Opened 5 years ago

Last modified 2 years ago

#834 new

Import of mzIdentML results

Reported by: Fredrik Levander Owned by:
Milestone: Proteios SE 2.20.0 Keywords:
Cc:

Description

Allow for import of search results in mzIdentML format from MS-GF+.

Change History (19)

comment:1 Changed 5 years ago by Fredrik Levander

First commit in [4555]

comment:2 Changed 5 years ago by Fredrik Levander

(In [4589]) Refs #834. Setting spectrum id of imported PSMs to MGF title if applicable.

comment:3 Changed 5 years ago by Fredrik Levander

(In [4590]) Refs #834. Correction to setting spectrum id of imported PSMs to MGF title if applicable.

comment:4 Changed 5 years ago by Fredrik Levander

(In [4596]) Refs #834. Cutting accession numbers at pipe character to comply with other proteios imports.

comment:5 Changed 5 years ago by Fredrik Levander

(In [4597]) Refs #834. Also trimming protein description string if it starts with accession to mimic default Mascot protein descriptions.

comment:6 Changed 5 years ago by Fredrik Levander

(In [4598]) Refs #834. Faster processing

comment:7 Changed 5 years ago by Fredrik Levander

(In [4599]) Refs #834. Logging more info.

comment:8 Changed 5 years ago by Fredrik Levander

(In [4600]) Refs #834. Removing slow file validation and adding progress message.

comment:9 Changed 5 years ago by Fredrik Levander

(In [4601]) Refs #834. Reverting commenting out of post processing.

comment:10 Changed 5 years ago by Fredrik Levander

(In [4602]) Refs #834. Commenting out of post processing.

comment:11 Changed 5 years ago by Fredrik Levander

(In [4605]) Refs #834. Faster annotation of retention times and total intensities to hits.

comment:12 Changed 5 years ago by Fredrik Levander

(In [4614]) Refs #834. Fix for Nterm mods

comment:13 Changed 5 years ago by Fredrik Levander

(In [4618]) Fixes #835 Refs #834 Faster results import, dictionary updates, init script update.

comment:14 Changed 5 years ago by Fredrik Levander

(In [4622]) Refs #834. Faster reading of data from MGF.

comment:15 Changed 5 years ago by Fredrik Levander

(In [4623]) Refs #834. Better handling of accession numbers delimited by pipes to support THISP database search. Handling negative infinity in tandem protein expect values.

comment:16 Changed 4 years ago by Fredrik Levander

(In [4630]) Refs #834. Some support for files generated by idconvert

comment:17 Changed 4 years ago by Fredrik Levander

(In [4631]) Refs #834. No given version of software supported

comment:18 Changed 4 years ago by Fredrik Levander

(In [4632]) Refs #834. Fix also for X!tandem if no given version for other software, leading to null as version.

comment:19 Changed 2 years ago by Fredrik Levander

In 4644:

Refs #834. X!tandem mzIdentML files from MGF searches have RTINSECONDS added to the spectrum ID. This results in ID mismatch, and this update cuts the spectrum ID before the RTINSECONDS if present.

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