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.

Description

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:

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.

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

Compiled class files (zipped jar file) (updated 2002-02-22)
Unix: unpack with unzip aminoseq-jar.zip
MS Windows: unpack with Info-Zip or Winzip.
Run with java -jar aminoseq.jar
You will need a Java runtime version 1.4, see http://java.sun.com/j2se/1.4/.
Source files (zipped jar file).
Developed with Sun's j2sdk version 1.4.
An example spectrum file taken from the Lutefisk Web site.
User manual
Documentation (forthcoming).

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:

There may problems with focus and arrow keys under MS Windows.
Currently one cannot save an edited spectrum window and continue editing later.

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