Brief descriptions are given for each downloadable file, each of which may be downloaded by clicking on its link. We suggest that you save download files to your disk into separate folder and then follow instructions to install. If it is a compressed file (with extension .zip) you need to first uncompress it into separate folder. Some antivirus and/or firewall software might interfere with normal installation process. It is standard practice to disable such software before installation. Don't forget to turn it back on!
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Updates to v.2.0f can be downloaded here. These are software-only updates. The NIST/EPA/NIH Mass Spectral Library is NOT included in any of these downloads. Update to v.2.2 is not available at present time.
OpenMS offers an open-source C++ library (+ Python bindings) for LC/MS data management, analysis and visualization. It empowers rapid development of mass spectrometry related software. OpenMS is freely available under the three clause BSD license and runs under Windows, macOS and Linux. The OpenMS members have a strong commitment to creating an open, inclusive, and positive community. Please read the OpenMS Code of Conduct for guidance on how to interact with others in a way that makes the community thrive.
OpenChrom is a software application to edit and analyze mass spectrometric chromatographic data. It is extensible in many different ways, depending on the demands of the users or the analytical procedures and algorithms. It offers a customizable graphical user interface. The software is independent of the operating system, due to the fact that the Rich Client Platform is written in Java. OpenChrom is released under the Eclipse Public License 1.0 (EPL). There are no license constraints regarding extensions. They can be published using open source as well as proprietary licenses. OpenChrom is available free of charge at
Software has become an integral part of analysis techniques. Especially in the area of gas chromatography/mass spectrometry, automatic samplers enable high throughput analyses. Software assists handling large amounts of data generated by automated and fast operating analytical instruments. Modern computer systems are inexpensive, powerful and allow analysis techniques that could not have been applied in the past. Deconvolution, a chromatographic quality enhancing technique, demonstrates for instance that increasing processor power makes new analysis techniques applicable. The technique of deconvolution has been described by Biller and Biemann [1, 2], Dromey et al. [3], Colby [4], Hindmarch et al. [5], Halket et al. [6], Kong et al. [7], Taylor et al. [8], Pool et al. [9, 10] and Davies [11] in various ways. Stein [12] published an enhanced deconvolution algorithm that has been implemented in the software AMDIS (Automated Mass Spectral Deconvolution and Identification System) [13]. AMDIS is available free of charge from the National Institute of Standards and Technology (NIST). Windig et al. [14, 15] described another approach to enhance chromatographic quality by a deconvolution method called CODA (Component Detection Algorithm). The commercially available software ACD/MS Manager [16] offers an implementation of this approach.
Increasing computational power enables new applications, but there is still a lack of interoperability. Instrument vendors, such as Agilent Technologies, Shimadzu, Thermo Fisher Scientific and Waters Corporation have created their own software and data format. Usually, the mass spectral data formats are binary and can only be accessed by the instrument vendors' proprietary software. Some commercial tools exist to convert the mass spectral data files into other formats, such as MASS Transit from PALISADE Corporation [17]. To avoid these limitations, some efforts have been made to design and implement interoperable data formats and software libraries as for example NetCDF [18] or mzXML [19, 20]. But even if it is possible to convert the data files to other formats, there are drawbacks in data processing as each software implements specific functions, has its own graphical user interface and is in most cases commercially available only, as for example the applicable software of ChemStation, Xcalibur or MassLynx. Hence, the users are forced to become familiar with different software systems, user interfaces and methods. Moreover, the software tools primarily target only specific operating systems, such as Microsoft Windows and Mac OSX. The number of software applications that are independent of the operating system and can also be run under Unix or Linux is limited. Linux systems are open source, available at no cost and their usage increases in scientific research (see Scientific Linux [21]), as well as in the public sector [22, 23]. Software applications, such as AMDIS, have been published to be used free of charge, but their source code is not disposable. Thus, it is not possible to evaluate the algorithms implemented in the software. Especially in the case of scientific research, it is not possible to figure them out and to extend them. Even if algorithms are described in published papers [2, 4, 9, 12, 24], it is often impossible to validate them manually due to the complexity of chromatographic data. Other applications like ChemStation, Xcalibur, ACD/MS Manager are proprietary and closed source. They are only commercially available. There is no means of revealing the correctness of their utilized algorithms. Efforts have been made to solve the problems of missing interoperability and restricted access to source codes and algorithms [25]. Bioclipse is a sophisticated project that is open source and is focused with its algorithms on metabolism analysis and gene sequencing. Its techniques are state-of-the-art. Some other projects are mMass [26], COMSPARI [27] and fityk [28], but they do have some restrictions regarding their interoperability and extensibility. BioSunMS [29] is a tool to read TOF (Time of Flight) mass spectral data files, but it is not able to read instrument vendors' native data files. The Chemistry Development Kit (CDK) [30] implements convenient features to edit chemical data and structures, but it has no appropriate user interface. The open source tool OpenMS [31] aims to edit mass spectrometric data, but it is not completely platform independent, as it is written in C++ programming language.
Increasing computational power enables new applications, but there is still a lack of interoperability. Instrument vendors, such as Agilent Technologies, Shimadzu, Thermo Fisher Scientific and Waters Corporation have created their own software and data format. Usually, the mass spectral data formats are binary and can only be accessed by the instrument vendors' proprietary software. Some commercial tools exist to convert the mass spectral data files into other formats, such as MASS Transit from PALISADE Corporation [17]. To avoid these limitations, some efforts have been made to design and implement interoperable data formats and software libraries as for example NetCDF [18] or mzXML [19,20]. But even if it is possible to convert the data files to other formats, there are drawbacks in data processing as each software implements specific functions, has its own graphical user interface and is in most cases commercially available only, as for example the applicable software of ChemStation, Xcalibur or MassLynx. Hence, the users are forced to become familiar with different software systems, user interfaces and methods. Moreover, the software tools primarily target only specific operating systems, such as Microsoft Windows and Mac OSX. The number of software applications that are independent of the operating system and can also be run under Unix or Linux is limited. Linux systems are open source, available at no cost and their usage increases in scientific research (see Scientific Linux [21]), as well as in the public sector [22,23]. Software applications, such as AMDIS, have been published to be used free of charge, but their source code is not disposable. Thus, it is not possible to evaluate the algorithms implemented in the software. Especially in the case of scientific research, it is not possible to figure them out and to extend them. Even if algorithms are described in published papers [2,4,9,12,24], it is often impossible to validate them manually due to the complexity of chromatographic data. Other applications like ChemStation, Xcalibur, ACD/MS Manager are proprietary and closed source. They are only commercially available. There is no means of revealing the correctness of their utilized algorithms. Efforts have been made to solve the problems of missing interoperability and restricted access to source codes and algorithms [25]. Bioclipse is a sophisticated project that is open source and is focused with its algorithms on metabolism analysis and gene sequencing. Its techniques are state-of-the-art. Some other projects are mMass [26], COMSPARI [27] and fityk [28], but they do have some restrictions regarding their interoperability and extensibility. BioSunMS [29] is a tool to read TOF (Time of Flight) mass spectral data files, but it is not able to read instrument vendors' native data files. The Chemistry Development Kit (CDK) [30] implements convenient features to edit chemical data and structures, but it has no appropriate user interface. The open source tool OpenMS [31] aims to edit mass spectrometric data, but it is not completely platform independent, as it is written in C++ programming language.
This software is free under the terms of the GNU General Public License (GPL). Please cite the above reference in any resulting publications. Read the FAQ and help screens within the software before contacting the Author with questions or before reporting bugs.
Problems with opening and working with QLD files are most probably having to do with no proper software compatible with QLD files being present on your machine. To address this issue, go to the MassLynx developer website, download the tool, and install it. It is that easy On the top of the page a list that contains all programs grouped based on operating systems supported can be found. One of the most risk-free method of downloading software is using links provided by official distributors. Visit MassLynx website and download the installer.
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