OpenChrom is an

open source software Open-source software (OSS) is Software, computer software that is released under a Open-source license, license in which the copyright holder grants users the rights to use, study, change, and Software distribution, distribute the software an ...

for the analysis and visualization of mass spectrometric and chromatographic data. Its focus is to handle native data files from several mass spectrometry systems (e.g. GC/MS, LC/MS, Py-GC/MS,

HPLC-MS High-performance liquid chromatography (HPLC), formerly referred to as high-pressure liquid chromatography, is a technique in analytical chemistry used to separate, identify, and quantify specific components in mixtures. The mixtures can origina ...

), vendors like

Agilent Technologies Agilent Technologies, Inc. is an American global company headquartered in Santa Clara, California, that provides instruments, software, services, and consumables for laboratories. Agilent was established in 1999 as a spin-off from Hewlett-Packar ...

, Varian,

Shimadzu is a Japanese public KK company, manufacturing precision instruments, measuring instruments and medical equipment, based in Kyoto, Japan. It was established in 1875. The American arm of the company, Shimadzu Scientific Instruments, was founde ...

Thermo Fisher Thermo Fisher Scientific Inc. is an American life science and clinical research company. It is a global supplier of analytical instruments, clinical development solutions, specialty diagnostics, laboratory, pharmaceutical and biotechnology s ...

PerkinElmer PerkinElmer, Inc., previously styled Perkin-Elmer, is an American global corporation that was founded in 1937 and originally focused on precision optics. Over the years it went into and out of several different businesses via acquisitions and di ...

and others. But also data formats from other detector types are supported recently. OpenChrom supports only the analysis and representation of chromatographic and mass spectrometric data. It has no capabilities for data acquisition or control of vendor hardware. OpenChrom is built on the Eclipse Rich Client Platform (RCP), hence it is available for various operating systems, e.g.

Microsoft Windows Windows is a Product lining, product line of Proprietary software, proprietary graphical user interface, graphical operating systems developed and marketed by Microsoft. It is grouped into families and subfamilies that cater to particular sec ...

macOS macOS, previously OS X and originally Mac OS X, is a Unix, Unix-based operating system developed and marketed by Apple Inc., Apple since 2001. It is the current operating system for Apple's Mac (computer), Mac computers. With ...

and

Linux Linux ( ) is a family of open source Unix-like operating systems based on the Linux kernel, an kernel (operating system), operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically package manager, pac ...

. It is distributed under the

Eclipse Public License The Eclipse Public License (EPL) is a free and open source software license most notably used for the Eclipse IDE and other projects by the Eclipse Foundation. It replaces the Common Public License (CPL) and removes certain terms relating t ...

1.0 (EPL). Third-party libraries are separated into single bundles and are released under various OSI compatible licenses.

History

OpenChrom was developed by Philip Wenig as part of his PhD thesis at the

University of Hamburg The University of Hamburg (, also referred to as UHH) is a public university, public research university in Hamburg, Germany. It was founded on 28 March 1919 by combining the previous General Lecture System ('':de:Allgemeines Vorlesungswesen, ...

, Germany. The focus of the thesis was to apply pattern recognition techniques on datasets recorded by analytical pyrolysis coupled with chromatography and mass spectrometry (Py-GC/MS). OpenChrom won the Thomas Krenn Open Source Award 2010 as well as the Eclipse Community Award 2011. The developers are also founding members of the Eclipse Science Working Group. After successful commercialization of contract development and services around the OpenChrom project, vendor Lablicate reinforced the commitment to Free/Libre/Open-Source Software with the release of ChemClipse in October 2016, which serves as the base for all OpenChrom products.

Supported data formats

Each system vendor stores the recorded analysis data in its own

proprietary format A proprietary file format is a file format of a company, organization, or individual that contains data that is ordered and stored according to a particular encoding-scheme, such that the decoding and interpretation of this stored data is easily ac ...

. That makes it difficult to compare data sets from different systems and vendors. Furthermore, it's a big drawback for interlaboratory tests. The aim of OpenChrom is to support a wide range of different

mass spectrometry data format Mass spectrometry is a scientific technique for measuring the mass-to-charge ratio of ions. It is often coupled to chromatographic techniques such as gas- or liquid chromatography and has found widespread adoption in the fields of analytical chem ...

s natively. OpenChrom takes care that the

raw data Raw data, also known as primary data, are ''data'' (e.g., numbers, instrument readings, figures, etc.) collected from a source. In the context of examinations, the raw data might be described as a raw score (after test scores). If a scientist ...

files can't be modified according to the

good laboratory practice The Principles of Good Laboratory Practice (GLP) establish rules and criteria for a quality system that oversees the organizational processes and conditions in which non-clinical (non-pharmaceutical) health and environmental safety–or simply toxi ...

. To help scientists OpenChrom supports several

open formats An open file format is a file format for storing Data (computing), digital data, defined by an openly published specification usually maintained by a standards organization, and which can be used and implemented by anyone. An open file format ...

to import and export the analysis results. In addition, OpenChrom offers its own open source format (*.ocb) that makes it possible to save the edited chromatogram as well as the peaks and identification results.

Mass selective detector

* Agilent ChemStation *.D (DATA.MS and MSD1.MS) * AMDIS Library (*.msl) * Bruker Flex MALDI-MS (*.fid) * Chromtech (*.dat) * CSV (*.csv) * Finnigan (*.RAW) * Finnigan MAT95 (*.dat) * Finnigan ITDS (*.DAT) * Finnigan ITS40 (*.MS) * Finnigan Element II (*.dat) *

JCAMP-DX JCAMP-DX are text-based file formats created by JCAMP for storing spectroscopic data. It started as a file format for Infrared spectroscopy. It was later expanded to cover Nuclear magnetic resonance spectroscopy, mass spectrometry, electron ma ...

(*.JDX) *

Microsoft Excel Microsoft Excel is a spreadsheet editor developed by Microsoft for Microsoft Windows, Windows, macOS, Android (operating system), Android, iOS and iPadOS. It features calculation or computation capabilities, graphing tools, pivot tables, and a ...

(*.xlsx) * mzXML (*.mzXML) * mzData (*.mzData) *

NetCDF NetCDF (Network Common Data Form) is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. The project homepage is hosted by the Unidat ...

(*.CDF) * NIST Text (*.msp) * Open Chromatography Binary (*.ocb) * Peak Loadings (*.mpl) * PerkinElmer (*.raw) * Varian SMS (*.SMS) * Varian XMS (*.XMS) * VG MassLab (*.DAT_001;1) * Shimadzu (*.qgd) * Shimadzu (*.spc) * Waters (*.RAW) * ZIP (*.zip) * Agilent ICP-MS (*.icp) * Finnigan ICIS (*.dat) *

mzML Mass spectrometry is a scientific technique for measuring the mass-to-charge ratio of ions. It is often coupled to chromatographic techniques such as gas- or liquid chromatography and has found widespread adoption in the fields of analytical che ...

(*.mzML) * mzMLb (*.mzMLb) * mz5 (*.mz5) * mzDB (*.mzDB) *

SVG Scalable Vector Graphics (SVG) is an XML-based vector graphics format for defining two-dimensional graphics, having support for interactivity and animation. The SVG specification is an open standard developed by the World Wide Web Consortium sin ...

(*.svg) * MassHunter (*.D) * Finnigan ICIS (*.dat) * MassLynx (*.RAW) * Galactic Grams (*.cgm) * AnIML (*.animl) * GAML (*.gaml) * ...

Flame ionization detector A flame ionization detector (FID) is a scientific instrument that measures analytes in a gas stream. It is frequently used as a detector in gas chromatography. The measurement of ions per unit time makes this a mass sensitive instrument. Standa ...

* Agilent FID (*.D/*.ch) * FID Text (*.xy) * NetCDF (*.cdf) * PerkinElmer (*.raw) * Varian (*.run) * Finnigan FID (*.dat) * Finnigan FID (*.raw) * Shimadzu (*.gcd) * Arw (*.arw) * AnIML (*.animl) * GAML (*.gaml) * ...

Diode-array detection

* Agilent DAD (*.UV/*.ch) * ABSciex * Chromulan * Shimadzu (*.lcd) * Waters Empower * AnIML (*.animl)

Fourier-transform infrared spectroscopy Fourier transform infrared spectroscopy (FTIR) is a technique used to obtain an infrared spectrum of absorption or emission of a solid, liquid, or gas. An FTIR spectrometer simultaneously collects high-resolution spectral data over a wide spectr ...

* Thermo Galactics (*.spc) * Thermo Fisher Nicolet (*.spa) * GAML (*.gaml)

Near-infrared spectroscopy Near-infrared spectroscopy (NIRS) is a spectroscopic method that uses the near-infrared region of the electromagnetic spectrum (from 780 nm to 2500 nm). Typical applications include medical and physiological diagnostics and research inc ...

* Bruker OPUS (*.0)

Other formats

* Peak Loadings (*.mpl) *

NIST The National Institute of Standards and Technology (NIST) is an agency of the United States Department of Commerce whose mission is to promote American innovation and industrial competitiveness. NIST's activities are organized into physical s ...

-DB (*.msp) * AMDIS (*.msl) * AMDIS (*.cal) * AMDIS (*.ELU) * MassBank (*.txt) * SIRIUS (*.ms)

Major features

OpenChrom offers a variety of features to analyze chromatographic data: * Native handling of chromatographic data (MSD and FID) *

Batch processing Computerized batch processing is a method of running software programs called jobs in batches automatically. While users are required to submit the jobs, no other interaction by the user is required to process the batch. Batches may automatically ...

support * Baseline detector support * Peak detector, integrator support * Peak deconvolution * Peaks and mass spectrum identifier support * Quantitation support * Filter support (e.g. Mass Fragment and Scan Removal, noise reduction, Savitzky–Golay smoothing, CODA, backfolding) *

Retention time In chemical analysis, chromatography is a laboratory technique for the separation of a mixture into its components. The mixture is dissolved in a fluid solvent (gas or liquid) called the ''mobile phase'', which carries it through a system ( ...

shift support * Retention index support * Chromatogram overlay mode * Support for

principal component analysis Principal component analysis (PCA) is a linear dimensionality reduction technique with applications in exploratory data analysis, visualization and data preprocessing. The data is linearly transformed onto a new coordinate system such that th ...

(PCA) * Do/

undo Undo is an interaction technique which is implemented in many computer programs. It erases the last change done to the document, reverting it to an older state. In some more advanced programs, such as graphic processing, undo will negate the las ...

/redo support * Integration of

OpenOffice OpenOffice or open office may refer to: Computing Software * OpenOffice.org (OOo), a discontinued open-source office software suite, originally based on StarOffice * Apache OpenOffice (AOO), a derivative of OOo by the Apache Software Foundation, ...

LibreOffice LibreOffice () is a free and open-source office productivity software suite developed by The Document Foundation (TDF). It was created in 2010 as a fork of OpenOffice.org, itself a successor to StarOffice. The suite includes applications ...

and

Microsoft Office Microsoft Office, MS Office, or simply Office, is an office suite and family of client software, server software, and services developed by Microsoft. The first version of the Office suite, announced by Bill Gates on August 1, 1988, at CO ...

* Extensible by plug-ins * Chromatogram peak pattern analysis * Chromatogram and peak database support * Update support * Subtract mass spectra support

Releases

The software was first released in 2010. Each release is named after a famous scientist.

References

External links

* {{Chemistry software Bioinformatics software Mass spectrometry software Chemistry software for Linux Science software for macOS Science software for Windows Chromatography software Eclipse software