View source for MicrobeMS - A Matlab Toolbox for Microbial Identification Based on Mass Spectrometry

== 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-MS&sup1; and ''in silico'' Databases|Identification analysis by means of LC-MS&sup1; 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]]