Configure FASTA database in PEAKS

Configuring FASTA databases in PEAKS is fairly easy especially if the FASTA file has the same header format as one of the public databases (e.g. NR, Swiss-Prot, IPI). It is just a matter of selecting the pre-defined format and the parsing rules will be automatically filled in.

There are also a large number of users use PEAKS to search on their in-house, customized FASTA databases. In this situation, the header format is very hard to predict and it varies case by case.

In PEAKS, the parsing rule is defined using regular expression. While regular expression is very powerful, it will take people quite a bit of time to master it. Since we got tons of searches to run every week, against FASTA files with so many different header formats, I created this lazy, generic parsing rule for internal use and in most cases, it worked good enough.

Accession. The regular expression tries to use everything before the first white space as the accession. If no white space were found within the first 30 characters, the first 30 characters will be used as accession.

>\([^\s|]{1,30}\)

Description. The whole line after ">" will be used as the description.

>\(.*\)

Use new / non-standard amino acids in PEAKS

Some researchers are looking for unknown amino acids in their proteomic studies. This requires the software to be able to take new theoretical AA into account. Although, PEAKS internally only use the 20 common amino acids residues, here is a trick we can use to add new AAs.

The general concept is to add this new amino acid X as a PTM of an existing amino acid Y. The existing amino acid Y should be picked so that the mass difference between X and Y is distinguishable from the mass of all PTMs in the search. In the analysis, on top of the normal PTMs you may set, set this special PTM as a variable modification. In the result, this new amino acid X will appear as a variable modification of Y.

Here is an example. Let's add the amino acid Pyrrolysine to PEAKS. Open the PTM configuration by click the menu "Window"-->"Configuration", then select the PTM tab. Click the "New" button on the lower right corner of the dialog. I am going to configure it as a modification of Alanine. The mass difference is 184.1212Da.
Click "OK" to complete the configuration. When performing a PEAKS search, the new PTM, Pyrrolysine, can then be selected in the "Customized" tab of the "PTM Options" dialog.
Use the same trick, we can substitute or remove an amino acid by setting it as a fixed modification in the search.