Terms used in PeptideAtlas Builds

PeptideAtlas builds are available for download as a group of three different file formats, each containing some unique information not found in the other file formats.

FASTA format file

A file of sequences from the PeptideAtlas build where the first line is ">" followed by the PeptideAtlas accession and the second line is the peptide amino-acid sequence.

>PAp0000001
AAHEEICTTNEGVMYR

Biosequence set

The FASTA file that we map the peptide sequences to.

It includes the database (including decoys) we use to do the searches, and may includes the ensemble database if available.

CDS coordinates file

A file containing the peptide accession, and the position of the peptide relative to protein start (CDS coordinates).

PeptideAtlas accession	Sequence length	Protein accession	Length of sequence match	% Identity (=% match of sequence)	Start of sequence in protein CDS	End of sequence in protein CDS	Difference between sequence and matched sequence
PAp00000135	10	ENSP00000315757	10	100	40	49	0

CDS and chromosomal coordinates file

A file containing the peptide accession, the peptide's position within a protein relative to protein start (CDS coordinates), and it's chromosomal coordinates.

PeptideAtlas accession	Sequence length	Protein accession	Length of sequence match	% Identity (=% match of sequence)	Start of sequence in protein CDS	End of sequence in protein CDS	Difference between sequence and matched sequence	Protein description	Strand	Start of sequence in chromosome	End of sequence in chromosome	Transcript ID	Gene ID
PAp00000135	10	ENSP00000315757	10	100	40	49	0	chromosome:NCBI35:13:1:114142980:1	-1	45631043	45631072	ENST00000323076	ENSG00000136167

Database export XML

This file contains the contents of the various tables in the Peptide Atlas schema for a specified build, exported in an XML format.

This format is suitable for loading into a preexisting PeptideAtlas schema using the SBEAMS DataImport.pl script. This format can be loaded into mysql or MS SQL Server databases, and could possibly be used for others.

mysqldump export file

Peptide Atlas schema and data for a given build exported using mysqldump utility.

The data can be loaded into an empty mysql instance with the mysql command-line utility as follows:
mysql -u username -D database < PA_export.mysql
This greatly accelerates loading the data info a mysql instance relative to the xml format above, but would probably require some changes to work with a database other than mysql (SQL dialect issues)