User Manual for KVL Aminosequencer

KVL Aminosequencer supports manual de novo sequencing of proteins by interpretation of tandem mass spectrometry data (MS/MS).

This page provides preliminary documentation of the user interface. Especially the description of the automatic sequence proposal mechanisms is incomplete.

Starting the program

First you must download and unpack the program. Your computer must have a Java runtime version 1.3 installed, see

Then start the program by executing, at the Unix or MS Windows command prompt:

   java -jar aminoseq.jar

Opening a spectrum file

Select File | Open to open and read a spectrum file. The spectrum file must be in Sequest DTA or Mascot format.

The user interface

Here is a screen dump of the user interface. The user interface has the following parts:

The spectrum window

The spectrum window shows the current spectrum with mass (in amu) on the x-axis and relative abundance on the y-axis.

An amino acid sequence can be found manually by marking peaks in the spectrum. At any point during this process, the spectrum will be decorated with zero or more subsequences, each consisting of:

with green marks on either side of the red mark, and blue marks only on the left and right fringes. The accepted (green) amino acids of two subsequences may meet but cannot overlap. The potential (blue) amino acids belonging to one subsequence may overlap with potential (blue) amino acids of another sequence. If one peak is decorated with potential amino acids from two different sequences, then clicking on it will accept both, and make the sequences meet in that peak.

Building a sequence

Keystroke commands

Key Effect
z Zoom in around the cursor
o Zoom out around the cursor
c Recenter around the cursor
r Reset to full view of the spectrum
arrows Step left or right
m Show masses of 10 more peaks; may be repeated
n Hide masses of 10 more peaks; may be repeated

Menu commands

File Open file ctrl-OOpen file and read a new spectrum
Save log ctrl-SSave log to file
Print ctrl-PPrint the spectrum window
Quit ctrl-QQuit the program
Edit Undo ctrl-ZUndo change to sequence
Redo ctrl-YRedo change to sequence
Add mirrored spectrum ctrl-M?
Settings Show errors ctrl-EShow spectrum backwards also
Show sequence backwards ctrl-BShow amino acid sequence backwards
Show local levels ctrl-LShow average local abundance (peak height)
Use log scale ctrl-WUse log scale for abundance (peak height)
Show backwards spectrum ctrl-RShow spectrum backwards also
Show reinterpreted spectrum Shift spectrum by an amino acid modification
Allow K and R ctrl-AAllow K and R amino acids inside sequence
Decrease tolerance ctrl-DDecrease macth tolerance for potential amino acids
Increase tolerance ctrl-IIncrease match tolerance for potential amino acids
Sequencing parameters Set parameters for automatic proposals
Help Help ctrl-F1Show brief help (outdated)
About Show brief program information
Amino acids Show monoisotopic amino acid masses
Ion types Show composition of amino acid modifications
About Show information about the current spectrum

Automatic sequence proposals

(This section yet to be written).

The program can generate sequence proposals automatically. If you press the Compute button in the Computed proposals field, purple marks will appear on a sequence of peaks that correspond well to a series of peptide fragments. Repeatedly pressing the Compute button will cycle through some proposals. Right-clicking on a purple-marked peak, you can select Follow proposal right to obtain a sequence corresponding to all the purple peaks to the right. This is the same as left-clicking on the all those peaks, from left to right.

Other information

The program uses the monoisotopic masses, found here and here; some differ by 0.00001 Dalton from those of AminoCalc from Protana.

Authors and credits

KVL Aminosequencer was developed by Niels Jørgen Østergaard Kokholm ( and Peter Sestoft ( Natascha Helena Beyer ( provided background in proteomics and comprehensive MS/MS data sets, and tested the program. Gerhard Saalbach ( provided the initial inspiration for this work.

Peter Sestoft ( 2002-01-04, 2002-01-15