DeNovoID Help Page


The indexed peptide databases available are listed on a pull down menu. They are named by organism, source and release number or date. Currently, all of the databases assume trypsin cleavage with no missed cleavages and peptide sizes from 800 to 3000 Da. An optional checkbox allows for the inclusion of detailed information about the database and its construction in the output file.

Input Data Format

The data is entered in a modified FASTA format. Each query begins with a header line which is followed by one or more sequence lines. The header line begins with the '>' symbol and is followed by text describing the query. The sequence lines consist of a combination of three types of data. Ordered sequence tags (runs of amino acids for which the order is known) are designated by single letter amino acid codes that are not enclosed in square brackets. DeNovoID will examine the database peptides with the closest matching amino acid compositions and highlight the presence of these ordered sequence tags. Disordered sequence tags (runs of amino acids for which the order is unknown) are designated by single letter amino acid codes that are enclosed in square brackets. Mass tags (masses that cannot be confidently assigned to a single peptide composition) are indicated by a numeric value in Da enclosed in square brackets. The mass value is used to generate all the possible amino acid compositions consistent with the given mass. The mass tolerance is entered below.

Email address

Results are returned by email. Enter the address to be used for returning results.

File Upload

Queries can be entered in the text box or uploaded as a text file. The format of the file is the same as for the text box. Multiple queries can be as a batch with a new header line separating each query.

Mass Tolerance

The value for the mass tolerance sets the limit of the match between the given mass and the average mass of the amino acid residues that are considered a match. The default mass tolerance (1 Da) is used unless the value is changed.

Cutoff Value

The cutoff value is the maximum Euclidean distance between the query peptide composition and the database match to be shown. A value of zero will show only exact matches. A value of 1 will show exact matches and peptides that differ slightly in composition (about 1 amino acid for each 10 residues). A value of 2 will often show related peptides as well as unrelated peptides. When used in conjunction with the sequence tag match, a higher value can find partial matches.

Sequence Tag Matches

The user can require that all, some , or none of the ordered sequence tags be present for a match to be shown.