add some info about skyline glyco

docs/tutorial_glyco.md

@@ -243,6 +243,16 @@ for a complete guide to the visualization tool, see the associated tutorial.
 
 ![](https://raw.githubusercontent.com/Nesvilab/FragPipe/gh-pages/images/PDV-FragPipe_vis-example.png)
 
+
+**Skyline**: new in 22.0  
+
+**DIA results** can be automatically visualized in Skyline by checking the "Generate Skyline Document" box on the Skyline tab.  
+*Skyline running mode*: set to "Use speclib as input" to the DIA-NN report.tsv as the input  
+*Special Modifications Mode*: set to N-glyco or O-glyco depending on the analysis  
+**DDA results** currently require a workaround method, but will be supported fully in future. To view DDA results in Skyline:
+1) On the MSFragger tab, under Open Search Options, set "Report mass shift as a variable mod" to "Yes, remove delta mass". **NOTE: this prevents using Glycan Composition Assignment or O-Pair search on the Glyco tab! Run a separate search to generate a Skyline document vs using those methods.** Note also that this means that the results viewed in Skyline will NOT have glycan FDR applied.   
+2) Set the *Skyline running mode* to "Use pep.xml as input" on the Skyline tab and the *Special Modifications Mode* according to your analysis type.  
+
 **The PSM Table:** Key columns for GlycoPSM information
 
 *If NOT using Glycan Assignment in PTM-Shepherd or O-Pair localization:*