Nina adding documentation for FastMASST

docs/FastMASST_Nina.md

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+## Overview
+
+Query a single MS/MS spectrum across all public GNPS datasets in just a few seconds. This is an updated version of the traditional [MASST search](https://ccms-ucsd.github.io/GNPSDocumentation/masst/). 
+
+## FastMASST Web Interface
+
+Click [here](https://fastlibrarysearch.ucsd.edu/fastsearch/) for the FastMASST search interface, to get this start page:
+
+![web_interface](https://user-images.githubusercontent.com/100324020/155648887-c5c9815d-3838-4806-89c1-6022f621d972.JPG)
+
+## Parameters
+
+### Spectrum Input
+
+You can input the peaks through either the spectrum USI or manual entry. See additional information on spectrum USI [here](https://ccms-ucsd.github.io/GNPSDocumentation/usi/). 
+
+For manual entry, the peaks input requires a peak mass per line followed by intensity, separated by a space or a tab. See a [demonstration](http://fastlibrarysearch.ucsd.edu/fastsearch/?usi1=mzspec%3AGNPS%3AGNPS-LIBRARY%3Aaccession%3ACCMSLIB00000001548&precursor_mz=299.1760&charge=1&library_select=gnpslibrary&analog_select=No&delta_mass_below=130&delta_mass_above=200&pm_tolerance=0.05&fragment_tolerance=0.05&cosine_threshold=0.7&use_peaks=1#%7B%22peaks%22%3A%20%22299.1744%5Ct2979.96%5Cn215.081%5Ct2382.46%5Cn187.0858%5Ct1273.06%5Cn241.0958%5Ct1089.87%5Cn256.119%5Ct907.52%5Cn243.1111%5Ct322.93%5Cn200.0685%5Ct198.52%5Cn100.113%5Ct168.6%5Cn170.0576%5Ct142.73%5Cn85.1002%5Ct103.75%5Cn198.0551%5Ct93.44%5Cn299.3268%5Ct91.46%5Cn94.0639%5Ct88.92%5Cn201.0788%5Ct86.23%5Cn57.0695%5Ct72.38%22%7D) input spectrum.
+
+![image](https://user-images.githubusercontent.com/100324020/155649417-614738d2-36d2-4f41-bd92-d65fb0e2e431.png)
+
+### Library Names
+
+| Parameter  | Description          |
+| ------------- |-------------|
+| massivekb_index | ??? |
+| massivedata_index | ??? |
+| gnpsdata_index | ??? |
+| gnpslibrary | search against the GNPS MS/MS spectra library |
+
+### Search Options
+
+| Parameter  | Description          | Default |
+| ------------- |-------------| -----|
+| PM Tolerance	| Precursor mass tolerance | 0.05 |
+| Fragment Tolerance | MS2 peak tolerance | 0.05 |
+| Cosine Threshold | Cosine score threshold to make a match | 0.7 |
+| Analog Search | Will search data for analogs to library spectra | No |
+| Delta Mass Below | Maximum mass shift between target and putative analog with lower PM | 130 |
+| Delta Mass Above | Maximum mass shift between target and putative analog with higher PM | 200 |
+
+## Results
+
+Query results are separated into two categories, spectral match results and grouped data exploration. The top scoring match to public GNPS datasets are listed in the "Data Exploration – Match Results".
+
+![Match_results_table](https://user-images.githubusercontent.com/100324020/155649996-3c09d7b4-d82f-4f32-86b5-34f44772a7f1.JPG)
+
+Select the match of interest to view the spectrum mirror plots:
+
+![Match_results_tableselection_mirrorplots](https://user-images.githubusercontent.com/100324020/155650020-34c5b4c5-b254-4a06-a558-7337aa4710fd.JPG)
+
+![Match_results_mirrorplots](https://user-images.githubusercontent.com/100324020/155650048-b60a65db-dc9b-40a3-a39b-ac7d32ea6c2a.JPG)
+
+The “Grouped Data” allows you to categorize the distributions of all the spectra matches based on delta mass, dataset, adduct form, or compound name.
+
+![image](https://user-images.githubusercontent.com/100324020/155650162-b27478cc-f85a-4976-b1b6-c8edd78e97aa.png)
+
+## Citation
+
+!!! cite "Recommended Citation"
+	[Wang, M., Jarmusch, A.K., Vargas, F. et al. Mass spectrometry searches using MASST. Nat Biotechnol (2020) doi:10.1038/s41587-019-0375-9](https://www.nature.com/articles/s41587-019-0375-9)
+
+
+## Page Contributions
+
+{{ git_page_authors }}