This tool is licensed under GPL v3 and completely free of charge! You don’t need to register anything or pay any money. All you need is the Java Runtime Environment form Sun (it is also free).

The code is hosted at SourceForge, so the latest sources can be found there: iso2l development.

If you just want to use the tool download the latest binaries: iso2l binaries.

Known Bugs

All known bugs are listed here and/or tracked by MantisBT. If you find further issues feel free to contact me or write a report to the bug tracking system.

Version 3

Version May 2011 by Martin Scharm

  • MassSpec mode, graphics as expected by MS instruments
  • anti aliasing
  • zooming
  • Table of isotopes is sortable
  • graphic issues
  • Bugs of previous versions are closed
  • lots of further small changes
  • The listed mass at the cross hairs are incorrect, fixed with version 3.0.1
Download: Java: iso2l-3.0.1.jar (executable JAR-binary) Java: iso2l.jar (executable JAR-binary) Java: Git@SourceForge (Java source code) (Please take a look at the man-page. Browse bugs and feature requests.)

Version 2

Version Jan 2011 by Martin Scharm (completely revisited)

  • Complete translation to English
  • Deleted various bugs, that killed the results
  • Higher accuracy in mass and abundance
  • Added amino acid feature, calculate isotopes of amino acid sequences
  • Smart visibility improvements (rendering stuff)
  • Some more functions, not mentioned here
  • When peaks are combined, e.g. in case of rounding the masses, the masses are summed..
  • Doesn't discard H2O in peptide bonds
Download: Java: iso2l-v2.jar (executable JAR-binary) Java: iso2l-v2.bin (Java binaries) Java: iso2l-v2.src (Java source code) (Please take a look at the man-page. Browse bugs and feature requests.)

Version 1

Version 2007 by Martin Scharm, Christoph Ruttkies and Steffi Dornfeldt.

Download binaries as .tgz or .zip archive. Source code is also available as .tgz or .zip archive.

We additionally authored a documentation in German, of course you can download it too.


This tool is known to fail for bigger molecules, read this to understand the reasons. I strongly recommend to use a newer version.

Download: Java: iso2l.binaries.tgz, binaries) Java: iso2l.src.tgz, source code) PDF: iso2l.pdf (German documentation) (Please take a look at the man-page. Browse bugs and feature requests.)

Martin Scharm

stuff. just for the records.

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