Update parse_settings_maxquant.toml

[mlocardpaulet]

Hey! I am sorry, I have an error on my side (when I run the PR locally):

It does not look like it comes from your changes, does it?

[mlocardpaulet]

Hey! I am sorry, I have an error on my side (when I run the PR locally): It does not look like it comes from your changes, does it?

Although I don't have the error when I run the main locally.

[mlocardpaulet]

Also, can your script handle other modifications than oxidation and acetylation? Because users can search with many others without us even knowing, right?

[RobbinBouwmeester]

There is no naming convention, so no essentially we will not normalize modifications not in the dictionary provided. We keep them as is. There is no solution I can think of for this.

[mlocardpaulet]

There is no naming convention, so no essentially we will not normalize modifications not in the dictionary provided. We keep them as is. There is no solution I can think of for this.

I think that this is completely fine. I just asked because in the toml, the field "modification_dict" only contains oxydation and acetylation.

[RobbinBouwmeester]

@mlocardpaulet latest push should fix your issues :)

[RobbinBouwmeester]

Ok, nope, did not fix it, will try to fix it ASAP :)

[RobbinBouwmeester]

@mlocardpaulet now it should work! 👍

[mlocardpaulet]

It does not, sorry. Here is what I have:

So I suspect that "[Oxidation (M)]" -> "[(M)]", and I don't see the acetylations.

[mlocardpaulet]

Remind me: why do we even change the value in the "Modified sequence" field if we keep the modifications as is? I know that this was necessary to do so with other outputs, specially when sequences are stripped (no modification) and modifications are listed in another field. But here, why do we do that? And I am still not sure I understand the "modification_dict". What happens if people search with phosphorylation? I am sorry I am a bit slow to understand...

[RobbinBouwmeester]

Ok, we decided to do this to make downstream analysis easier if we want to compare (different) search engine input.

If the modification does not exist it will use the same name that is reported, but it will be put in between braces. So, for example:

AAPAPEEMS(Phospho (S))EPK|Z=3

If the modification is not present it will be changed to:

AAPAPEEMS[Phospho (S)]EPK|Z=3

[mlocardpaulet]

Ok, we decided to do this to make downstream analysis easier if we want to compare (different) search engine input.

If the modification does not exist it will use the same name that is reported, but it will be put in between braces. So, for example:

AAPAPEEMS(Phospho (S))EPK|Z=3

If the modification is not present it will be changed to:

AAPAPEEMS[Phospho (S)]EPK|Z=3

OK, I think that what is the most important is to have the modifications in the correct position in the sentence. The way the modification is encoded won't be homogenised by us, indeed. We also want all the modifications in the intermediate file (the ones we have in "modification_dict" and the others) to be reported in a homogenous fashion, right? If not, it will make things a lot more difficult for people who would want to parse these intermediate files (and actually I plan to do so for the paper). What do you think?

[mlocardpaulet]

Hello! @RobbinBouwmeester you know that it still does not work well, right? Here is the output from the main, a file from MQ 2.5.1.0

The [(M)] is not the correct modification.