GutenTag

Tandem mass spectra can reveal the sequences of peptides. Generally, these spectra have been matched to peptide sequences through database search algorithms such as SEQUEST or Matrix Sciences' Mascot. An alternative method was proposed in 1994 by Matthias Mann (Mann, M.; Wilm, M. Anal. Chem. 1994, 66: 4390-4399). This technique, called "sequence tagging," infers a short region of sequence (the tag) directly from the spectrum. Then it searches a sequence database for sequences which match this sequence tag and the flanking masses. Several problems have prevented this technique from achieving wide use:

• Inferring sequence tags manually is slow and error-prone.
• Inferring sequence tags through software was less accurate than manual determination.
• Software to search sequence databases with tag sequences were not generally designed to process many tags at once.
• When multiple sequences in the database matched a sequence tag, no technique was proposed to discern which was the correct match.

GutenTag addresses all of these problems. It automates the process of sequence tag inference with a more accurate model of fragment ions than found elsewhere. It can retain multiple tags for each spectrum, ranking them by their scores. It can search a sequence database for all of these tags in a single pass. It can evaluate the candidate sequences returned from the database to determine which is the correct match for each spectrum. In short, GutenTag makes the sequence tagging approach usable on real-world data.

The program can now be licensed for use at your university, institute, or company. Academic and nonprofit use is free of charge. Commercial use is available for a license fee. To start the licensing process, fill out this form.

The manual for GutenTag is available here.