MZTab protein group reader

[lucas-diedrich]

MZTab aggregates information on

1. Experimental metadata
2. Proteins
3. Peptides
4. PSMs
5. Small molecules

in one file format. Protein information is reported in a block that starts with PRT. Protein intensities (protein_abundance_<...>) might not be reported

Example

MTD	mzTab-version	1.0 rc5
MTD	mzTab-mode	Summary
MTD	sample[1]-description	Biological replicate 1, P30
MTD	sample[1]-custom[1]	[GO, GO:0044456, synapse part, subsample1]
MTD	sample[1]-custom[2]	[EFO, EFO:0000916, visual cortex, subsample1]
MTD	assay[1]-sample_ref	sample[1]
MTD	assay[1]-ms_run_ref	ms_run[1]
...
PRH	accession	description	taxid	species	database	database_version	search_engine	best_search_engine_score[1]	search_engine_score[1]_ms_run[1]	num_psms_ms_run[1]	num_peptides_distinct_ms_run[1]	num_peptides_unique_ms_run[1]	ambiguity_members	modifications	protein_coverage	protein_abundance_assay[1]	protein_abundance_assay[2]	protein_abundance_assay[3]	protein_abundance_assay[4]
PRT	223462890	Spna2 protein [Mus musculus]	10090	Mus musculus (Mouse)	NCBInr_2010_10	nr_101020.fasta	[MS, MS:1001207, Mascot, ]	6539.67	6539.67	157	92	null	null	null	0	1	0.853	0.864	0.791
...

Implementation

Custom import_files logic due to specific file format.

Limitations

I currently do not try to extract the sample metadata from this file