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7 March 2024
- 11:0011:00, 7 March 2024 diff hist +1 Identification Analysis by Means of LC-MS¹ and ''in silico'' Databases →Requirements current
- 10:5910:59, 7 March 2024 diff hist +37 m Publications with MicrobeMS No edit summary current
- 10:5710:57, 7 March 2024 diff hist −4 m Publications with MicrobeMS →Relevant publications
- 10:5710:57, 7 March 2024 diff hist +11 Publications with MicrobeMS →Relevant publications
- 10:5410:54, 7 March 2024 diff hist −109 Publications with MicrobeMS →Relevant publications
- 10:5310:53, 7 March 2024 diff hist −1,312 Publications with MicrobeMS →Relevant publications
- 10:4310:43, 7 March 2024 diff hist +3,346 Publications with MicrobeMS →Relevant publications
21 March 2023
- 17:0217:02, 21 March 2023 diff hist +388 Frequently Asked Questions (FAQ) →I have installed MicrobeMS, but I would like to use also spectral databases current
- 16:5316:53, 21 March 2023 diff hist +2 Identification Analysis by Means of LC-MS¹ and ''in silico'' Databases →Introduction
- 16:5016:50, 21 March 2023 diff hist +6 m Frequently Asked Questions (FAQ) →I have installed MicrobeMS, but I would like to use also spectral databases
- 16:4916:49, 21 March 2023 diff hist +177 Frequently Asked Questions (FAQ) →I have installed MicrobeMS, but I would like to use also spectral databases
- 16:4516:45, 21 March 2023 diff hist +283 Publications with MicrobeMS →Relevant publications
- 16:3716:37, 21 March 2023 diff hist +332 m Publications with MicrobeMS →Relevant publications
- 16:3416:34, 21 March 2023 diff hist +7 m Create database spectra →Producing database spectra current
- 16:3216:32, 21 March 2023 diff hist −11 m Data Format of Spectral Multifiles No edit summary current
- 16:3116:31, 21 March 2023 diff hist −11 Data Format of Peak List Files No edit summary current
- 16:3016:30, 21 March 2023 diff hist −1 m Download MicrobeMS →Test Spectra and Databases current
- 16:3016:30, 21 March 2023 diff hist −18 Download MicrobeMS →Test Spectra and Databases
- 16:2716:27, 21 March 2023 diff hist +21 m The Log-File (logfile.txt) No edit summary current
- 16:2516:25, 21 March 2023 diff hist +1 The Log-File (logfile.txt) No edit summary
- 14:5414:54, 21 March 2023 diff hist −22 Mass Spectrometry Databases →MALDI-TOF MS databases current
- 14:5214:52, 21 March 2023 diff hist −84 m MicrobeMS - A Matlab Toolbox for Microbial Identification Based on Mass Spectrometry →Introduction current
- 14:5114:51, 21 March 2023 diff hist −27 m MicrobeMS - A Matlab Toolbox for Microbial Identification Based on Mass Spectrometry →Introduction
- 14:4514:45, 21 March 2023 diff hist −32 m Download MicrobeMS →Test Spectra and Databases
- 14:4314:43, 21 March 2023 diff hist −4 Download MicrobeMS →MicrobeMS pcode (Windows and Linux)
- 14:4014:40, 21 March 2023 diff hist −8 m Download MicrobeMS →MicrobeMS stand-alone (Windows)
- 14:3914:39, 21 March 2023 diff hist −2 Download MicrobeMS No edit summary
- 14:2114:21, 21 March 2023 diff hist −3 m Mass Spectrometry Databases →Introduction
- 14:2014:20, 21 March 2023 diff hist +3 Mass Spectrometry Databases →Introduction
- 14:1914:19, 21 March 2023 diff hist −3 Mass Spectrometry Databases →Introduction
- 14:1414:14, 21 March 2023 diff hist +15 Mass Spectrometry Databases →MALDI-TOF MS databases
- 14:1214:12, 21 March 2023 diff hist +3 m Mass Spectrometry Databases →LC-MS¹ databases
- 14:1114:11, 21 March 2023 diff hist +89 Mass Spectrometry Databases →MALDI-TOF MS databases
- 14:0914:09, 21 March 2023 diff hist −2 m MicrobeMS Wiki:General disclaimer No edit summary current
- 14:0814:08, 21 March 2023 diff hist +1 m MicrobeMS Wiki:General disclaimer No edit summary
- 14:0714:07, 21 March 2023 diff hist +1 m MicrobeMS Wiki:General disclaimer No edit summary
- 14:0514:05, 21 March 2023 diff hist +53 MicrobeMS Wiki:General disclaimer No edit summary
- 14:0414:04, 21 March 2023 diff hist +434 Mass Spectrometry Databases →MALDI-TOF MS databases
- 13:5913:59, 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
- 12:5012:50, 18 March 2023 diff hist +1 m Peak Detection →Peak picking - basic concepts current
- 12:4912:49, 18 March 2023 diff hist 0 N File:View-peak-list.jpg No edit summary current
- 12:4912:49, 18 March 2023 diff hist 0 N File:Threshold-for-peak-picking.jpg No edit summary current
- 12:4812:48, 18 March 2023 diff hist 0 N File:Peak-pick.jpg No edit summary current
- 12:4712:47, 18 March 2023 diff hist 0 m Identification Analysis by Neural Networks No edit summary current
- 12:4612:46, 18 March 2023 diff hist 0 m Identification Analysis by Neural Networks →Classification
- 12:4612:46, 18 March 2023 diff hist 0 m Identification Analysis by Neural Networks No edit summary
- 12:4512:45, 18 March 2023 diff hist 0 N File:Ann-html.jpg No edit summary current
- 12:4512:45, 18 March 2023 diff hist 0 N File:Ann-text.jpg No edit summary current
- 12:4512:45, 18 March 2023 diff hist 0 N File:Ann-settings.jpg No edit summary current
- 12:4412:44, 18 March 2023 diff hist 0 N File:Ann-main-figure.jpg No edit summary current
- 12:4412:44, 18 March 2023 diff hist 0 N File:Synthon-logo.jpg No edit summary current
- 12:4212:42, 18 March 2023 diff hist 0 N File:Wilcox-test-plot.jpg No edit summary current
- 12:4112:41, 18 March 2023 diff hist 0 m Microbial Identification based on Mass Spectral Libraries and Interspectral Distances No edit summary current Tag: Manual revert
- 12:4012:40, 18 March 2023 diff hist 0 N File:Compr-html.jpg No edit summary current
- 12:3912:39, 18 March 2023 diff hist 0 N File:Compr-txt.jpg No edit summary current
- 12:3312:33, 18 March 2023 diff hist 0 m Microbial Identification based on Mass Spectral Libraries and Interspectral Distances No edit summary Tag: Reverted
- 12:3112:31, 18 March 2023 diff hist 0 N File:Cmpr-main-figure.jpg No edit summary current
- 12:3112:31, 18 March 2023 diff hist 0 m Microbial Identification based on Mass Spectral Libraries and Interspectral Distances No edit summary
- 12:3012:30, 18 March 2023 diff hist 0 m Data Format of Peak List Files No edit summary
- 11:0411:04, 18 March 2023 diff hist 0 N File:Peak-frequency-plot.jpg No edit summary current
- 11:0111:01, 18 March 2023 diff hist 0 N File:Readlcmsres.jpg No edit summary current
- 10:5910:59, 18 March 2023 diff hist 0 N File:Cmpr-main-figure-linux.jpg No edit summary current
- 10:5710:57, 18 March 2023 diff hist 0 N File:UHCA.jpg No edit summary current
- 10:5610:56, 18 March 2023 diff hist 0 N File:Command-line-window.jpg No edit summary current
- 10:5510:55, 18 March 2023 diff hist 0 N File:T-test-plot.jpg No edit summary current
- 10:5410:54, 18 March 2023 diff hist 0 N File:T-test.jpg No edit summary current
- 10:5410:54, 18 March 2023 diff hist 0 N File:Gel-view.jpg No edit summary current
- 10:5410:54, 18 March 2023 diff hist 0 N File:Redes.jpg No edit summary current
- 10:5310:53, 18 March 2023 diff hist 0 N File:Autocalibrate.jpg No edit summary current
- 10:5310:53, 18 March 2023 diff hist 0 N File:Cut.jpg No edit summary current
- 10:5210:52, 18 March 2023 diff hist 0 N File:Load-mzXML.jpg No edit summary current
- 10:5210:52, 18 March 2023 diff hist 0 N File:ExportToND.jpg No edit summary current
- 10:5110:51, 18 March 2023 diff hist 0 N File:Exportascii.jpg No edit summary current
- 10:5010:50, 18 March 2023 diff hist 0 N File:Peaklist-format-C-struc.jpg No edit summary current
- 10:4910:49, 18 March 2023 diff hist 0 N File:Load-Bruker.jpg No edit summary current
- 10:4910:49, 18 March 2023 diff hist 0 N File:Array-spec-dbs.jpg No edit summary current
- 10:4810:48, 18 March 2023 diff hist 0 N File:Array-spec-avr.jpg No edit summary current
- 10:4810:48, 18 March 2023 diff hist 0 N File:Array-spec-ccl.jpg No edit summary current
- 10:4410:44, 18 March 2023 diff hist 0 N File:Multifile-format-spec-struc.jpg No edit summary current
- 10:4110:41, 18 March 2023 diff hist 0 N File:Batch-dbspectra.jpg No edit summary current
- 10:4110:41, 18 March 2023 diff hist 0 N File:Edit-header-info.jpg No edit summary current
- 10:4010:40, 18 March 2023 diff hist 0 N File:MicrobeMS-Main-Figure.jpg No edit summary current
- 10:4010:40, 18 March 2023 diff hist 0 N File:Edit-comment-III.jpg No edit summary current
- 10:3910:39, 18 March 2023 diff hist 0 N File:Edit-comment-II.jpg No edit summary current
- 10:3910:39, 18 March 2023 diff hist 0 N File:Edit-comment-I.jpg No edit summary current
- 10:3810:38, 18 March 2023 diff hist 0 N File:Assign-id.jpg No edit summary current
- 10:3510:35, 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
- 10:3510:35, 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
- 10:3410:34, 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
- 10:3410:34, 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
- 10:3310:33, 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
- 10:3210:32, 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
- 10:3210:32, 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
- 10:3110:31, 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
- 10:3110:31, 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
- 10:3010:30, 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..."
- 10:3010:30, 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..."
- 10:2910:29, 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..."
- 10:2910:29, 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
- 10:2810:28, 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..."