User contributions for Laschp
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18 March 2023
- 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
