User contributions for Laschp

7 March 2024

• 12:0012:00, 7 March 2024 diff hist +1‎ Identification Analysis by Means of LC-MS¹ and ''in silico'' Databases ‎ →‎Requirements current
• 11:5911:59, 7 March 2024 diff hist +37‎ m Publications with MicrobeMS ‎No edit summary current
• 11:5711:57, 7 March 2024 diff hist −4‎ m Publications with MicrobeMS ‎ →‎Relevant publications
• 11:5711:57, 7 March 2024 diff hist +11‎ Publications with MicrobeMS ‎ →‎Relevant publications
• 11:5411:54, 7 March 2024 diff hist −109‎ Publications with MicrobeMS ‎ →‎Relevant publications
• 11:5311:53, 7 March 2024 diff hist −1,312‎ Publications with MicrobeMS ‎ →‎Relevant publications
• 11:4311:43, 7 March 2024 diff hist +3,346‎ Publications with MicrobeMS ‎ →‎Relevant publications

21 March 2023

• 18:0218:02, 21 March 2023 diff hist +388‎ Frequently Asked Questions (FAQ) ‎ →‎I have installed MicrobeMS, but I would like to use also spectral databases current
• 17:5317:53, 21 March 2023 diff hist +2‎ Identification Analysis by Means of LC-MS¹ and ''in silico'' Databases ‎ →‎Introduction
• 17:5017:50, 21 March 2023 diff hist +6‎ m Frequently Asked Questions (FAQ) ‎ →‎I have installed MicrobeMS, but I would like to use also spectral databases
• 17:4917:49, 21 March 2023 diff hist +177‎ Frequently Asked Questions (FAQ) ‎ →‎I have installed MicrobeMS, but I would like to use also spectral databases
• 17:4517:45, 21 March 2023 diff hist +283‎ Publications with MicrobeMS ‎ →‎Relevant publications
• 17:3717:37, 21 March 2023 diff hist +332‎ m Publications with MicrobeMS ‎ →‎Relevant publications
• 17:3417:34, 21 March 2023 diff hist +7‎ m Create database spectra ‎ →‎Producing database spectra current
• 17:3217:32, 21 March 2023 diff hist −11‎ m Data Format of Spectral Multifiles ‎No edit summary current
• 17:3117:31, 21 March 2023 diff hist −11‎ Data Format of Peak List Files ‎No edit summary current
• 17:3017:30, 21 March 2023 diff hist −1‎ m Download MicrobeMS ‎ →‎Test Spectra and Databases current
• 17:3017:30, 21 March 2023 diff hist −18‎ Download MicrobeMS ‎ →‎Test Spectra and Databases
• 17:2717:27, 21 March 2023 diff hist +21‎ m The Log-File (logfile.txt) ‎No edit summary current
• 17:2517:25, 21 March 2023 diff hist +1‎ The Log-File (logfile.txt) ‎No edit summary
• 15:5415:54, 21 March 2023 diff hist −22‎ Mass Spectrometry Databases ‎ →‎MALDI-TOF MS databases current
• 15:5215:52, 21 March 2023 diff hist −84‎ m MicrobeMS - A Matlab Toolbox for Microbial Identification Based on Mass Spectrometry ‎ →‎Introduction current
• 15:5115:51, 21 March 2023 diff hist −27‎ m MicrobeMS - A Matlab Toolbox for Microbial Identification Based on Mass Spectrometry ‎ →‎Introduction
• 15:4515:45, 21 March 2023 diff hist −32‎ m Download MicrobeMS ‎ →‎Test Spectra and Databases
• 15:4315:43, 21 March 2023 diff hist −4‎ Download MicrobeMS ‎ →‎MicrobeMS pcode (Windows and Linux)
• 15:4015:40, 21 March 2023 diff hist −8‎ m Download MicrobeMS ‎ →‎MicrobeMS stand-alone (Windows)
• 15:3915:39, 21 March 2023 diff hist −2‎ Download MicrobeMS ‎No edit summary
• 15:2115:21, 21 March 2023 diff hist −3‎ m Mass Spectrometry Databases ‎ →‎Introduction
• 15:2015:20, 21 March 2023 diff hist +3‎ Mass Spectrometry Databases ‎ →‎Introduction
• 15:1915:19, 21 March 2023 diff hist −3‎ Mass Spectrometry Databases ‎ →‎Introduction
• 15:1415:14, 21 March 2023 diff hist +15‎ Mass Spectrometry Databases ‎ →‎MALDI-TOF MS databases
• 15:1215:12, 21 March 2023 diff hist +3‎ m Mass Spectrometry Databases ‎ →‎LC-MS¹ databases
• 15:1115:11, 21 March 2023 diff hist +89‎ Mass Spectrometry Databases ‎ →‎MALDI-TOF MS databases
• 15:0915:09, 21 March 2023 diff hist −2‎ m MicrobeMS Wiki:General disclaimer ‎No edit summary current
• 15:0815:08, 21 March 2023 diff hist +1‎ m MicrobeMS Wiki:General disclaimer ‎No edit summary
• 15:0715:07, 21 March 2023 diff hist +1‎ m MicrobeMS Wiki:General disclaimer ‎No edit summary
• 15:0515:05, 21 March 2023 diff hist +53‎ MicrobeMS Wiki:General disclaimer ‎No edit summary
• 15:0415:04, 21 March 2023 diff hist +434‎ Mass Spectrometry Databases ‎ →‎MALDI-TOF MS databases
• 14:5914:59, 21 March 2023 diff hist +549‎ N MicrobeMS Wiki:General disclaimer ‎ Created page with "You are using MicrobeMS at your own risk! There is no responsibility for damages, problems etc. resulting from use of this code. Furthermore, there is also no warranty for bug-free operation, fitness for a particular purpose or the appropriate behavior of the program. Please report software bugs, inconsistencies or suggestions for new functions to lasch at microbe-ms.com. The software is distributed under the CC BY-NC-SA 4.0 license (Creative Commons Attribution-NonComm..."

18 March 2023

• 13:5013:50, 18 March 2023 diff hist +1‎ m Peak Detection ‎ →‎Peak picking - basic concepts current
• 13:4913:49, 18 March 2023 diff hist 0‎ N File:View-peak-list.jpg ‎No edit summary current
• 13:4913:49, 18 March 2023 diff hist 0‎ N File:Threshold-for-peak-picking.jpg ‎No edit summary current
• 13:4813:48, 18 March 2023 diff hist 0‎ N File:Peak-pick.jpg ‎No edit summary current
• 13:4713:47, 18 March 2023 diff hist 0‎ m Identification Analysis by Neural Networks ‎No edit summary current
• 13:4613:46, 18 March 2023 diff hist 0‎ m Identification Analysis by Neural Networks ‎ →‎Classification
• 13:4613:46, 18 March 2023 diff hist 0‎ m Identification Analysis by Neural Networks ‎No edit summary
• 13:4513:45, 18 March 2023 diff hist 0‎ N File:Ann-html.jpg ‎No edit summary current
• 13:4513:45, 18 March 2023 diff hist 0‎ N File:Ann-text.jpg ‎No edit summary current
• 13:4513:45, 18 March 2023 diff hist 0‎ N File:Ann-settings.jpg ‎No edit summary current
• 13:4413:44, 18 March 2023 diff hist 0‎ N File:Ann-main-figure.jpg ‎No edit summary current
• 13:4413:44, 18 March 2023 diff hist 0‎ N File:Synthon-logo.jpg ‎No edit summary current
• 13:4213:42, 18 March 2023 diff hist 0‎ N File:Wilcox-test-plot.jpg ‎No edit summary current
• 13:4113:41, 18 March 2023 diff hist 0‎ m Microbial Identification based on Mass Spectral Libraries and Interspectral Distances ‎No edit summary current Tag: Manual revert
• 13:4013:40, 18 March 2023 diff hist 0‎ N File:Compr-html.jpg ‎No edit summary current
• 13:3913:39, 18 March 2023 diff hist 0‎ N File:Compr-txt.jpg ‎No edit summary current
• 13:3313:33, 18 March 2023 diff hist 0‎ m Microbial Identification based on Mass Spectral Libraries and Interspectral Distances ‎No edit summary Tag: Reverted
• 13:3113:31, 18 March 2023 diff hist 0‎ N File:Cmpr-main-figure.jpg ‎No edit summary current
• 13:3113:31, 18 March 2023 diff hist 0‎ m Microbial Identification based on Mass Spectral Libraries and Interspectral Distances ‎No edit summary
• 13:3013:30, 18 March 2023 diff hist 0‎ m Data Format of Peak List Files ‎No edit summary
• 12:0412:04, 18 March 2023 diff hist 0‎ N File:Peak-frequency-plot.jpg ‎No edit summary current
• 12:0112:01, 18 March 2023 diff hist 0‎ N File:Readlcmsres.jpg ‎No edit summary current
• 11:5911:59, 18 March 2023 diff hist 0‎ N File:Cmpr-main-figure-linux.jpg ‎No edit summary current
• 11:5711:57, 18 March 2023 diff hist 0‎ N File:UHCA.jpg ‎No edit summary current
• 11:5611:56, 18 March 2023 diff hist 0‎ N File:Command-line-window.jpg ‎No edit summary current
• 11:5511:55, 18 March 2023 diff hist 0‎ N File:T-test-plot.jpg ‎No edit summary current
• 11:5411:54, 18 March 2023 diff hist 0‎ N File:T-test.jpg ‎No edit summary current
• 11:5411:54, 18 March 2023 diff hist 0‎ N File:Gel-view.jpg ‎No edit summary current
• 11:5411:54, 18 March 2023 diff hist 0‎ N File:Redes.jpg ‎No edit summary current
• 11:5311:53, 18 March 2023 diff hist 0‎ N File:Autocalibrate.jpg ‎No edit summary current
• 11:5311:53, 18 March 2023 diff hist 0‎ N File:Cut.jpg ‎No edit summary current
• 11:5211:52, 18 March 2023 diff hist 0‎ N File:Load-mzXML.jpg ‎No edit summary current
• 11:5211:52, 18 March 2023 diff hist 0‎ N File:ExportToND.jpg ‎No edit summary current
• 11:5111:51, 18 March 2023 diff hist 0‎ N File:Exportascii.jpg ‎No edit summary current
• 11:5011:50, 18 March 2023 diff hist 0‎ N File:Peaklist-format-C-struc.jpg ‎No edit summary current
• 11:4911:49, 18 March 2023 diff hist 0‎ N File:Load-Bruker.jpg ‎No edit summary current
• 11:4911:49, 18 March 2023 diff hist 0‎ N File:Array-spec-dbs.jpg ‎No edit summary current
• 11:4811:48, 18 March 2023 diff hist 0‎ N File:Array-spec-avr.jpg ‎No edit summary current
• 11:4811:48, 18 March 2023 diff hist 0‎ N File:Array-spec-ccl.jpg ‎No edit summary current
• 11:4411:44, 18 March 2023 diff hist 0‎ N File:Multifile-format-spec-struc.jpg ‎No edit summary current
• 11:4111:41, 18 March 2023 diff hist 0‎ N File:Batch-dbspectra.jpg ‎No edit summary current
• 11:4111:41, 18 March 2023 diff hist 0‎ N File:Edit-header-info.jpg ‎No edit summary current
• 11:4011:40, 18 March 2023 diff hist 0‎ N File:MicrobeMS-Main-Figure.jpg ‎No edit summary current
• 11:4011:40, 18 March 2023 diff hist 0‎ N File:Edit-comment-III.jpg ‎No edit summary current
• 11:3911:39, 18 March 2023 diff hist 0‎ N File:Edit-comment-II.jpg ‎No edit summary current
• 11:3911:39, 18 March 2023 diff hist 0‎ N File:Edit-comment-I.jpg ‎No edit summary current
• 11:3811:38, 18 March 2023 diff hist 0‎ N File:Assign-id.jpg ‎No edit summary current
• 11:3511:35, 18 March 2023 diff hist +1,087‎ N Import Mass Spectra in a mzXML Data Format ‎ Created page with "400px|thumb|right|Import of mass spectral data files in the mzXML format This function allows loading of spectral data files stored in a [https://en.wikipedia.org/wiki/Mass_spectrometry_data_format#mzXML mzXML data format] which in principle allows analyzing also data obtained by the [http://www.biomerieux-diagnostics.com/vitek-ms VITEK® MS solution from bioMérieux]. The mzXML import function of MicrobeMS is based on the Matlab routine [htt..." current
• 11:3511:35, 18 March 2023 diff hist +3,338‎ N Store spectra (NeuroDeveloper format) ‎ Created page with "right|The dialog box ''export to NeuroDeveloper'' This function allows storing mass spectral data in a format which can be imported by the NeuroDeveloper software. The NeuroDeveloper is a software for teaching and validating artificial neural network models using spectra from various origins (e.g. IR, Raman, or mass spectra). The function ''export to NeuroDeveloper'' is available from the ''File'' menu bar and can be used for converting peak tabl..." current
• 11:3411:34, 18 March 2023 diff hist +1,162‎ N Export spectra to ASCII ‎ Created page with "This function allows storing mass spectral data in a standard two-column ASCII data format. The function ''export ASCII'' is available from the ''File'' menu bar and can be used to export individual original or pre-processed mass spectra (not peaklists!). Select first the spectra to be exported from the listbox denoted with ''MicrobeMS spectra ID`s'' and chose then ''export ASCII'' → ''original spectra'' or ''pre-processed spectra''. This will open a standard file b..." current
• 11:3411:34, 18 March 2023 diff hist +173‎ N Store spectra (Bruker format) ‎ Created page with "This function allows storing mass spectral data in the native Bruker spectra data format. Note that this function is still experimental - it should be used only for testing." current
• 11:3311:33, 18 March 2023 diff hist +946‎ N Load spectra (Bruker format) ‎ Created page with "520px|thumb|right|Select multiple directories for direct loading of MALDI-TOF mass spectra in a Bruker specific data format This function allows loading of spectral data files stored in a Bruker-specific data format. The function ''load spectra'' is available from the ''File'' menu bar and can be called also by using the shortcut key <Ctrl>+<L>. When pressing the button ''load'' the function is loading all spectra present in subdirectories of th..." current
• 11:3211:32, 18 March 2023 diff hist +5,024‎ N Wilcoxon Rank-Sum Test ‎ Created page with "__FORCETOC__ == Introduction == right|input parameters for univariate t-tests| [https://en.wikipedia.org/wiki/Wilcoxon_signed-rank_test| Wilcoxon rank-sum test] (Wikipedia) To be continued == Parameter of the Wilcoxon rank-sum test == * m/z range: boundaries of the m/z region in which the Wilcoxon rank-sum tests are performed * α: significance level of the Wilcoxon rank-sum test * dx (ppm): a parameter defining the width and the number of..." current
• 11:3211:32, 18 March 2023 diff hist +5,401‎ N Two-samples t-Tests ‎ Created page with "__FORCETOC__ == Introduction == right| input parameters for univariate t-tests| This function performs two-samples t-tests in each segment of the MALDI-TOF mass spectra using peak tables as inputs. t-tests are useful for biomarker screening in ensembles of mass spectra exhibiting certain degree of similarity. A two-samples t-test in a given m/z segment returns a test decision for the null hypothesis H(0) that the peak intensity data in class I and c..." current
• 11:3111:31, 18 March 2023 diff hist +5,335‎ N Peak Frequency Test ‎ Created page with "== Introduction == Peak frequency tests are useful for biomarker screening in ensembles of mass spectra exhibiting certain degree of similarity. These tests require pre-processed spectra with valid peak tables as inputs and are suitable to systematically determine the number of peaks and their relative abundance throughout the spectral m/z intervals. For peak frequency tests it is required to compile a mass spectral data set and to perform pre-processing including peak..." current
• 11:3111:31, 18 March 2023 diff hist +2,669‎ N Creating Pseudo-Gel Views ‎ Created page with "When dealing with large spectral databases which sometimes comprise hundreds of individual mass spectra, data inspection and data assessment cannot be done by manual screening of the individual spectra alone. In these instances simulated pseudo-gel views for visual analysis of the data set are popular means. In gel view representations, spectral peak intensities are converted to color, or gray scales and plotted as a function of the m/z values. Gel views are usually gene..." current
• 11:3011:30, 18 March 2023 diff hist +4,631‎ N Identification Analysis by Neural Networks ‎ Created page with "__FORCETOC__ == Introduction == The function ''Identification by Neural Networks'' is basically an interface between MicrobeMS and Synthon's NeuroDeveloper™, a software for teaching and validating ANN models with microbial mass spectra. Based on pre-defined neural network models, the interface can be used to classify mass spectra into pre-defined categories (i.e. microbial genera, species, subspecies, etc.). Spectral pre-processing, features selection and ANN cla..."
• 11:3011:30, 18 March 2023 diff hist +20,521‎ N Microbial Identification based on Mass Spectral Libraries and Interspectral Distances ‎ Created page with " == Introduction == * In the MicrobeMS software package microbial identification based on mass spectral libraries and interspectral distances, or similarity measures such as D-values, is carried out by means of the subfunction cmpr ('''c'''o'''mp'''a'''r'''e). The cmpr function is available from the ''Analysis'' menu bar (select ''compare with database''), or by pressing the button ''compare with DB'' in the ''ANALYSIS'' tab (see Screenshot_of_MicrobeMS|Screenshot of..."
• 11:2911:29, 18 March 2023 diff hist +3,841‎ N Create database spectra ‎ Created page with "== Introduction == Database spectra are the preferred type of database entries in MicrobeMS. Such database spectra constitute the spectral references of a microbial library. Ideally database spectra are obtained from multiple measurements of the bacterial isolate under study in order to cover the spectral variability contained in the spectra of biological and technical replicates. The concept of database spectra involves automated generation of peak tables from spectra..."
• 11:2911:29, 18 March 2023 diff hist +5,985‎ N Unsupervised Hierarchical Cluster Analysis ‎ Created page with "__FORCETOC__ == Introduction == Because of its simplicity and ease of interpretation agglomerative unsupervised hierarchical cluster analysis (UHCA) enjoys great popularity for analysis of microbial mass spectra. Agglomerative UHCA is a method of cluster analysis in which a ''bottom up'' approach is used to obtain a hierarchy of clusters. The main idea of UHCA is to organize patterns (spectra) into meaningful or useful groups using some type of similarity measure. The..." current
• 11:2811:28, 18 March 2023 diff hist +1,295‎ N The Log-File (logfile.txt) ‎ Created page with "When starting MicrobeMS the main window and a command line window (see screen shot below) will appear. While the main window allows to interact with the program, the command line window shows input parameters and displays non-standard errors. These messages are stored in a log-file (''logfile.txt''), which can be found in the following directories: MicrobeMS '''standalone version''', Windows operating system (W7/W8/W8.1/W10): user directory, usually ''C:\User..."
• 11:2811:28, 18 March 2023 diff hist +3,276‎ N Display MS Metadata ‎ Created page with "The function ''display MS metadata'' (aka ''display spectra entries'') is available from the ''View'' pulldown menu and allows users to retrieve spectral metadata stored in the MS data files. The requested metadata information will be displayed in the command line window of MicrobeMS. The output of the command line window is stored per default in a logfile (''logfile.txt'', see the log-file for details).<br>   <br> To retrieve the met..." current
• 11:2711:27, 18 March 2023 diff hist +1,211‎ N Class Assignment ‎ Created page with "Class assignment, or '''labelling''' of individual mass spectra is a procedure in which selected spectra are grouped by an operator. The class assignment procedure is a prerequisite for the following functions of the MicrobeMS program: * Averaging mass spectra * Create database spectra from individual microbial mass spectra * Peak frequency tests * Two-samples t-tests..." current
• 11:2711:27, 18 March 2023 diff hist +2,098‎ N Averaging Mass Spectra ‎ Created page with "Various reasons exist to create average, or mean spectra, from individual mass spectra. First and foremost, averaging allows to improve the spectral signal-to-noise ratio (SNR). A second goal of spectra averaging is to eliminate the degree of spectral variability when measuring spatially inhomogeneous samples from different sample spots. Finally, spectra averaging may be useful when prepraring illustrations for presentations or scientific publications. '''IMPORTANT''':..." current
• 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.<br> 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. <br> 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):<br> * 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) ==  <br> <b>Prerequisites</b> 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. <br> 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) === <font color="red">'''NEW'''</font> - 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 "<b> Pcode toolbox of the MicrobeMS software (v.082)</b> * 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