Here are the answers to the questions:

1. What tool was used for pathway enrichment analysis?
The article does not specifically mention a tool used for pathway enrichment analysis, but it mentions that "we were able to statistically verify new phenomena" and "systems-wide mapping of these co-modified peptides suggests", which implies that some kind of analysis was performed. However, the tool used is not described.

2. Was a tool version number provided?
Not described.

3. What gene set library was queried (eg: GO, KEGG, Reactome or other)?
Not described.

4. Was a background gene list defined for pathway enrichment analysis?
Not described.

5. What statistical test was used for enrichment analysis?
Not described.

6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?
Not described.

It appears that the article does not provide detailed information on the pathway enrichment analysis methodology. The authors may have used a specific tool or approach, but it is not explicitly stated in the text.