docs: web service README added

README.md

@@ -17,7 +17,7 @@ highlights the affected PNP fragment in the interactive report. The MS/MS peaks
 You can read more about the modification-tolerant PNP matching in [Gurevich et al, 2018](https://www.nature.com/articles/s41564-017-0094-2).
 
 
-![](img/NPvis_pipeline.png)
+![](img/pipeline.png)
 
 NPvis was developed in the [Center for Algorithmic Biotechnology (CAB)](http://cab.spbu.ru), St. Petersburg State University 
 within the [RSF 20-74-00032 project](https://cab.spbu.ru/grant/rsf-20-74-00032/).
@@ -58,7 +58,7 @@ You can use ProteoWizard's [msconvert](https://proteowizard.sourceforge.io/tools
 
 ## Output (NPvis reports)
 
-![](img/sample_NPvis_report.png)
+![](img/sample_report.png)
 
 The Figure above shows an NPvis report for the [CCMSLIB00000839197](https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00000839197#%7B%7D) spectrum from the [GNPS spectral library](https://ccms-ucsd.github.io/GNPSDocumentation/gnpslibraries/) matched with 
 the [surugamide A](https://pubchem.ncbi.nlm.nih.gov/compound/71764189) structure in the "PNP with modification" mode. 

webservice/README.md

@@ -0,0 +1,57 @@
+## Web service usage
+
+**NB!** This file provides hints on the NPvis [web service](http://cab.cc.spbu.ru/npvis/) usage. 
+Please first read the [main README](../README.md) to get the general info about the tool and its inputs/outputs.  
+
+### Controls
+
+Most of the web service controls are located on a foldable left panel. The visible set depends on the selected data types, 
+the figure below shows two possible views.  
+![](../img/web_controls.png)
+
+You can provide a spectrum (MS/MS) via a [Universal Spectra Identifier](https://www.nature.com/articles/s41592-021-01184-6) (USI) 
+or a file in the [MGF](https://fiehnlab.ucdavis.edu/projects/lipidblast/mgf-files), 
+[mzXML](http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML), and 
+[mzML](https://www.psidev.info/mzML) format. The provided USI should be resolvable via the [Metabolomics Spectrum Identifier Resolver](https://metabolomics-usi.ucsd.edu/).
+If a spectra file contains more than one spectrum, please specify the desired Scan ID (the first spectrum is used by default).
+
+You can provide a compound chemical structure via 
+a [SMILES](https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system) string 
+(both canonical and isomeric SMILES are supported) or a file in the  
+[MDL MOL V3000](http://biotech.fyicenter.com/1000250_What_Is_SDF_Mol_V3000_File_Format.html) format. 
+If the compound name is specified, it will pop up in the report Metadata panel.
+
+The advanced settings panel allows users to select 
+* the NPvis running mode ("PNP" for exact compound-spectrum matches or "PNP with modification" where exact compound is unknown)
+* max allowed MS/MS peak annotation error (the value and the relative/absolute type)
+* ionisation adduct (H, Na, K)
+* spectrum charge (only positively charged ions are currently supported)
+
+The Load Sample Data button prefills the controls with the [CCMSLIB00000839197](https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00000839197#%7B%7D) spectrum from the [GNPS spectral library](https://ccms-ucsd.github.io/GNPSDocumentation/gnpslibraries/) (via USI) 
+and the [surugamide A](https://pubchem.ncbi.nlm.nih.gov/compound/71764189) structure (via SMILES). The match is supposed for the "PNP with modification" mode and all other parameters set as default, 
+but you can tweak them if you want!
+
+The Reset button reset all controls to default values.
+
+The Submit button starts the processing, the resulting report will appear on the right within a few seconds.
+
+### GET Requests
+
+Our server supports HTML GET Requests. A valid request should contain a spectrum specified via USI, 
+a compound in the SMILES format and the NPvis running parameters. 
+The web server handles incoming requests and generates the NPvis reports in return. 
+
+Valid examples are:
+* CCMSLIB00000839197 vs surugamide A  
+
+      http://cab.cc.spbu.ru/npvis/?smiles=CC[C@H](C)[C@H]1C(=O)N[C@@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@@H](C(=O)N[C@@H](C(=O)N[C@H](C(=O)N[C@@H](C(=O)N1)C)[C@@H](C)CC)CC(C)C)CC2=CC=CC=C2)[C@@H](C)CC)CCCCN)[C@H](C)CC&gusi=mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00000839197&errthr=0.05&errtype=da
+
+* CCMSLIB00000839197 vs surugamide B 
+
+      http://cab.cc.spbu.ru/npvis/?smiles=CC[C@H](C)[C@@H]1NC(=O)[C@@H](C)NC(=O)[C@@H](NC(=O)[C@@H](CC(C)C)NC(=O)[C@@H](CC2=CC=CC=C2)NC(=O)C(NC(=O)[C@@H](CCCCN)NC(=O)[C@H](NC1=O)C(C)C)[C@@H](C)CC)[C@@H](C)CC&gusi=mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00000839197&errthr=0.05&errtype=da
+
+So, you should prepend your request with `http://cab.cc.spbu.ru/npvis/?` and use the following keywords joined via the `&` sign:
+* `smiles=` to specify the structure SMILES
+* `gusi=` to specify the spectrum USI
+* `errthr=0.05` to specify the maximum allowed MS/MS peak annotation error
+* `errtype=da` to switch between the absolute (`da`) and relative (`ppm`) error threshold type