Achroma software tool was designed as an expandable software solution for new analytical approaches or a-typical experimental evaluations, e.g. negative product trace in enzymatic assays via Liquid Chromatography – Mass Spectrometry (LC-MS)(Krappmann, M. and T. Letzel (2012). "Achroma: a software strategy for analysing (a-)typical mass-spectrometric data." Analytical Methods 4: 1060-1071.)
Calculating negative signals was the initial problem of Thomas Letzel and his analytical working group and the lack of vendor software, which can’t calculate these signals. To close this gap Achroma has been developed with Students of the Faculty of Biotechnology and Bioinformatics since 2004. At the moment five modules and an additional file converter are available:
Showing chromatograms: Showing mass spectra:
Chromatogram Comparison Module:
This module compares the intensities of chosen chromatograms over the time and calculates a quotient chromatogram to show for example the stability of two internal standards of an experimental set up or the forming of inhibitor-enzyme complex (“Protein and Peptide Analysis by LC-MS: Experimental Strategies”, Chapter 11, ed. T. Leztel, Royal Society of Chemistry, Cambridge, UK, DOI: 10.1039/9781849733144-00142).
Signal Recognition Module:
In between this module the calculation of positive and negative signals and its areas are possible. Also, the calculations can be done in normal and in smoothing mode.
(a) Loading of experimental data into Achroma
(b) Settings for extracted ion chromatogram (EIC)
(c) Settings for the smoothing of the graph and showing signal areas
(d) Settings for the detection of positive or negative signals
(e) Manually manipulation of the automatically detected signals
(f) Settings for spectra comparison (the next module, see below)
Calculating and showing continous flow areas for experiments with no signal peaks, e.g. continuous flow enzymatic activity measurement by increasing of the reaction temperature.
Difference Spectrum Module:
The spectrum comparison module starts from the signal recognition module. This is a very special and new module, which compares the intensities of a spectrum from the top (positive signal) or the bottom (negative signal) of a peak with the intensities of an time point from the base line before the peak. The module calculates a difference spectrum and shows this in an own new view. The difference is built by subtracting the intensity at the maximum/minium of the peak from the intensity at the selected time point at the same m/z value.
Achroma works with ASCII-Text files. The files have a defined format – see example files. There are several possibilities to convert raw data into the right Achroma format:
- Waters Data Bridge (Software tool from Waters MassLynx software) – converting into Waters ASCII-file
- Converting from excel (csv-file) into Achrom text-file via achromaConverter software.
- Converting Thermo Scientific data files via file converter tool of Xcalibur software and achromaConverter software. First converting step: raw data-file in text file via file converter of Xcalibur software. Second converting step: Thermo Scientific text file via achromaConverter in the right text file form for analyzing data with Achroma software.
Future development of Achroma software modules:
Achroma was the first idea of modular development of analytical software, but since the implementation of the first module a lot of time elapsed and new software architectures are better suited for our idea of an open software platform. The functionality of Achroma will be transferred to openMASP and future developments will only be done for openMASP.
Thanks to the students of bioinformatics for implementing Achroma modules:
Wolfgang Hollweck, Oliver Schmidt, Andrea Heidenreich, Patrick Schulte-Middelich and Manuel Erhardt