Is there any freeware alternative to Agilent Chemstation or Masshunter that can handle Agilent files? As the community edition is available as free software, I suggest you just give it a try.
Related: Masshunter Software Latest Versions - Adp Pc Payroll Software Versions - C Sharp Software Versions - Fas Inventory Software Versions - Fast Download Software Versions
- License: Shareware
Nowadays software update is quite a usual thing: new patches are released, software errors are fixed, vulnerabilities are removed and new functions are added. It is not possible to follow all the updates manually. Carambis Software Updater Pro will scan your system automatically and find downloadable softwareversions and updates after any potential threats of viruses, Trojans, vulnerabilities and data loss are excluded. Carambis Software Updater Pro advantages: 1. All computer software (portable software included) is regularly checked for updates as scheduled.
- Platform: Windows
- Publisher:Carambis
- Date: 12-05-2011
- Size: 17525 KB
- License: Freeware
Keep track of the difference between Softwareversions on your PC and the Internet.
With just one click on the 'Web Update' button this program will check all the programs in its list to see if there are newer versions on the internet..
Mass Hunter software, free download Windows 7
- Platform: WinOther
- Publisher:littlegems
- Date:
- Size: 215 KB
- License: Freeware
Free PC Inventory is a freeware information tool that grabs details of everything about your computer, from the hardware components through to the installed softwareversions. It even offers up a list of processes that are running. It's the kind of tool that could be invaluable if you're trying to hunt down a driver or errant component replacement. Definitely one for the toolbox. Free PC Inventory does not require installation and can be used as a portable application. It can be run from a removable storage device such as a CD-ROM drive, USB flash drive, flash card, or floppy disk.
Mass Hunter software, free download For Windows 7
- Platform: Windows
- Publisher:Network Mosaic
- Date: 07-12-2009
- Size: 1012 KB
- License: Freeware
www.FileREX.COM is one of the best sites from where you can download high-quality software. We launched FileREX Update Checker , which is a small utility that scans your computer registry for installed software and display a list of updates. Only takes secons to help you get the most up-to-date, more steady and functional software.
Main Features:
1) Automatically search for installed softwares.
2) Automatically display download links to newest softwareversions.
3) Check for updates periodically.
- Platform: Windows
- Publisher:BitCoder
- Date: 04-08-2011
- Size: 666 KB
- License: Shareware
In the event of a computer crash, you lose hundreds of dollars in software if you cannot find your product keys, with 'Backup Key Recovery' you can prevent losing your investment and money. 'Backup Key Recovery' recovers over popular software product keys from a crashed hard disk drive! In order to install or reinstall Microsoft Office, Windows, or other commercial software, you must have access to a product serial key (CD Key) for that product. Backup Key Recovery retrieves product key for over 4500 other softwareversions installed on your crashed or secondary hard disk drive.
- Platform: Windows
- Publisher:Nsasoft US LLC
- Date: 01-09-2014
- Size: 2135 KB
- License: Freeware
An intuitive MediaGallery for PHPNuke based Websides. Full featured and full customizable. Works with most PHPNuke based SoftwareVersions from (6.5?) 7.x to 8.1. You can't see the Download now Button from here??? Please go to the Project page on fi.
- Platform: Linux, Mac, Windows
- Publisher:phpmediagallery.sourceforge.net
- Date: 16-08-2012
- Size: 7388 KB
- License: Freeware
SimOS is an OS that will be based on the OSKIT function library. In addition we will be maintaining the oskit as a seperate release, updated as the core of the kernel. This OS will be easy to use, with numerous softwareversions on it..
- Platform: Linux, Unix
- Publisher:simosdev.sourceforge.net
- Date: 19-09-2012
- Size: 11119 KB
- License: Freeware
WWSM is a login-script program that determines whether software is installed, updated or removed by testing for Operating System, registry keys, softwareversions and machine name..
- Platform: WinOther
- Publisher:wwsm.sourceforge.net
- Date: 24-11-2012
- Size: 33 KB
- License: Freeware
Music Live TV stations from Videowebgate TV portal, on your desktop. All Live TV stations broadcasting music online, in a single software TV shaped with Remote control and manual scanner. Software is free and will updated through the web constantly. no need for software update however More softwareversions will be released in the future. The software is a single part of the videowebgate TV portal and allow the user to have his own provate copy without having to browse the web for a specific page.
- Platform: Windows
- Publisher:Amitm.com
- Date: 26-08-2006
- Size: 903 KB
- License: Shareware
VirtualLab Mac Data Recovery Software is on the cutting edge of data recovery software. The versatility of this program is surpassed by none! No matter how big or small your problem VirtualLab will quickly recover your data so you can get on with what you really need to be doing, not worrying about lost data.Works with both OS 9 and OS X and now includes support for Intel Based Macs, too! Forget having to use different softwareversions for different recoveries, VirtualLab does it all in one! We have different pricing available depending on the amount of data you want to buy.
- Platform: Mac
- Publisher:BinaryBiz
- Date: 6-2-0808
- Size: 2130 KB
- License: Comercial
ElecKey is the complete solution for software copy protection and software licensing.
Key Features:
Effortless and No Programming: The wizard style makes it very simple and easy to protect your application. You can create a protected version of your application within a few minutes. There is no need to modify any single line of source code.
Limits and Modular Protection: Allows you to create a variety of softwareversions and marketing options, such as an evaluation version.
- Platform: Windows
- Publisher:Sciensoft Research
- Date: 02-01-2011
- Size: 12807 KB
- License: Freeware
Z=GRDREAD2('filename.grd') will return the data as a matrix in Z [X,Y,Z]=GRDREAD2('filename.grd') will also return X and Y vectors suitable for use in Matlab commands such as IMAGE or CONTOUR. e.g., imagesc(X,Y,Z); axis xy This function will load COARDS compliant netCDF grdfiles, the standard format in GMT 4 and later, as well as GMT v3 netCDF formats. The data matrix Z will have a MATLAB data type appropriate to the data type used in the netCDF file. Although both gridline and pixel registered grids can be read, pixel registration will be converted to gridline registration for the x- and y-vectors in MATLAB.
- Platform: Matlab, Scripts
- Publisher:Kelsey Jordahl
- Date: 03-01-2013
- Size: 10 KB
- License: Shareware
TeeCal is a shop management software solution specifically designed for the ScreenPrinting and Embroidery industry. Designed to be the most user friendly software in this industry TeeCal provides you with easy ways to manage your business. With features from the TeeCal Console to the TeeCal Reporting we provide a product that will keep you informed and also allow you to manage your production workflow accurately. The TeeCal Console will help you track your production jobs from start to finish. Using the Console will also allow you to view the current status of each production job.
- Platform: Windows
- Publisher:TeeCal
- Date:
- Size: 53166 KB
- License: Freeware
Gallery is a web based software product that lets you manage your photos onyour own website. You must have your own website with PHP and database support in order to install and use it. With Gallery you can easily create and maintain albums of photos via an intuitive interface. Photo management includes automatic thumbnail creation, image resizing, rotation, ordering, captioning, searching and more. Albums and photos can have view, edit, delete and other permissions per individual authenticated user for an
additional level of privacy.
- Platform: Windows
- Publisher:BitNami
- Date:
- Size: 55736 KB
- License: Freeware
A unique scanning algorithm quickly analyzes the data about any outdated software on your PC and immediately displays the list of programs to be updated. Using the latest versions of programs makes your system more secure and minimizes vulnerabilities which may jeopardize your data. You also benefit from all the advantages of the extended functionality featured by the updated programs.With Soft4Boost Update Checker, you will no longer spend your time tracking down the obsolete programs and searching for the updates - Soft4Boost Update Checker will take care of that! Additionally, the utility will automatically notify you about any new softwareversions as soon as they are released.
- Platform: Windows
- Publisher:Sorentio Systems Ltd.
- Date: 05-05-2016
- Size: 14197 KB
- License: Shareware
Screen capture software for recording computer screen and audio. Video tutorials included to get you started fast. This screen capture recording software allows a user to record their voice and their computer desktop. Great for demos and tutorials. If you have a product for sale, membership site or just something to explain to others and you don't want to do it over and over again... Record your demonstration on your computer screen. A computer screen recording can be delivered online or through email.
- Platform: Windows
- Publisher:Cambrian House, LLC
- Date: 12-05-2010
- Size: 10524 KB
- License: Shareware
Email Sentinel Pro smoothly prevents malware emails from reaching your mailbox folders and running viruses, worms or exploit attacks. It intercepts emails before they reach your Inbox email folders, thus reducing the infection risk to zero. While some of the latest email softwareversions include attachment protection features, these features are subject to programming bugs and exploits. If you don't feel like relying on the security features of your email software, then use Email Sentinel Pro to block virus attachments before they reach the Inbox folders of your email software, thus eliminating the risk of HTML email exploits.
- Platform: Windows
- Publisher:emailaddressmanager.com
- Date:
- Size: 3112 KB
- License: Freeware
Stay up to date in the world of Android with Android Authority. Get all the latest Android news, rumors, hot Android apps, tips & tricks and device reviews!
You can expect excellent up to date coverage on the following topics:
* * Software updates
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* * Android wallpapers
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* * Android widgets
* * Android tools
* * Android manuals and guides
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* * Firmware updates
We cover all the latest and most popular Android phones & tablets including:
* Samsung Galaxy S2
* Samsung Galaxy S3
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* * Android Authority App supports the following Android Software...
- Platform: Android, Windows
- Publisher:AndroidAuthority.com
- Date:
- Size: 2355 KB
- License: Shareware
Email Sentinel Pro smoothly prevents malware emails from reaching your mailbox folders and running viruses, worms or exploit attacks. It intercepts emails before they reach your Inbox email folders, thus reducing the infection risk to zero. While some of the latest email softwareversions include attachment protection features, these features are subject to programming bugs and exploits. If you don't feel like relying on the security features of your email software, then use Email Sentinel Pro to block virus attachments before they reach the Inbox folders of your email software, thus eliminating the risk of HTML email exploits.
- Platform: Windows
- Publisher:DS Development
- Date: 17-11-2004
- Size: 2492 KB
- License: Freeware
DAEMON Tools needs a 1:1 Copy to run!! DAEMON Tools is used to RUN GAMES, NOT TO BURN THEM!!! Means emulation must be active while you want to play a game, not while burning the copy (except for you want to use DAEMON Tools' 'fastdump' feature on a safedisc protected CD). If you want to run a copy protected application from an image mounted to a Generic DVD-ROM enabling the copy protection emulation(s) is NOT necessary!! Generic DVD-ROM is able to run nearly every protected or unprotected CD image (SafediscT«, SecuromT«, LaserlockT«, LockblocksT« etc.
- Platform: Windows
- Publisher:DAEMON Tools
- Date: 21-07-2009
- Size: 504 KB
Mass spectrometry software is software used for data acquisition, analysis, or representation in mass spectrometry.
- 1Proteomics software
Proteomics software[edit]
In protein mass spectrometry, tandem mass spectrometry (also known as MS/MS or MS2) experiments are used for protein/peptide identification. Peptide identification algorithms fall into two broad classes: database search and de novo search. The former search takes place against a database containing all amino acid sequences assumed to be present in the analyzed sample, whereas the latter infers peptide sequences without knowledge of genomic data.
Database search algorithms[edit]
| Name | Type | Description |
|---|---|---|
| Andromeda (part of MaxQuant) | freeware | Andromeda is a peptide search engine based on probabilistic scoring. On proteome data, Andromeda performs as well as Mascot, a widely used commercial search engine, as judged by sensitivity and specificity analysis based on target decoy searches. It can handle data with arbitrarily high fragment mass accuracy, it is able to assign and score complex patterns of post-translational modifications, such as highly phosphorylated peptides, and accommodates extremely large databases. Andromeda can function independently or integrated into MaxQuant. This combination enables analysis of large datasets on a desktop computer. Identification of co-fragmented peptides improves the number of identified peptides. Developed by Jürgen Cox and others at the Max Planck Institute of Biochemistry.[1] |
| Byonic | proprietary | Database search algorithm released in 2011 by Protein Metrics Inc. with original developments at PARC[2] that searches MS/MS data from all types of instruments and internally employs the program Combyne,[3] which combines peptide identifications to produce protein scores and identification probabilities. |
| Comet | open source | Database search algorithm developed at the University of Washington available for Windows and Linux. Note that Comet is just a single command line binary that does MS/MS database search. It takes in spectra in some supported input format and writes out .pep.xml, .pin.xml, .sqt and/or .out files. You will need some other support tool(s) to actually make use of Comet results (A GUI for Windows only is available).[4] |
| Tide (rewrite of Crux) | open source | Tide is a tool for identifying peptides from tandem mass spectra. It is an independent reimplementation of the SEQUEST algorithm, which identifies peptides by comparing the observed spectra to a catalog of theoretical spectra derived in silico from a database of known proteins. The immediate ancestor of Tide is Crux, but Tide has been completely re-engineered to achieve a thousandfold improvement in speed while exactly replicating SEQUEST XCorr scores. Developed at the University of Washington.[5] |
| Greylag | open source | Database search algorithm developed at the Stowers Institute for Medical Research designed to perform large searches on computational clusters having hundreds of nodes. |
| InsPecT | open source | A MS-alignment search algorithm available at the Center for Computational Mass Spectrometry at the University of California, San Diego[6] |
| Mascot | proprietary | Performs mass spectrometry data analysis through a statistical evaluation of matches between observed and projected peptide fragments.[7] |
| MassMatrix | freeware | MassMatrix is a database search algorithm for tandem mass spectrometric data. It uses a mass accuracy sensitive probabilistic scoring model to rank peptide and protein matches. |
| MassWiz | open source | Search algorithm developed at Institute of Genomics and Integrative Biology available as a windows commandline tool. |
| MS-GF + | open source | MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database. It supports the HUPO PSI standard input file (mzML) and saves results in the mzIdentML format, though results can easily be transformed to TSV. ProteomeXchange supports Complete data submissions using MS-GF+ search results. Developed at Center for Computational Mass Spectrometry at the University of California, San Diego, with later work at Pacific Northwest National Laboratory (PNNL) |
| MyriMatch | open source | Database search program developed at the Vanderbilt University Medical Center designed to run in a single-computer environment or across an entire cluster of processing nodes.[8] |
| OMSSA | freeware | The Open Mass Spectrometry Search Algorithm (OMSSA) is an efficient search engine for identifying MS/MS peptide spectra by searching libraries of known protein sequences. OMSSA scores significant hits with a probability score developed using classical hypothesis testing, the same statistical method used in BLAST. It is developed at the National Center for Biotechnology Information.[9][10] |
| PEAKS DB | proprietary | Database search engine, run in parallel with de novo sequencing to automatically validate search results, allowing for a higher number of found sequences for a given false discovery rate. In addition to providing an independent database search, results can be incorporated as part of the software’s multi-engine (Sequest, Mascot, X!Tandem, OMSSA, PEAKS DB) consensus reporting tool, inChorus.[11] The tool also provides a list of sequences identified exclusively by de novo sequencing. |
| pFind | freeware | pFind Studio is a computational solution for mass spectrometry-based proteomics, it germinated in 2002 in Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China. |
| Phenyx | proprietary | Developed by Geneva Bioinformatics (GeneBio) in collaboration with the Swiss Institute of Bioinformatics (SIB). Phenyx incorporates OLAV, a family of statistical scoring models, to generate and optimize scoring schemes that can be tailored for all kinds of instruments, instrumental set-ups and general sample treatments.[12] |
| ProbID | open source | PI is a powerful suite on analysis of tandem mass spectrum. ProbID seeks to fill the need for the deep analysis of tandem mass spectrum, including the fragmentation rules, preference of cleavage, neutral losses, etc. Developed at the Bioinformatics Group, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.[13] |
| ProLuCID | freeware | ProLuCID is a fast and sensitive tandem mass spectra-based protein identification program recently developed by Tao Xu and others in the Yates laboratory at The Scripps Research Institute.[14] |
| ProteinPilot Software | proprietary | Uses Paragon database search algorithm that combines the generation of short sequence tags (‘taglets’) for computation of sequence temperature values and estimates of feature probabilities to enable the peptide identification considering hundreds of modifications, non-tryptic cleavages and amino acid substitutions. Uses the Pro Group Algorithm for protein inference analysis to report the minimal set of proteins justified based on the peptide evidence. Supports quantification for label-based workflows (iTRAQ reagents, mTRAQ reagents and SILAC labeling). A translation layer translates user interface controls in the language of the proteomics experimental scientist to underlying complex informatics parameters.[15] |
| Protein Prospector | open source | Protein Prospector is a package of about twenty proteomic analysis tools developed at the University of California San Francisco. The tandem mass spectrometry searching software is Batch-Tag / Batch-Tag Web, with the results processed and displayed using Search Compare. It uses scoring systems tailored to instrument and fragmentation mode to optimize analysis of different types of fragmentation data. |
| RAId | lost | Developed at the National Center for Biotechnology Information, Robust Accurate Identification (RAId)[16] is a suite of proteomics tools for analyzing tandem mass spectrometry data with accurate statistics.[17] |
| SEQUEST | proprietary | Identifies collections of tandem mass spectra to peptide sequences that have been generated from databases of protein sequences.[18] |
| SIMS | open source | SIMS (Sequential Interval Motif Search) is a software tool design to perform unrestrictive PTM search over tandem mass spectra; users do not have to characterize the potential PTMs. Instead, users only need to specify the range of modification mass for each individual amino acid.[19] |
| SimTandem | freeware | A database search engine for identification of peptide sequences from LC/MS/MS data; the engine can be used as an external tool in OpenMS/TOPP.[20] |
| SQID | open source | SeQuence IDentification (SQID) is an intensity-incorporated protein identification algorithm for tandem mass spectrometry. |
| X!Tandem | open source | Matches tandem mass spectra with peptide sequences. |
De novo sequencing algorithms[edit]
De novo peptide sequencing algorithms are based, in general, on the approach proposed in Bartels et al. (1990).[21]
| Name | Type | Description |
|---|---|---|
| CycloBranch | open source | A stand-alone, cross-platform and open-source de novo engine for identification of nonribosomal peptides (linear, cyclic, branched and branch-cyclic) from accurate product ion spectra.[22] |
| DeNovoX | proprietary | De novo sequencing on CID spectra acquired with ion trap mass spectrometers delivering complete and/or partial peptide sequences (sequence tags).[23] |
| DeNoS | Sequencing of peptides using all information from CAD and ECD spectra; part of the software tool Proteinmatching Analysis Software (PAS) which in turn is part of the software package Medicwave Bioinformatics Suite (MBS).[24] | |
| Lutefisk | open source | Software for the de novo interpretation of peptide CID spectra. |
| Novor | proprietary, free for academic research | Real-time de novo peptide sequencing engine that is fast, accurate and easy to be integrated into research pipelines. Novor can de novo sequence more than 300 MS/MS spectra per second on a Macbook Pro laptop computer.[25] |
| PEAKS | proprietary | De novo sequencing for each peptide, confidence scores on individual amino acid assignments with manually assisted modeand automated de novo sequencing on an entire LC run processed data faster than 1 spectrum per second.[26][27] |
| Supernovo | proprietary | A unique, hands-free solution for end-to-end de novo sequencing of monoclonal antibodies |
Homology searching algorithms[edit]
| Name | Type | Description |
|---|---|---|
| MS-Homology | open source | MS-Homology is a database search program within the Protein Prospector package that permits searching with strings that combine masses and amino acid stretches, where one can specify the number of amino acid mismatches allowed. |
| SPIDER | proprietary | The SPIDER algorithm matches sequence tags with errors to database sequences for the purpose of protein and peptide identification and can be used in conjunction with PEAKS mass spectrometry data analysis software. |
MS/MS peptide quantification[edit]
| Name | Type | Description |
|---|---|---|
| MarkerView Software | proprietary | Commercial software for statistical analysis for quantitative mass spec data sets from metabolomics and proteomic profiling applications. |
| Mascot Distiller | proprietary | Software for peak picking and raw data preprocessing. Has an optional toolbox for label-free quantification as well as isobaric labeling and isotopic labeling. Supports raw file formats from all major instrument vendors. |
| Mascot Server | proprietary | The search engine supports quantification based on isobaric labeling as long as all the required information is part of the MS/MS spectrum. |
| MassChroQ | open source | Peptide quantification analysis of label free or various isotopic labeling methods (SILAC, ICAT, N-15, C-13 …), works with high and low resolution spectrometer systems, supports complex data treatments as peptide or protein fractionation prior to LC-MS analysis (SCX, SDS-PAGE, etc.). |
| MaxQuant | freeware | Quantitative proteomics software developed by Jürgen Cox and others at the Max Planck Institute of Biochemistry in Martinsried, Germany written in C# that allows the analysis of label free and SILAC based proteomics experiments. |
| MultiQuant Software | proprietary | Can process quantitative data sets from TripleTOF or QTRAP systems, including MRM and SWATH Acquisition. |
| OpenMS / TOPP | open source | Software C++ library for LC-MS/MS data management and analysis that offers an infrastructure for the development of mass spectrometry related software. Allows peptide and metabolite quantification, supporting label-free and isotopic-label based quantification (such as iTRAQ and TMT and SILAC) as well as targeted SWATH-MS quantification.[28] |
| ProtMax | freeware | ProtMAX[29] is a software tool for analyzing shotgun proteomics mass spectrometry data sets, developed by Volker Egelhofer at the University of Vienna. |
| Spectronaut | proprietary | Commercial software for quantitative proteomics developed by Biognosys AG (Schlieren, Switzerland) based on the mProphet algorithm[30] that allows the targeted analysis of data independent acquisition (DIA) data sets for label-free peptide quantitation, also called SWATH acquisition.[31] |
| Skyline | open source | Open source (Apache 2.0) Windows client software developed in the MacCoss lab at University of Washington[32] that supports building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM - Targeted MS/MS), Data Independent Acquisition (DIA/SWATH) and targeted DDA with MS1 quantitative methods and analyzing the resulting mass spectrometer data. |
| SWATH Software 2.0 | proprietary | Commercial software processing tool within PeakView that allows targeted data processing of SWATH acquisition data. Using a protein/peptide ion library, fragment ion extracted ion chromatograms (XICs) are generated, scored and quantified for peptides from the library. After false discovery rate analysis (FDR), results are filtered and quantitative peptide/protein data can be exported for statistical analysis. |
| BACIQ | open source | BACIQ is a mathematically rigorous approach that integrates peptide intensities and peptide-measurement agreement into confidence intervals for protein ratios (BACIQ). The main advantages of BACIQ are: 1) it removes the need to threshold reported peptide signal based on an arbitrary cut-off, thereby reporting more measurements from a given experiment; 2) confidence can be assigned without replicates; 3) for repeated experiments BACIQ provides confidence intervals for the union, not the intersection, of quantified proteins; 4) for repeated experiments, BACIQ confidence intervals are more predictive than confidence intervals based on protein measurement agreement. |
Other software[edit]
| Name | Type | Description |
|---|---|---|
| ArtIST by Clover Biosoft | proprietary | (Artificial Intelligence Straing Typing) MALDI-TOF MS data analysis and biomarker discovery tools, based on artificial intelligence and machine learning algorithms. ArtIST is an online service. |
| Advanced Chemistry Development | proprietary | Commercial solutions for the interpretation of MS and xC/MS data with spectrum/structure matching, identification of known and unknown metabolites, as well as for the identification of compounds through spectral comparison. |
| Analyst | proprietary | Software by AB Sciex, a division of The Danaher Corporation. |
| AnalyzerPro | proprietary | A vendor independent software application for processing mass spectrometry data that can analyze both GC-MS and LC-MS data using both qualitative and quantitative data processing and is used for metabolomics data processing using MatrixAnalyzer for the comparison of multiple data sets. |
| Chromeleon | proprietary | Software by Thermo Fisher Scientific used with mass spectrometry instruments, as well as chromatography instruments. |
| Crosslinx | open source | Identify cross-linked peptides from mzML files. Python script or standalone executables for Linux and Windows. Feasible for bigger databases with a two-step approach.[33] |
| DeNovoGUI | open source | Software with a graphical user interface for running parallelized versions of the freely available de novo sequencing software tools Novor and PepNovo+.[34] |
| Easotope | open source | Software for archiving, organizing, and analyzing mass spectrometer data. Currently oriented toward clumped CO2 analysis but also useful for bulk CO2 work and expandable to other isotopic systems. |
| [El-MAVEN] | open-source | Desktop software by Elucidata for processing labeled LC-MS, GC-MS and LC-MS/MS data in open-formats (mzXML, mzML, CDF). The software has a graphical and command line interface with integration to a cloud platform for storage and further analyses like relative flux and quantification.[35] |
| ESIprot | Enables the charge state determination and molecular weight calculation for low resolution electrospray ionization (ESI) mass spectrometry (MS) data of proteins.[36] | |
| KnowItAll Spectroscopy Software & Mass Spectral Library | proprietary | Software from Bio-Rad Laboratories, Inc. with solutions for mass spectrometry including: spectral analysis, database searching (spectrum, structure, peak, property, etc.), processing, database building (MS or multiple techniques including IR, Raman, NMR, UV, Chromatograms), spectral subtraction, plus tools for reporting and ChemWindow structure drawing. |
| LabSolutions LCMS | proprietary | Software by Shimadzu Corporation used with mass spectrometry and HPLC instruments. |
| Mass++ | open source | Analysis software for mass spectrometry that can import and export files with open-formats (mzXML, mzML) and load some instrument vendor formats; users can develop and add original functions as Mass++ plug-ins. |
| MassBank.jp | website | website hosted by the Institute for Advanced Biosciences, in Keio University, Tsuruoka City, Yamagata, Japan with mass spectrometric data for organic compounds. |
| MassBank.eu | website | European MassBank server. The website is maintained and hosted by the Helmholtz Centre for Environmental Research (Leipzig, Germany) |
| MassBank | open source | MassBank and RMassBank development website provided by the MassBank consortium. MassBank data is shared under a Creative Commons license. |
| MassCenter | proprietary | Software by JEOL used with mass spectrometry instruments. |
| Mass Frontier | proprietary | Software by HighChem used for interpretation and management of mass spectra of small molecules. |
| MassLynx | proprietary | Software by Waters Corporation. |
| MassMap | proprietary | General-purpose software suite for automated evaluation of MS data by MassMap GmbH & Co. KG, suitable for LC/MS and GC/MS data of all kinds of molecules, the analysis of intact mass spectra of proteins, the analysis of general HDX experiments and the HDX fragment analysis of peptides, with particular method for the identification of unexpected/unknown components in even very complex mixtures. |
| Mass-Up | open-source | Utility for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data that loads data from mzML, mzXML and CSV files and allows users to apply baseline correction, normalization, smoothing, peak detection and peak matching. In addition, it allows the application of different machine learning and statistical methods to the preprocessed data for biomarker discovery, unsupervised clustering and supervised sample classification.[37] |
| massXpert | open source GPL | Graphical user interface-based (GUI) software for simulating and analyzing mass spectrometric data obtained on known bio-polymer sequences.[38] Successor to polyxmass. |
| METLIN Database and Technology Platform | proprietary | Created in 2003, METLIN now includes over a million molecules ranging from lipids, steroids, plant & bacteria metabolites, small peptides, carbohydrates, exogenous drugs/metabolites, central carbon metabolites and toxicants. The metabolites and other small molecules have been individually analyzed to provide both empirical and in silico MS/MS data. |
| mMass | open source | Multi-platform package of tools for mass spectrometric data analysis and interpretation written in Python. |
| MolAna | MolAna was developed by Phenomenome Discoveries Inc, (PDI) for use in IONICS Mass Spectrometry Group's 3Q Molecular Analyzer, Triple quadrupole mass spectrometer | |
| ms2mz | freeware | Utility for converting between mass spectrometer file formats, e.g. to convert proprietary binary files to MGF peak list files to prepare files for upload to Proteome Cluster. |
| MSGraph | open source | |
| MSight | freeware | Software for mass spectrometry imaging developed by the Swiss Institute of Bioinformatics.[39] |
| MSiReader | freeware | Vendor-neutral interface built on the Matlab platform designed to view and perform data analysis of mass spectrometry imaging (MSI) data.[40] Matlab is not required to use MSiReader. |
| mspire | open-source | Mass spectrometry informatics developers toolbox written in ruby that includes an mzML reader/writer, in-silico digestion and isotopic pattern calculation etc.; submodules such as mspire-lipidomics, mspire-sequest, and mspire-simulator extend the functionality.[41] |
| Multimaging | Software for mass spectrometry imaging designed to normalize, validate and interpret MS images. | |
| multiMS-toolbox | open source | ms-alone and multiMS-toolbox is a tool chain for mass spectrometry data peak extraction and statistical analysis. |
| mzCloud | website | Web-based mass spectral database that comprises a collection of high and low resolution tandem mass spectrometry data acquired under a number of experimental conditions. |
| MZmine 2 | open source | An open-source software for mass-spectrometry data processing, with the main focus on LC-MS data. |
| OmicsHub Proteomics | OmicsHub Proteomics combines a LIMS for mass spec information management with data analysis functionalities on one platform. | |
| OpenChrom | open source | Chromatography and mass spectrometry software that can be extended using plug-ins and is available for several operating systems (Microsoft Windows, Linux, Unix, Mac OS X) and processor architectures (x86, x86_64, ppc). with converters for the native access of various data files, e.g. converters for mzXML, netCDF, Agilent, Finnigan and Varian file formats. |
| ORIGAMI | open source | Software suite for analysis of mass spectrometry and ion mobility mass spectrometry datasets. ORIGAMI was originally developed to improve the analysis workflows of activated IM-MS/collision induced unfolding (CIU) datasets and allow seamless visualisation of results. Recently, ORIGAMI was modified to be more accepting of non-MS centric and enables visualisation of results from other sources as well as enables exporting of all results in an interactive format where the user can share any dataset and visualise in an internet browser.[42] |
| PatternLab | freeware | Software for post-analysis of SEQUEST, ProLuCID or Comet database search results filtered by DTASelect or Census.[43] |
| pyOpenMS | open source | pyOpenMS is an open-source Python library for mass spectrometry, specifically for the analysis of proteomics and metabolomics data in Python. |
| SIM-XL | freeware | Spectrum Identification Machine for Cross-linked Peptides (SIM-XL) is a fast and sensitive XL search engine which is part of the PatternLab for proteomics environment, to analyze tandem mass spectrometry data derived from cross-linked peptides.[44] |
| Peacock | open source | Mac OS X application developed by Johan Kool that can be used to interpret gas-chromatography/mass-spectrometry (GC/MS) data files. |
| PeakInvestigator | proprietary | 3-4X effective resolution improvement in post-processing of raw profile data output from mass specs. Veritomyx advanced signal processing software for peak detection, deconvolution, and centroiding of raw profile mass spec data reveals multiple peaks hidden in overlapped data. Notable features: order-of-magnitude improvements in mass and abundance precision for deconvolved peaks; local dynamic baselining; advanced thresholding algorithm increases sensitivity across wide dynamic range; statistically-driven and completely automated (no user-to-user variation). More complete and precise resulting mass lists facilitate faster and cost-efficient subsequent determination of correct biomolecular identifications. |
| Pinnacle | Proprietary | From comprehensive quantitation of 10,000s of proteins across of 100s of samples using DDA, DIA, PRM or SRM with fully integrated statistics and biological interpretation, to complete N-linked glycoprotein identification routine, to a very in-depth analysis in protein characterization, including peptide mapping, error tolerant search and disulfide analysis, all of this is available in a single software. Analyzing 100s of samples brings big challenges of LC and MS variation when run over months of acquisition, and the software can automatically correct for this. The visualization, editing and annotation capabilities can be tailored to be at the high level of proteins or at a much lower level of transitions or isotopes. |
| PIQMIe | web | Proteomics Identifications/quantitations data management and integration service is a web-based tool that aids in reliable and scalable data management, analysis and visualization of semi-quantitative (SILAC) proteomics experiments.[45] |
| POTAMOS | open source | Web application that provides calculated mass spectrometry data independently of instrumentation focused on a well known protein family of histones whose PTMs are believed to play a crucial role in gene regulation; calculates the kind, the number and the combinations of the possible PTMs corresponding to a given peptide sequence and a given mass. |
| PROTRAWLER | LC/MS data reduction application that reads raw mass spectrometry vendor data (from a variety of well-known instrument companies) and creates lists of {mass, retention time, integrated signal intensity} triplets summarizing the LC/MS chromatogram. | |
| ProteoIQ | proprietary | Software for the post-analysis of Mascot, SEQUEST, or X!Tandem database search results.[46][47][48] |
| Proteomatic | Freeware | Data processing pipeline created for the purpose of evaluating mass spectrometric proteomics experiments.[49] |
| ProteomicsTools | open source | Software for the post-analysis of MASCOT, SEQUEST, Comet, XTandem, PFind, PeptidePhophet, MyriMatch, MSGF, OMSSA, MSAmanda or Percolator database search result.[50] |
| ProteoWizard | open source | Link library and tools that are a set of modular and extensible open-source, cross-platform tools and software libraries that facilitate proteomics data analysis. |
| ProteoWorker | proprietary | Cloud-based software for proteomics data analysis including COMET, Peptide Prophet, ProteinProphet and extensive data sorting, filtering and annotation tools. |
| pymzML | open source | Python module to interface mzML data in Python based on cElementTree with additional tools for MS-informatics.[51] |
| Pyteomics | open source | A Python framework for proteomics data analysis.[52] |
| Quantinetix | Software for mass spectrometry imaging designed to quantify and normalize MS images in various study types that is compatible with a variety of MSI instruments, including Bruker, Sciex, Thermo and with iMZML. | |
| Rational Numbers Excel Add-In | proprietary | De novo identification tool that works with Microsoft Excel 2010, Excel 2013, and Excel 2016. |
| Rational Numbers Search | proprietary | Identification of small molecules by comparison of accurate-mass fragmentation data to a database of 250000 molecules represented as mathematical partitions |
| REGATTA | LC/MS list comparison application that works with ProTrawler (but accepts input in Excel/CSV form) to provide an environment for LC/MS results list filtering and normalization {mass, retention time, integrated intensity} lists. | |
| RemoteAnalyzer | proprietary | Software by SpectralWorks Limited for vendor independent 'Open Access' client/server based solutions to provide a walk-up and use LC-MS and GC-MS data system; instrument control and data processing support for multiple vendors' hardware is provided. |
| Scaffold | proprietary | Suite of proteomics tools for analyzing spectra, peptides and proteins across multiple samples. |
| SCIEX OS | proprietary | Next generation software by SCIEX controlling the X-series mass spectrometers and support for data analysis acquired using the Analyst software suite. |
| SCiLS Lab | Statistical analysis of MALDI imaging mass spectrometry data that integrates with Bruker MALDI imaging. | |
| SimGlycan | proprietary | Predicts the structure of glycans and glycopeptides using mass spectrometry MS/MS data. |
| SIMION | proprietary | Ion optics simulation program |
| Spectrolyzer | Spectrolyzer is a Microsoft Windows-based software package that provides bioinformatics data analysis tools for different mass spectrometers that focuses on finding protein biomarkers and detecting protein deviations. | |
| Spectromania | proprietary | Software for analysis and visualization of mass spectrometric data.[53] |
| StavroX | freeware | Software to identify cross-linked peptides from mass spectrometric data written in Java that can be used for a wide variety of cross linkers and proteases used in the cross linking MS experiment; it compares theoretical peptide-peptide cross link combinations for the analyzed proteins to MS/MS data.[54] |
| Swiss Mass Abacus | open source | Swiss Mass Abacus is a calculator of peptide and glycopeptide masses. It is purposefully kept as simple as a basic calculator executing arithmetic operations. |
| TOF-DS | proprietary | Software by Markes International used with BenchTOF time-of-flight mass spectrometers |
| TurboMass | proprietary | GC/MS software by PerkinElmer. |
| Trans-Proteomic Pipeline (TPP) | open source | The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics that includes PeptideProphet for the Statistical validation of PSMs using search engine results, iProphet for distinct peptide sequence validation, using PeptideProphet results (can also combine the results of multiple search engines) and ProteinProphet for Protein identification and validation, using PeptideProphet OR iProphet results. TPP does also Protein Quantification with XPRESS (Calculation of relative abundances of peptides and proteins from isotopically labeled MS/MS samples), ASAPRatio (Automated Statistical Analysis on Protein Ratio; an alternative to XPRESS) and Libra (Quantification of isobarically-labeled samples (e.g. iTraq, TMT, etc.) for any number of channels). The TPP currently supports Sequest, Mascot, ProbID, X!Tandem, Comet, SpectraST, MSGF+, Inspect, MyriMatch, and Phenyx. Developed at the Seattle Proteomic Centre (SPC).[55] |
| Universal Mass Calculator | Universal Mass Calculator (UMC) for Windows written in C++ is a proprietary toolbox for calculating relevant information from sum formulae, e.g. isotope distribution, mass differences, mass deviations and mass/isotope information of the elements, degree of deuteration. | |
| VIPER | Analysis of accurate mass and chromatography retention time analysis of LC-MS features (accurate mass and time tag approach).[57] | |
| Xcalibur | proprietary | Software by Thermo Fisher Scientific used with mass spectrometry instruments. |
| XCMS Online (Cloud-Based) | proprietary | Freely available and the most widely used metabolomic and lipidomic data processing platform with over 21,000 users as of 2017. |
See also[edit]
- Mass spectrometry data format: for a list of mass spectrometry data viewers and format converters.
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- ^Deutsch, Eric W.; Mendoza, Luis; Shteynberg, David; Farrah, Terry; Lam, Henry; Tasman, Natalie; Sun, Zhi; Nilsson, Erik; Pratt, Brian; Prazen, Bryan; Eng, Jimmy K.; Martin, Daniel B.; Nesvizhskii, Alexey I.; Aebersold, Ruedi (2010). 'A guided tour of the Trans-Proteomic Pipeline'. Proteomics. 10 (6): 1150–1159. doi:10.1002/pmic.200900375. ISSN1615-9853. PMC3017125. PMID20101611.
- ^Monroe, M. E.; Tolić, N.; Jaitly, N.; Shaw, J. L.; Adkins, J. N.; Smith, R. D. (2007). 'VIPER: an advanced software package to support high-throughput LC-MS peptide identification'. Bioinformatics. 23 (15): 2021–3. doi:10.1093/bioinformatics/btm281. PMID17545182.
External links[edit]
- Mass Spectrometry Software at Curlie
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