in the evidence.txt. And the modification:PTM:K:biotinylation(lowercase). And saved. However, when I run the artmsQuantification in R, it always has the error: The PTM name used in the evidence file, and the third position in PTM:K:BIOTINYLATION must be all lowercase characters Error in artmsQualityControlEvidenceBasic(evidence_file = config$files$evidence, : Error: unexpected format for specifying a user-defined modification typePTM:K:BIOTINYLATION.

Another question is that: can I use the artMS to perform the semi-quantification of pepetides (by intensity) without label-free method, which means no repeat experiment of each group. I input the result from MaxQuant, and run the artmsQuantification with the AB modification. But only shows QC result, no quantification result.

Looking forward your reply.

With best wishes, Wang.

[biodavidjm]

Hi @Wang-Xuejun

This should be easy to fix. The question is, how is the biotinylation annotated in the Modified.sequence column of the evidence file? for example, for ubiquitination, the modification is annotated in that column like this:

_AAAALVK(gl)GR_

Therefore, the mod_type options should be like this:

mod_type = "PTM:K:gl")

Do the same for Biotinylation.

Please, let us know how it goes.

[Wang-Xuejun]

Thanks for your reply.

The modified.sequence is AAAATAAASRPK(biotinylation). So I set the modifications: PTM:K:biotinylation in myconfig file. But it still resulted in the error which I described before.

[biodavidjm]

Thanks!

The problem is exactly the same as this one #189

Please, do what is suggested in that issue, i.e.,

For a site-specific quantification:

1. Use the function artmsProtein2SiteConversion() to generate the site-specific evidence file.
2. Add the resulting site-specific evidence file in the yaml configuration file in the evidence section and mark the modification option as "AB"
3. Run artmsQuantification function

For global quantification:

you have to filter first the evidence file and create a new version with only the biotinylation peptides. Then use that evidence file in the yaml configuration file and again, use "AB" in the modification section.

We are working on generating a new version that will allow the use of the customized version in the "modification" section. It will be notified here when ready. But in the meantime, I recommend any of the options described above.

Thanks!

[Wang-Xuejun]

Thanks for your suggestions! I tried the site-specific quantification first:

> artmsProtein2SiteConversion(evidence_file = "C:/Users/Emily/Documents/MSproject/data/evidence.txt",
+ ref_proteome_file = "C:/Users/Emily/Documents/MSproject/data/reference_proteome.txt",
+ output_file = "C:/Users/Emily/Documents/MSproject/data/biotinylation-sites-evidence.txt",
+ mod_type = 'PTM:K:(biotinylation)')
The PTM name used in the evidence file, and the third position in PTM:K:(biotinylation) must be all lowercase characters
Error in artmsProtein2SiteConversion(evidence_file = "C:/Users/Emily/Documents/MSproject/data/evidence.txt",  : 
  Error: unexpected format for specifying a user-defined modification typePTM:K:(biotinylation)

However, I already changed the information of modification in the evidence.txt file(by using the replace function of txt): like AAAATAAASRPK(biotinylation)

I think the reason is mainly on the evidence.txt format. But I have no idea about this.

Looking forward your reply and the new version of artMS.

[biodavidjm]

Not sure why is not working

Could you please share the first 100 lines of the modified evidence file so I can debug it? If so, please, send it to artms.help@gmail.com

Thanks

[Wang-Xuejun]

I send you the file.

Thanks a lot.

[biodavidjm]

It was easy to fix: we were writing the mod_type option incorrectly. It should be...

mod_type = "PTM:K:biotinylation"

without the parentheses!

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

[Wang-Xuejun]

Hi,

I just tried! It works well! Thank you so much! But another error occurs:

- Protein <O00418> not in the sequence database
- Protein <P42229> not in the sequence database
- Protein <P51692> not in the sequence database
- Protein <O15230> not in the sequence database
Error in artmsProtein2SiteConversion(evidence_file = "C:/Users/Emily/Documents/MSproject/data/evidence.txt",  : 
  Protein IDs from evidence file and sequence database do not match. 
         Are you sure that you are using the right sequence database?

What's the meaning of sequence database in this error? I used the human database from Uniprot. Why this kind of error exists? Looking forward to your reply!

With best wishes, Wang.