Compare which features are included in the Community and Enterprise Edition. To get the full functionality for the Community Edition a number of plug-ins need to be fetched and installed from the Marketplace after Installation of OpenChrom®.
Several vendor-specific MS data formats can be imported natively into OpenChrom®
including Agilent (*.D), Bruker Flex MSD, Chromtech, Finnigan ITS40, Finnigan ITDS, Finnigan MAT, Finnigan RAW, Perkin-Elmer MSD, Shimadzu QGD, Waters MSD, Varian SMS, Varian XMS and VG. Further vendor formats currently supported are Agilent FID and Shimadzu SPC (Database). Note, that FID files can only be visualized and converted to an open xy-format, but not be edited in the current release. This will be available in our next release. Further vendor formats, including other detector types (e.g. UV, DAD), are on our agenda for the next release. If you run into problems with any converter or you are interested to get a vendor format included, feel free to contact us
Several open MS data formats can be imported into OpenChrom®
. Next to the open OpenChrom®
data formats *.chrom and *.ocb these include NetCDF, mzXML (v2.1), JCAMP-DX and CSV. Note, that the CSV-files need to have a particular format, which is described in the Wiki and documentation. Furthermore, xy-data (column 1: RT, column 2: Intensity) can be imported. The files have to be renamed to *.xy files. Note, that XY file types can currently only be visualized. Editing (peak detection etc.). will be available in our next release. If you run into problems with any converter or you are interested to get another format included, feel free to contact us
MS data can be exported in several open data formats. Next to the open OpenChrom®
formats *.chrom and *.ocb these include NetCDF, Microsoft Excel (*.xlsx) and CSV. Note, that data saved as *.ocb files also include all processing details (peak detection, identifications, etc.). Furthermore, detected peaks can be exported in the peak library formats of NIST MS Search (*.msp) and AMDIS (*.msl). For the export of snapshots of a TIC chromatograms a pdf-converter is available. If you run into problems with any converter or you are interested to get another format included, feel free to contact us
Various filters allow you to process your chromatographic and mass spectrometric data including Ion Remover, Savitzky-Golay Smoothing, CODA Filter, Backfolding Filter, Retention Time Shifter, Denoising Filter, Substract MS Filter and Scan Removal Filter
The only classifier currently included is the WNC classifier (Water, Nitrogen, Carbon Dioxide), which sums up the intensities of selected ions over a selected RT range (determined by the RT window displayed in the Chromatogram view). The default ions analyzed are 18, 28 and 44 (nominal m/z of water, nitrogen and carbon dioxide), but other ions may be selected instead.
Currently two background detection algorithms are implemented which are only applied on the TIC signal. The SNIP Baseline Detector usually works better than the Smoothed Background Detector. The detected background can be quantified when peak integration is performed. Note, that the detected background can not be subtracted from the chromatographic signal, yet. This is scheduled for the upcoming release.
The implemented automated peak detection is a simple detector based on the first derivative. Overlapping peaks are not recognized well. A remedy is the implemented Manual Peak Detector. Improved peak detection including deconvolution is planned for an upcoming release. Note, that peak detection and integration are separate procedures in OpenChrom® to allow higher flexibility. Hence, peak integration has to be performed as a separate step.
Currently three different kinds of integration are implemented. If peaks were detected with the preceding peak detection step, the „Integrator #1“ determines the peak areas according to the trapezoid rule. The „PeakMax integrator“ does not determine any area but takes the intensity at the peak maximum as an estimate of peak abundance. This measure may be helpful, when heavily overlapping peaks are assumed to have gaussian shape and the the individual maxima can be determined. Note, that if the actual peak area of gaussian peaks was to be estimated with the peak maximum the full width at half maximum height (FWHM) would have to be determined as well.
The „Sum Area Chromatogram Integrator“ sums up all m/z channels according to the retention time window selected in the Chromatogram Explorer (main chromatogram view). If a background detection has been applied previously in the workflow, the summed area is divided into the chromatogram and background area. Note, that also the summed intensities of each m/z channel is reported. This integrator may be particularly useful for direct insertion probe - mass spectrometry (DIP-MS), pyrolysis – mass spectrometry (Py-MS) or evolved gas analysis (EGA).
If NIST libraries are available to the user, these can be used for identification of detected peaks via the NIST Database connector. Peaks can be identified one by one or batchwise. To set up the NIST Database Connector appropriately please query the Wiki
or ask us
The plug-in PeakIdent®
allows setting up and query user-specific databases/libraries to facilitate identification and comparison of components/peaks. Note, that the libraries can also be made accessible for all users within a network.
With the aid of the plug-in user-relevant databases/libraries for mass spectra can be established and e.g. utilized, analogous to the NIST or Wiley libraries, to identify peaks in a sample. If you want to learn more about the plug-in, feel free to contact us
The plug-in MultiScanIdent®
allows setting up and query user-specific databases/libraries to facilitate identification and comparison of complex samples. These databases can also be made accessible for all users within a network.
With the aid of the plug-in databases for complete mass spectrometric fingerprints can be established and e.g. utilized to elucidate the composition of unknown complex mixtures or the similarities between samples. Note, that in contrast to the plug-in ChromIdent®
the mass spectral information of individual peaks in a chromatogram are summarized. The plug-in MultiScanIdent®
may be particularly useful to categorize samples measured with direct insertion probe - mass spectrometry (DIP-MS) or pyrolysis – mass spectrometry (Py-MS). If you want to learn more about the plug-in, feel free to contact us
The plug-in ChromIdent®
allows setting up and query user-specific databases/libraries to facilitate identification and comparison of complex samples. Note, that the databases can also be made accessible for all users within a network.
With the aid of the plug-in databases for complete chromatographic fingerprints can be established and e.g. utilized to elucidate the composition of unknown complex mixtures or the similarities between samples. This may be of interest to analysts of the fragrant, flavor or polymer industry and could aid quality control. It is particularly useful for measurements conducted with thermodesorption – gas chromatography/mass spectrometry (TD-GC/MS) or pyrolysis – gas chromatography/mass spectrometry (Py-GC/MS). If you want to learn more about the plug-in, feel free to contact us
If you decide to acquire an OpenChrom®
Enterprise Edition you can opt between single and multiple license support subscriptions. Rapid support will be guaranteed. learn more
With the implemented quantitation support it is possible to use a set of selected peaks to set up calibrations. These can be saved and subsequently used to quantify the selected components in your target samples. Soon you will find more details about Quantitation in the Wiki
enables you to perform your data processing and reporting batchwise on numerous data files. Once you have edited a chromatogram to your liking you can automate the editing process which will save you a lot of time. This also includes the identification of detected peaks via a NIST database or via one of our available database plug-ins PeakIdent®
. Find more details in the Wiki
You can generate a default text report containing quantitative details on all detected and integrated peaks. Furthermore, identification and quantitation results are reported. If you need custom-made reports feel free to contact us
. Soon you will find more details about Reporting in the Wiki
While editing your chromatograms it may be handy for your work-flow to copy data tables into excel sheets or write reports including e.g. snapshots. The Office Integration Editor enables to open and use Microsoft Word and Excel or any of the Open Office modules within the OpenChrom®
workbench. Find more details about how to install and set up the Office Integration Editor in the Wiki