PGATK File Formats

The ProteoGenomics Analysis ToolKit is based on standard proteomics formats developed by HUPO-PSI and Genomics Standard file formats. This section is to highlight in 10 minutes the most important features of those file formats, How they are used in PGATK and you can contribute to their development.

Note

It is important to notice that this Help page only provides the fundamentals of each file format used in PGATK, for more details we provide links to the original documentation of the File format.

BED Format

BED

BED *(Browser Extensible Data) format provides a flexible way to define the data lines that are displayed in an annotation track UCSC Bed Definition. BED lines have three required fields and nine additional optional fields. The number of fields per line must be consistent throughout any single set of data in an annotation track. The order of the optional fields is binding: lower-numbered fields must always be populated if higher-numbered fields are used.

Note

If your data set is BED-like, but it is very large (over 50MB) and you would like to keep it on your own server, you should use the bigBed data format.

The pedBed Fields and Properties supported by PGATK:

Field (bold are required)	Description	Example
chrom	The name of the chromosome	chr3
chromStart	The starting position of the feature in the chromosome or scaffold	1000
chromEnd	The ending position of the feature in the chromosome or scaffold	5000
name	Defines the label of the BED line. GPATK annotate peptide sequence	K(Phospho)SR
score	A score between 0 and 1000.	1000
strand	Defines the strand. Either “.” (=no strand) or “+” or “-“.
thickStart	The starting position at which the feature is drawn thickly.
thickEnd	The ending position at which the feature is drawn thickly	5000
itemRgb	An RGB value that will determine the display color of BED line color	(0,0,255)
blockCount	The number of blocks (exons) in the BED line.
blockSizes	A comma-separated list of the block sizes.
blockStarts	A comma-separated list of block starts.
proteinAccession	Protein accession number
transcriptAccession	Transcript Accession
peptideSequence	Peptide Sequence with no PTMs added
proteinUniqueness	Peptide uniqueness (See color code color)
transcriptUniqueness	Peptide uniqueness (See color code color)
genomeReferenceVersion	Genome reference version number
psmScore	Best PSM score
fdr	False-discovery rate
modifications	Coma separated list of Post-translational modifications
peptideRepeatCount	Peptide Counting
datasetAccession	Dataset Identifier
uri	Uniform Resource Identifier

Hint

If the field content is to be empty the space should be field with a “.”

Note

BED input files (and input received from stdin) are tab-delimited. The following types of BED files are supported by PGATK:

• BED4: A BED file where each feature is described by chrom, start, end, and name. (e.g. chr1 11873 14409 VLADIMIR)
• BED6: A BED file where each feature is described by chrom, start, end, name, score, and strand. (e.g. chr1 11873 14409 VLADIMIR 0 +)
• BED12: A BED file where each feature is described by all twelve columns listed above. (Default option in all tools)
• BED12+11: A complete Bed file including required fields and optionals.

Color

Uniqueness Colors:

Colour	Description
	Peptide is unique to single gene AND single transcript
	Peptide is unique to single gene BUT shared between multiple transcripts
	Peptide is shared between multiple genes

Modified Peptides Colors:

Like BED but containing the location of the post-translational modification on the genome. Thick parts of the peptide blocks indicate the position of the post-translational modification on a single amino acid (short thick block) while longer blocks indicate the occurrence of the first and last post-translational modification and residues in between. In the PTMBED the colour code is changed to indicate the type of modification.

Colour	Post-translational Modification
	Phosphorylation (phospho)
	Acetylation (acetyl)
	Amidation (amidated)
	Oxidation (oxidation)
	Oxidation (oxidation)
	Methylation (methyl)
	Ubiquitinylation (glygly; gg)
	Sulfation (sulfo)
	Palmitoylation (palmitoyl)
	Formylation (formyl)
	Deamidation (deamidated)
	Any other post-translational modification

Additional Files formats

Peptide Atlas Peptide List

PeptideAtlas released every month/year a list of peptides that has been found/identified by MS/MS (see the list here). The PGATK support the output list as input of some of the tools such as pepgenome .

Column	Field	Description
1	peptide_accession	Peptide Accession (PAp06389395)
2	peptide_sequence	Peptide Sequence
3	best_probability	Best Peptide Probability
4	n_observations	Spectral counting
		More properties not used

Hint

For our pipelines and tools the order of the column is important.

Note

A full pipeline to map the PeptideAltas peptide evidences to Genome Coordinates can be found here.