bigbio / bigbio/quantms

OpenMS and frequently mass shifts in Unimod

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#411 12 comments 0 reactions 0 assignees View on GitHub
enhancement
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Nextflow
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83
Forks
57
Avg merge
4h 14m
Merged PRs (30d)
1

Description

### Description of feature

@MaLLLiYA @timosachsenberg @jpfeuffer @daichengxin :

We have been analysing some of the datasets and we found some interesting unexpected PTMs (mass shits), most of them are here:

https://unimod.org/modifications_list.php?a=search&value=1&SearchFor=Unidentified+modification+of&SearchOption=Contains&SearchField=

```
1970 |   | Unknown:162 | Unidentified modification of 162.1258 found in open search | 162.125595 | 162.2267 | H(18) C(8) O(3)
```

Can we make sure these mods works in OpenMS? Also, Can you let us know @timosachsenberg how you can search with OpenMS tools for a delta mass when the mod is not defined on OpenMS?

Contributor guide

Open the contributing guide

Research direction

Start by reviewing the Unimod search linked in the issue and the OpenMS tools relevant to searching for undefined delta masses. The issue is complete only when the handling of the listed modifications and the workflow for undefined mass shifts are clearly established; no repository files or tests are named.

Written by the indexing model from the issue text.

Assessment

Domain
bioinformatics
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

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