Crosslinking experiments model [DO NOT MERGE]

[ypriverol]

Here, Im trying to introduce a model for cross-linking experiments. Feedback needed. @diogobor can you give feedback here. The proposal is the following:

Cross-linking experiments

MS-based cross-linking experiments are used to study protein-protein interactions and protein structures. Currently, multiple MS-based cross-linking methods are available including hydrogen−deuterium exchange (HDX-MS), cross-linking mass spectrometry (XL-MS), and ion-mobility MS (IM-MS).

In the case of cross-linking experiments, the first thing that needs to be annotated in the SDRF-proteomics in the sample metadata is the enrichment process. The enrichment process SHOULD be provided:

• characteristics[enrichment process]: The enrichment process is a characteristic that describes the enrichment process of the sample. In the case of cross-linking experiments, the value SHOULD be one of the following: enrichment of cross-linked Protein. This will help the users to understand that the samples are enriched in cross-linked proteins.

In the data side, multiple columns SHOULD be added to the SDRF-proteomics to describe the cross-linking experiment. The following columns are SHOULD be provided:

• comment[cross-linking method]: The method used for the cross-linking experiment. The value SHOULD be one of the following: hydrogen−deuterium exchange, cross-linking mass spectrometry, and ion-mobility mass spectrometry. All these terms are added to PRIDE ontology.
• comment[cross-linker]: The cross-linker is a compound that can link to two or more polymer chains (https://www.ebi.ac.uk/ols4/ontologies/xlmod/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FXLMOD_00004?lang=en[see reference]). The value SHOULD be the accession of the cross-linker in the XL-MS ontology or PRIDE ontology. In addition to the cross-linker accession provided as NT=DSSO;AC=XLMOD:02126 the user can provide additional information about the linker:

Property	Key	Example	Mandatory(:white_check_mark:)/Optional(:zero:)	Comment
Cross-linker Accession	AC	AC=XLMOD:02126	✅	Accession in XL-MS or PRIDE ontologies.
Cross-linker Name	NT	NT=DSSO	✅	Name of the cross-linker term.
Cross-linker Target	TA	TA=K	0️⃣	Target amino acid

Some remaining questions:

• what other properties from the cross-liker will be good to capture, mass diff, C or N terminal cleavage site?
• What would be the relation between the cross-linker and the PTMs, should we annotate it together or split them?

[diogobor]

"what other properties from the cross-liker will be good to capture, mass diff, C or N terminal cleavage site?"
Besides the name and XLMOD, the following info

1. Cleavable or Non-cleavable
2. Mass Shift
   2.1) for cleavable: (mandatory) Heavy fragment mass & Light fragment mass
   2.2) for non-cleavable: (optional) Hydrolyzed mass (Dead-end mass)
3. is it n-term cleavage site?

"What would be the relation between the cross-linker and the PTMs, should we annotate it together or split them?"
In general , it can be annotated together.
However, for isobaric labelled PTMs, e.g. TMT, the behavior of the XL is different because TMT reacts in N-term as well as DSSO, for instance. Scout knows how to handle it.