MS ANA STANDALONE USAGE INSTRUCTION

MSAna.exe -spec [spectrumFile] -lib [spectrumLibrary] -para [settings.xml]

***Required: -spec spectrumFile ... single .MGF spectrum file or folder with multiple files
	- Specify files with query spectra that will be identified.
	- All search results will be combined in one CSV output file.
	- After completed search the result file will be at the location of the spectra files. 
	
	- SUPPORTED SPECTRUM FILE TYPES: [MGF]
	- You can use MSCONVERT software to convert your data into MGF
	(  https://proteowizard.sourceforge.io/tools/msconvert.html  )

***Required: -lib spectrumLibrary ... single .mgf library file or folder with multiple files
	- Specify files with library spectra that will construct the search space.
	- All library files will be combined to one single target library.
	- A new decoy library is created upon running a search with a library for the first time.

	- SUPPORTED LIBRARY FILE TYPES: [MGF]
	- You can download state-of-the-art spectral libraries from MASSIVE
	(  https://massive.ucsd.edu/ProteoSAFe/static/massive-kb-libraries.jsp  )

***Required: -para settings.xml ... single .xml file with parameter settings
	- Requires MS Ana settings.xml as provided with the download.
	- See settings.xml for search parameters such as match tolerance etc.
	- A new decoy library is created when running a search with changed settings for the first time.


DEFAULT PARAMTERS (used when no arguments are given)

MSAna.exe -spec .\spectra\ -lib .\library\ -para settings.xml


EXAMPLE SEARCH

Download includes small sample data in the .\spectra\ and .\library\ folder.
Execute MS Ana with default parameters to run example search.
After completed search the result file CSV will be in the .\spectra\ folder.


SEARCH RESULT OUTPUT

After completed search a CSV result file MSAnaSearch_XX-XX-XX-XX.csv is created at the location of the searched spectra.

Search results include combined identification results for all query spectrum files and target-decoy search.