IMPORT MODIFICATION FILE

[kazbek966]

Is there intelligent way of importing Custom Modification file ? I am in particular interested in O- and N-glycan libraries that currently has very limited build-in options. I was trying to locate MOdification file in the SearchGUI folder itself to make amends and could not find it, thus the only way either to add one-by-one, which is a bit lengthy exercise or find a way to import the file or add it in the next version. Will be happy to provide a list.

[hbarsnes]

Modifications are stored in a json file that you can find here: "username"\.compomics\modificationFactory-5.0.42.json.

You could potentially make your own version of this file. Not sure how easy it would be though.

There should also be a command line option to add custom modifications (java -cp utilities-5.1.18.jar com.compomics.cli.modifications.ModificationsCLI), but it does not seem to be working. But if you think that this would be an option, I can try to fix it and release a new version.

Here is the description of the ModificationsCLI command line:

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Compomics Modifications - Command Line
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The ModificationsCLI command line allows the command line management of modifications. It can be used to create and edit json files containing modifications compatible with CompOmics tools.

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OPTIONS
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Input and Output:

-in                                  An input file (.json).
-out                                 The destination modifications file (.json).
-l                                   Lists all modifications implemented. All other options than in will be ignored.


Remove modification:
-rm                                  The name of a modification to remove.


Add modification:
-type                                The type of the modification to add. Modification at specific amino acids.: Modification at specific amino acids.; Modification at the N-terminus of a protein: Modification at the N-terminus of a protein; Modification at the N-terminus of a protein at specific amino acids.: Modification at the N-terminus of a protein at specific amino acids.; Modification at the C-terminus of a protein.: Modification at the C-terminus of a protein.; Modification at the C-terminus of a protein at specific amino acids.: Modification at the C-terminus of a protein at specific amino acids.; Modification at the N-terminus of a peptide: Modification at the N-terminus of a peptide; Modification at the N-terminus of a peptide at specific amino acids.: Modification at the N-terminus of a peptide at specific amino acids.; Modification at the C-terminus of a peptide.: Modification at the C-terminus of a peptide.; Modification at the C-terminus of a peptide at specific amino acids.: Modification at the C-terminus of a peptide at specific amino acids..
-name                                The name of a modification to add.
-short_name                          The short name of the modification to add.
-composition_added                   The atomic composition of the modification to add.
-composition_removed                 The atomic composition of the modification to remove.
-pattern                             For modifications that target specific amino-acids, the pattern of amino-acids targetted. E.g. N[ACDEFGHIKLMNQRSTYUOVW][ST] for a modification targetting N followed by any amino acid but P followed by S or T.
-pattern_index                       For modifications targetting a pattern of amino-acids longer than one amino acid, the index on the patter where the modification is located, 0 being the first amino acid. E.g. 0 in N[ACDEFGHIKLMNQRSTYUOVW][ST] means that the modification is located on N, 2 means that the modification is located on S or T. 0 by default.

[kazbek966]

Yes, seems like JSON is a bit of a monster to put it mildly. Upon attempt to upload it to Claude it immediately went beyound all token limits. Is there any other way to upload those modifications ? I would really love to add a bit of O- and N-Glycans and by a bit I mean around 200 each. Doing it by hand is a bit of an issue .... If you think CL will help then lets try it. But how this file was created in the first place ? Through same CL ?

[hbarsnes]

If you think CL will help then lets try it.

Ok, I will see if I get the time to look at it later this week.

But how this file was created in the first place ? Through same CL ?

The modification objects are created inside our Java code. We've added them one by one over time, largely as a manual process and when needed. The json file came later and is automatically created from the code.

[kazbek966]

On further thinking it occurred to me that it will be much simpler to format one of very first JSON modif file , that do not have SILACs, TMT and all other modifications I have no use for. IN practice I really need a couple of common modifications ( oxidation, deamidation, ammonia/water loss, carbamylation) and thats pretty much it. Though I would love to drastically expand list of glycans: both N- and O-. And that would have been my top priority. SO in case I have relatively clean JSON modif file, I can put into Claude and make it populate with all I need in one go. It does have some token limitations, but I can do this is a couple of iterations. Just not sure how and whether itis possible to automate CL . I guess it is possible as well. But letting Claude do the job sounds more straightforward.

[hbarsnes]

Both solutions should work. Well, given that I get the command line up and running again. I already made a quick fix. Will try to find the time to release a new version next week.