User contributions for Laschp

11:2611:26, 18 March 2023 diff hist +6,999‎ N Peak Detection ‎ Created page with "== Introduction == Peak picking is an essential (and the final) step of the spectral pre-processing pipeline. The result of peak picking is a peak table which is attached to the mass spectra. In MicrobeMS peak picking can be started via the ''find peaks'' command of the ''Peak pick'' pulldown menu (shortcut <ctrl>+P), or by pressing the ''peak'' button located in the ''Peak pick'' tab. right|Screenshot of the peak pick window == Peak picking - b..."
11:2611:26, 18 March 2023 diff hist +9,050‎ N Spectral Pre-processing ‎ Created page with " == Introduction == Spectral data analysis is a challenging task of the MALDI-TOF MS-based workflow for microbial identification. Considering that a MALDI-TOF mass spectrum is a complex signal which usually consists of hundreds of peaks and certain level of noise, adequate spectral pre-processing is required prior to peak detection and classification analysis. The quality of microbial mass spectra should be assessed visually immediately after data acquisition with r..." current
11:2511:25, 18 March 2023 diff hist +10,446‎ N Description of MicrobeMS' main parameter file 'microbems.opt' ‎ Created page with "== Introduction == '''Important notice''': With MicrobeMS v. 0.82 the format of the parameter file ''microbems.opt'' has changed! The file ''microbems.opt'' is a simple text file which is read upon initialization by MicrobeMS. The file ''microbems.opt'' contains a number of program-wide parameters and parameters required for auto-preprocessing and auto-peak detection from raw (original) mass spectra. Auto-preprocessing and auto-peak detection is carried when generating..." current
11:2511:25, 18 March 2023 diff hist +8,042‎ N Data Format of Peak List Files ‎ Created page with "Peak list files combine multiple peak lists in one single file. These files are stored in a Matlab™ specific data format and contain the peak lists as well as the respective metadata. In Matlab peak list files can be loaded by entering the following command at the Matlab command prompt: >> load('ecoli-peaklist-oct16.pkf','-mat') This command will open ''ecoli-peaklist-oct16.pkf'', an example peak list file consisting of 16 individual peak lists from spectra of f..."
11:2411:24, 18 March 2023 diff hist +8,424‎ N Data Format of Spectral Multifiles ‎ Created page with "Spectral multifiles combine multiple spectra in one single file. These files are stored in a Matlab™ specific data format and contain the spectral as well as the respective metadata. Spectral multifiles can be loaded in Matlab by entering the following command: >> load('ecoli-filelist-oct16.muf','-mat') This command will open ''ecoli-filelist-oct16.muf'', an example multifile containing 16 individual MALDI-TOF mass spectra acquired from five different strains of..."
11:2311:23, 18 March 2023 diff hist +109‎ N Management of Sample Information ‎ Created page with "800px|thumb|left|Screenshot of the window "''Edit spectra header information''"" current
11:2211:22, 18 March 2023 diff hist +7,624‎ N Adding / Editing Metadata of MALDI-TOF Mass Spectral Data ‎ Created page with "== Introduction == When analyzing MALDI-TOF mass spectra from microorganisms it is often important to have direct access to taxonomic information, parameters of cultivation, of the sample preparation method and other relevant data associated with mass spectra acquisition in the context of microbiology. Historically, MALDI-TOF mass spectrometry was developed in the late 1980s and beginning of the 1990s from physicists for physicists and chemists. None of the developers a..." current
11:2211:22, 18 March 2023 diff hist +8,917‎ N Frequently Asked Questions (FAQ) ‎ Created page with "== What is MicrobeMS? == The MicrobeMS software package is a program initially designed for the analysis of MALDI-TOF mass spectra of microbial samples. The MicrobeMS software was developed by Peter Lasch at the [http://www.rki.de/EN/Home/homepage_node.html: Robert-Koch-Institute (RKI)] in Berlin, Germany, and can be used to identify microbial strains and species based on their mass spectral patterns. == What is the most actual version of MicrobeMS? == The most actual..."
11:2111:21, 18 March 2023 diff hist +7,632‎ N Publications with MicrobeMS ‎ Created page with "== Acknowledgements == MicrobeMS is a software project that has been developed by [http://www.peter-lasch.de Peter Lasch] at the [http://www.rki.de/EN/Content/Institute/DepartmentsUnits/CenterBioSafety/zbs6/zbs6_node.html ''Proteomics and Spectroscopy''] unit at the [http://www.rki.de ''Robert Koch-Institute''] (Berlin/Germany). MicrobeMS is not open source but is provided for free, for testing or non-commercial use. Please send us references to any publications, presen..."
11:2011:20, 18 March 2023 diff hist +10,842‎ N Identification Analysis by Means of LC-MS¹ and ''in silico'' Databases ‎ Created page with "__FORCETOC__ == Introduction == Microbial identification analysis by means of LC-MS¹ data and an ''in silico'' database represents an alternative bottom-up proteomics approach that involves (i) efficient extraction of proteins from cultivated microbial samples, (ii) digestion by trypsin and (iii) LC-MS measurements. Next steps in the analytical pipeline are (iv) extraction of MS¹ data followed by (v) systematic tests of MS¹ data against a library of strai..."
11:1911:19, 18 March 2023 diff hist +3,908‎ N Mass Spectrometry Databases ‎ Created page with "__FORCETOC__ == Introduction == Library-based MS approaches for microbial identification require labeled sets of microbial mass spectra. Starting with version 0.82 MicrobeMS can deal with experimental MALDI-TOF or LC-MS¹ mass spectra and the respective MS databases. The RKI databases of microbial MALDI-TOF mass spectra contain mass spectral entries from highly pathogenic (biosafety level 3, BSL-3) bacteria such as ''Bacillus anthracis'', ''Yersinia pestis'',..."
11:1811:18, 18 March 2023 diff hist +1,172‎ N How to Obtain a License ‎ Created page with " Once you have accepted all terms of the license agreement you can download a free version of MicrobeMS. In order to run MicrobeMS an additional license key file ('keygen.gen') must be obtained and copied into the toolbox directory of MicrobeMS. This individual license key is NOT included in the MicrobeMS installation package and will be send to you only on request. Please e-mail your request together with your name and an institutional address to the following e-mail..." current
11:1811:18, 18 March 2023 diff hist +3,969‎ N MicrobeMS Wiki:General disclaimer ‎ Created page with "MicrobeMS - A Matlab Toolbox for Analysis of Microbial MALDI-TOF Mass Spectra '''License Agreement''' MicrobeMS is willing to license this software to you only upon the condition that you accept all of the terms and conditions contained in the following license agreement. Please read the terms and conditions carefully as continuing with the setup procedure will indicate your acceptance of all of the terms and conditions of the license agreement ("agreement"). If you..." current
11:1711:17, 18 March 2023 diff hist +4,800‎ N Install MicrobeMS ‎ Created page with "__FORCETOC__ == Preface == MicrobeMS is a Matlab-based application which can be installed in two different versions (with basically the same functionality): * The stand-alone version requires installation of the MATLAB Compiler Runtime (MCR R2014a 64-bit). * MicrobeMS as a Matlab pcode toolbox. For this a licensed version of Matlab will be required. == Install MicrobeMS as a stand-alone application (Windows) == Prerequisites MicrobeMS is Matla..." current
11:1611:16, 18 March 2023 diff hist +3,695‎ N MALDI-TOF Mass Spectrometry Database ‎ Created page with "__FORCETOC__ == Introduction == Library-based MS approaches for microbial identification require labeled sets of microbial mass spectra. Starting with version 0.82 MicrobeMS can deal with experimental MALDI-TOF or LC-MS¹ mass spectra and the respective MS databases. The RKI databases of microbial MALDI-TOF mass spectra contain mass spectral entries from highly pathogenic (biosafety level 3, BSL-3) bacteria such as ''Bacillus anthracis'', ''Yersinia pestis'',..." current
11:1511:15, 18 March 2023 diff hist +3,014‎ N Download MicrobeMS ‎ Created page with "MicrobeMS is available in two different editions: in (i) a stand-alone Windows 64-bit version requiring the Matlab Compiler Runtime (MCR) 64-bit and (ii) a Matlab pcode toolbox version requiring Matlab R2014 (Windows / Linux) or later. Please note that you accept with downloading the [http://www.microbe-ms.com/microbe-ms/license.txt: license conditions] of MicrobeMS. === MicrobeMS stand-alone (Windows) === '''NEW''' - Microbe MS 0.84 stand-al..."
11:1511:15, 18 March 2023 diff hist +92‎ N Screenshot of MicrobeMS ‎ Created page with "1000px|thumb|Screenshot of main window of MicrobeMS v.082" current
11:1411:14, 18 March 2023 diff hist +1,883‎ N Computer specification ‎ Created page with " Pcode toolbox of the MicrobeMS software (v.082) * Processor: 32-bit or 64-bit CPU from Intel or AMD * Operating system: Microsoft Windows 7/8/8.1/10 (64-bit version prefered), or * LINUX, MicrobeMS has been tested under Debian version 10 (codenamed Buster) * Matlab R2014a (The Mathworks) or newer * The Statistics and the Bioinformatics Toolbox of Matlab (the latter toolbox will be required only for mzXML data import). * MicrobeMS will be installed as a Matlab t..." current
11:1311:13, 18 March 2023 diff hist +4,867‎ N MicrobeMS - A Matlab Toolbox for Microbial Identification Based on Mass Spectrometry ‎ Created page with "== Introduction == The MicrobeMS software package is a program specifically designed for the analysis of MALDI-TOF mass spectra of microbial samples. The MicrobeMS software was developed by [http://www.peter-lasch.de: Peter Lasch] at the [http://www.rki.de/EN/Home/homepage_node.html: Robert-Koch-Institute (RKI)] in Berlin/Germany and can be used to identify microbial strains and species based on their mass spectral patterns. The program is a comprehensive [http://www.ma..."
11:1211:12, 18 March 2023 diff hist −657‎ Main Page ‎ Redirected page to MicrobeMS - A Matlab Toolbox for Microbial Identification Based on Mass Spectrometry current Tag: New redirect

User contributions for Laschp

18 March 2023

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