KVL Aminosequencer

KVL Aminosequencer is a program for de novo protein sequencing. It permits graphical interactive interpretation of spectra obtained from fragmentation of tryptic peptides by tandem mass spectrometry (MS/MS). Ease of use and machine assistance were important design goals.


KVL Aminosequencer permits manual interactive de novo protein sequencing, via an easy-to-use graphical user interface.

The program reads a spectrum from a text file and displays it graphically. The program combines manual and automatic interpretation of the spectrum:

This way, fragmented tryptic peptides analysed by MS/MS can be interpreted interactively. The interpretation is illustrated graphically.

Several starting points are allowed when interpreting the spectrum. Thus, sections of the peptide can be interpreted while ambiguous parts of the spectrum are ignored. This procedure generates several short amino acid stretches per spectrum. Consequently, several database searches can easily be made of incompletely fragmented peptides. This may increase the identification percentages.

The program has been tested mainly with spectra obtained from electrospray ionization (ESI).

Downloading and unpacking

To do

This is the initial release of the program, and feedback on usability and desirable improvements is most welcome.

Here are some known problems and issues:

Authors and credits

KVL Aminosequencer was developed by Niels Jørgen Østergaard Kokholm (kokholm@dina.kvl.dk) and Peter Sestoft (sestoft@dina.kvl.dk).

Natascha Helena Beyer (nhbeyer@mail.dk) provided background in proteomics and comprehensive MS/MS data sets, and tested the program.

Gerhard Saalbach (g.saalbach@risoe.dk) provided the initial inspiration for this work.

Peter Sestoft (sestoft@dina.kvl.dk) 2002-01-04, 2002-02-22