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
- The user can manually select peaks that are an amino acid mass
away from peaks already selected. The program assists this selection
by indicating the best potential peaks.
- The program can automatically generate proposals for
interpretation of longer stretches of the spectrum. These proposals
can then be used in the manual interpretation.
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
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:
- There may problems with focus and arrow keys under MS Windows.
- Currently one cannot save an edited spectrum window and continue
Authors and credits
KVL Aminosequencer was developed by Niels Jørgen Østergaard Kokholm
and Peter Sestoft (email@example.com).
Natascha Helena Beyer (firstname.lastname@example.org) provided background
in proteomics and comprehensive MS/MS data sets, and tested the
Gerhard Saalbach (email@example.com) provided
the initial inspiration for this work.
Peter Sestoft (firstname.lastname@example.org)