Protein table format
====================

Use cases
---------

The Protein table is a
`Parquet <https://github.com/apache/parquet-format>`__ file that
contains the details of the proteins identified and quantified .

-  Store proteins identified and quantified from mzTab file, with the
   corresponding abundance and search engine scores.
-  Enable easy visualization and scanning on protein level.

Format
------

-  ``protein_accession``: A list protein’s accessions ->
   ``list[string] (e.g. [P02768, P02769])``
-  ``best_id_score``: The best search engine score for the given protein
   as a key value pair -> ``string``
-  ``abundance``: The protein’s abundance as measured in the given
   sample -> ``float``
-  ``sample_accession``: A unique sample accession corresponding to the
   source name in the SDRF-> ``string``
-  ``global_qvalue``: Global q-value from quantms -> ``double``
-  ``is_decoy``: Indicates whether the protein is decoy ->
   ``boolean (0/1)``

Optional fields:

-  ``gene_accessions``: A list of gene accessions ->
   ``list[string] (e.g. [ENSG00000139618, ENSG00000139618])``
-  ``gene_names``: A list of gene names ->
   ``list[string] (e.g. [APOA1, APOA1])``
-  ``number_of_peptides``: Number of peptides for the protein in the
   given sample ``sample_accession`` -> ``int``
-  ``number_of_psms``: Number of PSMs for the protein in the given
   sample ``sample_accession`` -> ``int``
-  ``number_of_unique_peptides``: Number of unique peptides for the
   protein in the given sample ``sample_accession`` -> ``int``