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== 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 [https://www.rki.de 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.mathworks.com: Matlab]-based package that operates under Windows 7/8/8.1/10/11 and LINUX (Debian, MicrobeMS versions later than 0.81). Original MALDI-TOF mass spectra in the format defined by [http://www.bdal.com: Bruker Daltonics] or by [http://www.shimadzu.com: Shimadzu] (via the mzXML data format) can be imported, processed and converted into a Matlab data matrix format specific to the MicrobeMS program. | |||
The software allows standard mass spectrometry manipulations such as smoothing, baseline correction, normalization, peak detection, auto-calibration and some other functions. Since the software also runs in a full Windows or LINUX 64-bit environment, the number of spectra in the data sets is limited only by the amount of available memory (RAM).<br> | |||
== Getting Started == | |||
* [[computer_specification|Specification of computer configuration]] | |||
* [[Screenshot_of_MicrobeMS|Screenshot of MicrobeMS]] | |||
* [[download_MicrobeMS|Downloading MicrobeMS]] | |||
* [[install_MicrobeMS|How to install MicrobeMS]] | |||
* [[MicrobeMS_Wiki:General_disclaimer |License conditions]] | |||
* [[How_to_Obtain_a_License|How to obtain a license?]] | |||
* [[Mass Spectrometry Databases|Mass spectrometry databases]] | |||
* [[Publications_with_MicrobeMS|Acknowledgements, relevant publications]] | |||
* [[Frequently_Asked_Questions_(FAQ)|Frequently asked questions (FAQ)]] | |||
== Preparing Mass Spectra == | |||
* [[Adding / Editing Metadata of MALDI-TOF Mass Spectral Data|Adding / editing metadata of MS data files]] | |||
* [[Management of Sample Information|Management of sample information (spectral metadata)]] (taxonomic information, culture conditions, sample preparation methods, etc.) | |||
== Description of the Data File Formats == | |||
* [[Data_Format_of_Spectral_Multifiles|Description of the format of spectral multifiles (*.muf)]] | |||
* [[Data_Format_of_Peak_List_Files|Description of the format of peak list files (*.pkf)]] | |||
* [[Description of MicrobeMS' main parameter file 'microbems.opt'|Description of the parameter file 'microbems.opt']] | |||
== Import and Export of Mass Spectra and Mass Spectral Libraries == | |||
* [[Load spectra (Bruker format)|Load spectral data files]] acquired by using Bruker's mass spectrometers | |||
* [[Data_Format_of_Spectral_Multifiles|Load / store spectral multifiles (*.muf)]] | |||
* [[Data_Format_of_Peak_List_Files|Load / store peak list files (*.pkf)]] | |||
* [[Store spectra (Bruker format)|Store spectra in a Bruker-specific data format]] | |||
* [[Export spectra to ASCII|Store spectra in a standard ASCII data format]] (export to ASCII) | |||
* [[Store spectra (NeuroDeveloper format)|Store peaklist data in a format specific to the NeuroDeveloper software]] (export to NeuroDeveloper) | |||
* [[Import Mass Spectra in a mzXML Data Format|Import mass spectral data from mzXML data]] (allows importing spectra from Shimadzu/bioMérieux systems) | |||
== Spectral Analysis and Visualization == | |||
* [[Spectral Pre-processing|Spectral pre-processing]]: smoothing, baseline correction, normalization, cut, auto-calibration, data reduction | |||
* [[Peak Detection|Peak detection]] | |||
* [[Averaging Mass Spectra|Averaging mass spectra]] | |||
* [[Class Assignment|Class assignment]] | |||
* [[Display MS Metadata|Display spectral metadata]] | |||
* [[The Log-File (logfile.txt)|The log-file]] (logfile.txt) | |||
== Identification and Classification == | |||
* [[Unsupervised Hierarchical Cluster Analysis|Unsupervised hierarchical cluster analysis]] | |||
* [[Create database spectra|Creating database spectra from individual microbial mass spectra]] | |||
* Compiling mass spectral databases | |||
* [[Microbial Identification based on Mass Spectral Libraries and Interspectral Distances|Microbial identification based on mass spectral libraries and interspectral distances]] | |||
* [[Identification Analysis by Neural Networks|Identification analysis by artificial neural networks (ANN,]] requires the NeuroDeveloper software package from [http://www.synthon-analytics.de: Synthon Analytics]) | |||
* [[Identification Analysis by Means of LC-MS¹ and ''in silico'' Databases|Identification analysis by means of LC-MS¹ and ''in silico'' databases]] | |||
== Identification of MS Biomarker Peaks == | |||
* Generation of [[Creating Pseudo-Gel Views|pseudo-gel views]] from microbial mass spectra | |||
* [[Peak Frequency Test|Peak frequency tests]] | |||
* [[Two-samples t-Tests|Two-samples t-tests]] | |||
* [[Wilcoxon Rank-Sum Test|Wilcoxon rank-sum tests]] |
Latest revision as of 15:52, 21 March 2023
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 Peter Lasch at the 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 Matlab-based package that operates under Windows 7/8/8.1/10/11 and LINUX (Debian, MicrobeMS versions later than 0.81). Original MALDI-TOF mass spectra in the format defined by Bruker Daltonics or by Shimadzu (via the mzXML data format) can be imported, processed and converted into a Matlab data matrix format specific to the MicrobeMS program.
The software allows standard mass spectrometry manipulations such as smoothing, baseline correction, normalization, peak detection, auto-calibration and some other functions. Since the software also runs in a full Windows or LINUX 64-bit environment, the number of spectra in the data sets is limited only by the amount of available memory (RAM).
Getting Started
- Specification of computer configuration
- Screenshot of MicrobeMS
- Downloading MicrobeMS
- How to install MicrobeMS
- License conditions
- How to obtain a license?
- Mass spectrometry databases
- Acknowledgements, relevant publications
- Frequently asked questions (FAQ)
Preparing Mass Spectra
- Adding / editing metadata of MS data files
- Management of sample information (spectral metadata) (taxonomic information, culture conditions, sample preparation methods, etc.)
Description of the Data File Formats
- Description of the format of spectral multifiles (*.muf)
- Description of the format of peak list files (*.pkf)
- Description of the parameter file 'microbems.opt'
Import and Export of Mass Spectra and Mass Spectral Libraries
- Load spectral data files acquired by using Bruker's mass spectrometers
- Load / store spectral multifiles (*.muf)
- Load / store peak list files (*.pkf)
- Store spectra in a Bruker-specific data format
- Store spectra in a standard ASCII data format (export to ASCII)
- Store peaklist data in a format specific to the NeuroDeveloper software (export to NeuroDeveloper)
- Import mass spectral data from mzXML data (allows importing spectra from Shimadzu/bioMérieux systems)
Spectral Analysis and Visualization
- Spectral pre-processing: smoothing, baseline correction, normalization, cut, auto-calibration, data reduction
- Peak detection
- Averaging mass spectra
- Class assignment
- Display spectral metadata
- The log-file (logfile.txt)
Identification and Classification
- Unsupervised hierarchical cluster analysis
- Creating database spectra from individual microbial mass spectra
- Compiling mass spectral databases
- Microbial identification based on mass spectral libraries and interspectral distances
- Identification analysis by artificial neural networks (ANN, requires the NeuroDeveloper software package from Synthon Analytics)
- Identification analysis by means of LC-MS¹ and in silico databases
Identification of MS Biomarker Peaks
- Generation of pseudo-gel views from microbial mass spectra
- Peak frequency tests
- Two-samples t-tests
- Wilcoxon rank-sum tests
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