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nistAutoSearch

This repository provides tools to perform library searches against electron ionization mass spectral (EI-MS) databases using the API provided by NIST MS Search software. It includes R scripts for:

1. Automating spectral library searches.
2. Processing mass spectral data in MSP (NIST) format.
3. Handling large datasets by splitting lists into manageable blocks.
4. Automatic MSP (NIST) file itergrity fix.
5. Exporting search results and processed data to CSV files.
6. Automatic installation all dependencies.

How to run the tool

Run the Tool

1. Start the tool by running the launcher.bat file.
2. Make sure the NIST MS Search program is installed in its deafult location (C:\NIST$\MSSEARCH) and running.
3. NIST MS Search must be open and ready to communicate with its API.
4. Make sure the launcher can locate the R engine. You need to specify the path to the R executable in the launcher.bat file. Update the following line if you have an alterantive path:

rem path to R.exe folder
set "R_location=C:\Program Files"

Enable Automatic Search

1. In NIST MS Search, navigate to Options -> Library Search Options menu -> Automation tab.
2. Enable Automatic Search On to allow the tool to communicate with the NIST MS Search API.

Set the Number of Hits to Print

1. In the Automation tab of the Library Search options, find the Number of hits to print field.
2. Adjust this value to control how many search results are displayed for each query.
3. Let the tool perform the analysis of your input MSP (NIST) data automatically.

Once configured, the tool will automate spectral library searches, process your mass spectral data, and export results as needed.

Output csv table:

rda name	name	mf	rmf	prob	lib	cas	formula	mw	id	ri
input metabolite name	nist metabolite name	match score	reverse match score	probability	library	cas #	formula	molecular weight	id #	retention index

nistAutoSearch tool requires listed open source CRAN packages: mssearchr