computer science

OpenChrom

OpenChrom is a computer science topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand OpenChrom rather than just read about it. In short: OpenChrom is an open source software 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.

Key takeaways

OpenChrom belongs to computer science; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect OpenChrom to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of OpenChrom from memory before moving on to harder problems.

Reference excerpt

OpenChrom is an open source software 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), vendors like Agilent Technologies, Varian, Shimadzu, Thermo Fisher, PerkinElmer 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, macOS and Linux. It is distributed under the Eclipse Public License 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, 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. 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 formats natively. OpenChrom takes care that the raw data files can't be modified according to the good laboratory practice. To help scientists OpenChrom supports several open formats 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 (*.JDX) Microsoft Excel (*.xlsx) mzXML (*.mzXML) mzData (*.mzData) NetCDF (*.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 (*.mzML) mzMLb (*.mzMLb) mz5 (*.mz5) mzDB (*.mzDB) SVG (*.svg) MassHunter (*.D) Finnigan ICIS (*.dat) MassLynx (*.RAW) Galactic Grams (*.cgm) AnIML (*.animl) GAML (*.gaml) ...

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

Near-infrared spectroscopy Bruker OPUS (*.0)

Other formats Peak Loadings (*.mpl) NIST-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 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 shift support Retention index support Chromatogram overlay mode Support for principal component analysis (PCA) Do/undo/redo support Integration of OpenOffice/LibreOffice and Microsoft Office 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 renowned scientist. Within each major version weekly new releases are published.

References

External links Official website

Illustrations

Worked examples

Example 1 — a first encounter with OpenChrom

Start with the simplest possible case. Write down what OpenChrom claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In computer science, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to OpenChrom before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about OpenChrom ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of OpenChrom

In research: OpenChrom appears in computer science research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses OpenChrom in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: OpenChrom is common in secondary-school and first-year university syllabi. It links to neighbouring topics Bioinformatics software, Chemistry software for Linux, Chromatography software, so understanding it makes those chapters shorter.
In everyday life: Look for OpenChrom outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study OpenChrom in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what OpenChrom means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain OpenChrom out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is OpenChrom in simple terms?

Why does OpenChrom matter?

Because it connects several computer science ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study OpenChrom?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on OpenChrom.