Peptide table format¶
Use cases¶
The Peptide table aims to cover detail on peptide level including peptide intensity. The most of content are from peptide part of mzTab.
Store peptide intensity to perform down-stream analysis and integration.
Enable easy visualization and scanning on peptide level.
Format¶
For large-scale datasets, a peptide section would be very large. Therefore, a Parquet format is adopted and its data section mainly consists of the following column:
sequence
: Peptide sequence ->string
protein_accessions
: A list protein’s accessions ->list[string] (e.g. [P02768, P02769])
unique
: Indicates whether the peptide is unique for this protein in respect to the searched database ->boolean (0/1)
best_id_score
: A key value pair of the best search engine score selected by the algorithm(e.g. "MS-GF:RawScore": 234.0)
->string
posterior_error_probability
: Posterior Error Probability scores ->double
modifications
: A list of modifications for a give peptide ->[modification1, modification2, ...]
. A modification should be recorded as string similarly to mztab like: -{position}({Probabilistic Score:0.9})|{position2}|..-{modification accession or name}
-> e.g
1(Probabilistic Score:0.9)|2|3-UNIMOD:35
charge
: Precursor charge ->int
exp_mass_to_charge
: The precursor’s experimental mass to charge (m/z) ->double
peptidoform
: Peptidoform of the peptidePEPTIDE[+80.0]FORM
->string
sample_accession
: A unique sample accession corresponding to the source name in the SDRF->string
abundance
: The peptide’s abundance in the given sample ->float
is_decoy
: Indicates whether the peptide sequence is decoy ->boolean (0/1)
Optional fields:
number_of_psms
: Number of PSMs for the peptide in the given samplesample_accession
->int
retention_time
: Retention time (seconds), it can be the median across all retention times in the Peptide quantification features ->float
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])
consensus_support
: Global consensus support scores for multiple search engines ->float
id_scores
: A list of identification scores, search engine, percolator etc. Each search engine score will be a key/value pair(e.g. "MS-GF:RawScore": 78.9)
->list[string]
reference_file_name
: The reference file name that contains the spectrum. ->string
scan_number
: The scan number of the spectrum. The scan number or index of the spectrum in the file ->string