Here is a collation of the requested information regarding the pathway enrichment analysis from the scientific article, based on the Methods section and other relevant parts:

1. **Tool Used for Pathway Enrichment Analysis**:  
   - The tool used was an R package named “q-value” as mentioned in the Proteome Data Analysis subsection.
   
2. **Tool Version Number Provided**:  
   - No specific version number of the "q-value" tool is provided.

3. **Gene Set Library Queried**:  
   - Libraries queried included Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG).

4. **Background Gene List Defined for Pathway Enrichment Analysis**:  
   - The background gene list was defined using all the proteins as mentioned in the Proteome Data Analysis section.

5. **Statistical Test Used for Enrichment Analysis**:  
   - Fisher’s exact test was used to calculate p-values during enrichment analysis.

6. **False Discovery Rate Correction Used**:  
   - Yes, false discovery rate (FDR) correction was applied using the "q-value" package to control the number of false positives, with a significance threshold defined as FDR < 0.05.

These details can be used to create a table for easier reference:

| Question                                                                 | Answer                                  |
|--------------------------------------------------------------------------|-----------------------------------------|
| Tool Used for Pathway Enrichment Analysis                                | "q-value" R package                     |
| Tool Version Number Provided                                             | Not described                           |
| Gene Set Library Queried                                                 | GO, KEGG                                |
| Background Gene List Defined                                             | All proteins used as background         |
| Statistical Test Used for Enrichment Analysis                             | Fisher’s exact test                     |
| False Discovery Rate Correction Used                                     | Yes (FDR < 0.05)                        |

If you have any further questions or need additional details, feel free to ask!