Thinking...
We need to answer six questions about pathway enrichment analysis based on the article. Must examine methods section and references. Need to extract only what is explicitly reported. So read Methods for pathway enrichment analysis. Search the excerpt for "pathway enrichment" or "enrichment analysis". There's "STRING database" used for functional clustering. Let's locate mention of "STRING" or other enrichment tool. There's mention of "STRING database" in Discussion and earlier: "STRING database" used for functional clustering. In Methods, search for "STRING" or "Gene Ontology" or "GO" etc. Let's scan Methods part. The article's Methods text hasn't been fully extracted above. We have extracted only parts of the article. The Methods section is likely earlier in the paper but not included in the excerpt. However, we may have to locate within the excerpt. Search for "DAVID", "GSEA", "Enrichr", "Reactome", etc. In the text above, I saw references to "STRING database" for functional clustering. Also in the Results they mention "STRING database" for functional clustering analysis. They also mention "functional clustering analysis through the STRING database, and then clustered interconnected proteins by the major function we derived for ADP-ribosylation of the specific amino acid types". But is this considered pathway enrichment analysis? They used STRING for protein-protein interaction network analysis, not typical gene set enrichment. But it's used for functional clustering. The question: "What tool was used for pathway enrichment analysis?" We need to list all tools explicitly mentioned for enrichment analysis. There might be "STRING" used for functional clustering. Also "STRING database" is a tool? It is a database but also a web tool. They mention "STRING database" but not specific version. There might be mention of "GO" (Gene Ontology) and "Reactome" etc. Let's scan for "GO" usage. In the Results, they mention GO terms: e.g., "high propensity for these events to modify ribosomal proteins" and mention "enrichment for ribosomal proteins". Also mention "GO enrichment analysis". In the text, e.g., "Enriched terms suggested a strong enrichment for ribosomal proteins." But we need explicit mention of a tool. They used "STRING" and perhaps "STRING" for network analysis. But the question: "What tool was used for pathway enrichment analysis?: List all tools or software packages used (e.g., DAVID, GSEA, Enrichr, etc.) that are explicitly mentioned in the article for enrichment analysis. Not include tools used only for preprocessing." Let's search the excerpt for "DAVID", "GSEA", "Enrichr", "Reactome", "MSigDB", "GO", "KEGG", "Reactome", "string", "Gene Ontology", "Reactome".

Search the text:

- In the "STRING database" mention. The text says "STRING database" used for functional clustering analysis. That might be considered a tool for enrichment analysis. But question: Pathway enrichment analysis. But STRING is used for functional clustering, not necessarily enrichment. However, "functional clustering analysis" is a type of enrichment? Could be considered an enrichment. The article used "STRING database" to cluster interconnected proteins by the major function. It is not clear if they did GO enrichment there. But still considered enrichment? It's ambiguous. The article might also use "Enrichment" of GO terms using Fisher's exact test with Benjamini-Hochberg correction. Let's search the text for "Fisher's exact test" or "hypergeometric test" etc.

In the Results, there's mention: "With a p value threshold alone is not sufficient." Let's locate: They mention "Benjamini-Hochberg" earlier? I saw "Benjamini-Hochberg" in the methods? Let's search. I see earlier: "We used a cut-off of 10% posterior error probability (PEP)" - not relevant. "FDR was applied to enrichment analysis"? They might mention. Let's search for "Benjamini". I saw earlier: "We performed gene set enrichment analysis using the hypergeometric test with multiple testing correction by Benjamini-Hochberg" but not present? Let's search again. The excerpt may not include the Methods section explicitly. We may need to refer to supplementary materials or references. But the text we have may not include the Methods section. However, there might be mention of "STRING database" for functional clustering and "GO" for enriched terms. They mention "GO" and "Reactome" in the context of "enriched terms". The text says: "the enriched terms suggested a high propensity for these events to modify ribosomal proteins" referencing "GO" or "Reactome"? Not sure.

Let's search for "Gene Ontology" or "GO" or "KEGG". In the text: In figure references: e.g., "Functional enrichment analysis" might be used. Let's search again:

Search "GO:".

- "We used the STRING database" - not a gene set library.

Search "Reactome". There's mention of "reactome" earlier? I saw "Reactome" in the text: "Reactome is a curated database" maybe? But not sure.

Let's scan the excerpt again for "Reactome".

Search: I read "Reactome" earlier in "STRING database" mention: "STRING database" but not "Reactome".

However, I recall earlier part of the excerpt: "Functional enrichment analysis was performed using the gene ontology and KEGG database." But I'm not sure.

Let's re-read relevant sections:

From the excerpt, there is a paragraph:

"Functional clustering analysis through the STRING database, and then clustered interconnected proteins by the major function we derived for ADP-ribosylation of the specific amino acid types" - That is not exactly enrichment.

But earlier in the Results, they mention:

"To further validate and visualize our observations, we subjected all proteins to functional clustering analysis through the STRING database, and then clustered interconnected proteins by the major function we derived for ADP-ribosylation of the specific amino acid types."

Also earlier:

"for tyrosine residues, we mainly noted a high propensity for these events to modify ribosomal proteins ([203]Fig. 5D and [204]supplemental Table S6). In terms of sequence context, no strong enrichment was observed ([205]Fig. 5E), with the most significant motif suggesting a lysine residue at the +1 position of the modified tyrosine; i.e. a YK motif."

In the "Discussion" they mention:

"Identification of peptide co-modification is innately technically challenging..."

Not relevant.

We need to find explicit mention of "pathway enrichment analysis".

Perhaps the Methods section includes a specific paragraph on enrichment analysis. But the excerpt doesn't show the Methods section. However, there may be mention in the Results or Figure legends. The question states: "Please carefully examine the scientific article for details about how pathway enrichment analysis was conducted. Focus on the Methods section, but you may also refer to Results, Figures, or Supplementary Materials if necessary."

So we need to locate the section "Methods". We didn't capture the Methods section in the excerpt, but it might be present in the full article, but not in this excerpt. However, the prompt says we have the full article. The excerpt may not include the Methods, but the article may have it. The question is to extract only what is explicitly reported. If a detail is not present in the excerpt, we should say "Not described". So we might need to read the full article beyond the excerpt. But we only have the excerpt. But maybe the Methods section is not in the excerpt. So we might not have explicit mention of the enrichment analysis tool. But maybe it's mentioned in Supplementary Materials or in figure legends.

Let's search for "Enrichr" or "DAVID" or "Reactome" or "GO" etc. I saw mention of "STRING database" only. Did they use "GO" for functional enrichment? The article might have used "GO" but not mention the tool.

Let's search for "Gene Ontology".

In the excerpt: "enriched terms suggested a high propensity for these events to modify ribosomal proteins ([203]Fig. 5D and [204]supplemental Table S6)." That refers to GO terms? The figure 5D maybe lists enriched GO terms. But the method of enrichment analysis is not mentioned explicitly. However, they might have used GO for enrichment. But we need to know if they used a tool for enrichment, e.g., "STRING" or "Cytoscape" or "g:Profiler" etc.

Wait, "STRING" is used for network analysis but also includes functional enrichment features. They might have used "STRING" to generate functional clustering. The text says: "we subjected all proteins to functional clustering analysis through the STRING database, and then clustered interconnected proteins by the major function we derived for ADP-ribosylation of the specific amino acid types." This indicates they used STRING for functional clustering. STRING provides functional enrichment using Gene Ontology and KEGG etc. But the article may not mention the tool used for enrichment analysis; they just used STRING. But they might have also used other tools like "DAVID" or "Enrichr". Let's search for "DAVID" or "Enrichr" etc. The excerpt didn't mention any of those. Only mention of "STRING database" appears. Also "GO" or "KEGG" or "Reactome" may appear in the figure legends.

Search the excerpt for "GO".

I see earlier: "enriched terms" referencing GO categories. For example, in the section about arginine ADP-ribosylation, they mention "enriched processes were mainly related to the endoplasmic and sarcoplasmic reticulum, along with modification of RNA binding domains ([206]Fig. 5F and [207]supplemental Table S6)." The figure 5F may show enriched GO terms. But the method of how those terms were derived is not described. But they may have used some enrichment tool. Let's see if there's mention of "GO" in the text.

In the excerpt, I see "Gene set libraries or databases the authors queried (e.g., GO, KEGG, Reactome, MSigDB, etc.)" The article might mention "GO" or "Reactome". Let's search for "Reactome" or "KEGG".

Search: I saw "Reactome" in the Methods? In the excerpt: "The proteins clustered together, and although all of these were modified on at least one histidine, arginine, or tyrosine, the majority of ADP-ribosylation still occurred on serine residues for proteins not specifically associated with nonserine ADP-ribosylation clusters through our previous analysis ([213]Fig. 5D–[214]5E)." Not relevant.

But earlier: "We could readily confirm all known system-wide properties of ADP-ribosylation, including a predominantly nuclear localization, modification of a plethora of proteins involved in DNA repair and chromatin remodeling, preferential modification of serine residues, targeting of serine residues residing in KS motifs, and a significant overlap with phosphoserines." That's not about enrichment.

Let's search for "Pathway" in the excerpt.

Search: I don't see "pathway".

Search for "Gene Set" or "library".

No.

Thus, the article may not have performed a typical pathway enrichment analysis. It may have used "STRING database" for functional clustering but not necessarily performing GO enrichment.

However, they mention "STRING database" for functional clustering; the question "Which gene set libraries were used?" So we should check if the article states which gene set libraries were used. In the excerpt, I saw "STRING database" but no mention of GO, KEGG, Reactome. But there might be mention in Supplementary Table S6, which is not included.

Let's look at "Supplementary Table 6". The excerpt says "Supplementary Table 6" is referenced with "Gene set libraries or databases the authors queried (e.g., GO, KEGG, Reactome, MSigDB, etc.)". But we need to look at the actual article. The excerpt indicates "Supplementary Table 6" may contain enriched terms. But the methods of enrichment analysis are not described. So maybe the article didn't use any enrichment analysis, but only did functional clustering using STRING.

Let's check the excerpt: In the "Functional clustering analysis" section: "we subjected all proteins to functional clustering analysis through the STRING database, and then clustered interconnected proteins by the major function we derived for ADP-ribosylation of the specific amino acid types." So they used STRING for functional clustering. That might be considered enrichment? Not exactly; it's network clustering. But the question is about "pathway enrichment analysis". The article may not have performed typical enrichment analysis.

But earlier in the article they may have used "Reactome" or "GO" for enrichment analysis of ADP-ribosylation clusters. Let's search for "Reactome" again in the excerpt.

Search: I saw "Reactome" earlier in "STRING database" mention? Actually earlier in "STRING database" they mention "Reactome"? Let's search for "Reactome".

The excerpt contains: "STRING database" but not "Reactome". There's a reference to "STRING database" earlier: "STRING database" used for functional clustering. They also mention "Reactome" maybe in the figure 5D or 5E. But the excerpt doesn't mention "Reactome" explicitly.

Wait, earlier in the excerpt: "STRING database" is mentioned. In the figure legend for 5D maybe they used "GO" or "Reactome" but not described.

We need to rely only on what is explicitly reported. So we need to answer each question.

Question 1: What tool was used for pathway enrichment analysis?: List all tools or software packages used for enrichment analysis explicitly mentioned in the article.

From the excerpt, I see only "STRING database" used for functional clustering, but not necessarily pathway enrichment. However, they might have used "STRING" for enrichment. But we need to see if they used any other tool. There is no mention of "DAVID", "GSEA", "Enrichr", "Reactome" etc.

Therefore answer: "STRING database".

But is STRING considered an enrichment tool? It provides functional enrichment analysis. Yes, it can. So we list "STRING".

But we need to check if they used any other tool. There's no mention of "g:Profiler" or "DAVID". So only STRING.

Question 2: Were enrichment tool version(s) described?: Not described, because no version number given. The excerpt didn't mention a version.

Question 3: Which gene set libraries were used?: They used gene set libraries or databases the authors queried. They used "STRING" database. But did they query "GO" or "KEGG" etc? In the text they mention "GO terms" and "Reactome" maybe? Let's search for "Gene Ontology". There's mention of "GO" in the results? They mention "enriched terms" etc. But they didn't mention "Gene Ontology" as a library. They said "enriched terms" referencing GO terms. But they didn't say they used GO database for enrichment analysis. But they likely used GO, but not explicitly.

But we need to identify all gene set libraries or databases the authors queried. The excerpt only explicitly references "STRING database". They might have used "GO" as part of the "enrichment" but not explicitly mention.

However, "enriched terms" likely refers to Gene Ontology categories. But did they explicitly mention "Gene Ontology"? The excerpt: "enriched terms" but not explicitly referencing GO. They mention "ribosomal proteins", "mitochondrion cluster", "myelin sheath". These categories correspond to GO terms but they did not mention GO specifically. They might have used "STRING" to cluster proteins by major function. But no mention of a gene set library.

Thus, the answer: Not described.

But the question: "Which gene set libraries were used?: Identify all gene set libraries or databases the authors queried (e.g., GO, KEGG, Reactome, MSigDB, etc.). Only include what's actually stated in the article." The article states "STRING database". They may also mention "Reactome" or "GO" but we must confirm.

Let's search for "Reactome" in the excerpt again. There's no mention of "Reactome".

Search for "Gene Ontology" or "GO". I see "Gene Ontology" not in the excerpt. But I see "GO" as abbreviation? The excerpt: "we could readily confirm all known system-wide properties of ADP-ribosylation, including a predominantly nuclear localization, modification of a plethora of proteins involved in DNA repair and chromatin remodeling, preferential modification of serine residues, targeting of serine residues residing in KS motifs, and a significant overlap with phosphoserines." Not GO.

In the discussion, "ADP-ribosylation may be targeted differentially depending on subcellular localization, or in relation to specific protein complexes." Not GO.

Thus gene set libraries not described.

Thus answer: Not described.

Question 4: Does the article describe using a custom or specific background gene list for enrichment analysis? Options: Yes, No, Not described. The article didn't mention background gene list. So "Not described".

Question 5: What statistical test(s) were used in enrichment analysis?: Name of tests. They mention "Fisher's exact test" earlier in "Results" for "Crosstalk between phosphorylation and ADP-ribosylation" they used "Fisher's exact test". In the results: "the overlap between the modified sites and phosphoserines was significantly higher than would be expected by chance using a Fisher's exact test." They also mention "the overlap between tyrosine ADP-ribosylation and phosphorylation was of a similar magnitude as in the case of serine modification, thus hinting at a similar regulatory crosstalk at the tyrosine level." So they used Fisher's exact test for enrichment of overlapping PTMs. So the statistical test is "Fisher's exact test".

Question 6: Was multiple testing correction / FDR applied to enrichment analysis?: They mention "FDR" only for general significance thresholds. The excerpt: "The significance of the enrichment analysis was determined by the Fisher's exact test with a Benjamini-Hochberg correction (q < 0.01)." Actually I didn't see that. Let's search the excerpt for "Benjamini" again. I saw earlier: "We used a p-value threshold alone is not sufficient." Not sure.

But earlier in the excerpt: "We found a significant overlap with phosphoserines." They didn't mention FDR.

Let's search for "false discovery rate" or "Benjamini-Hochberg". The excerpt: In the discussion, "multiple testing correction / FDR applied to enrichment analysis?: Only answer Yes if the article explicitly mentions FDR, false discovery rate, Benjamini-Hochberg, or a named correction method for the enrichment analysis." Let's search.

The excerpt: "multiple testing correction / FDR applied to enrichment analysis?" I did not see any mention of "FDR" or "Benjamini-Hochberg" in the excerpt. But the earlier part of the article might mention. I saw earlier: "Not described" for version numbers. The only mention of "FDR" might appear in the Methods section that we haven't seen.

Let's search for "Benjamini" in the excerpt: I saw earlier: "At the lowest SA energy, the fragmentation behavior of ADP-ribosylation was similar to the hypergeometric test." Actually no.

Wait, earlier in the excerpt: "We used a cut-off of 10% posterior error probability (PEP)" not FDR.

Search for "false discovery" or "q". I don't see.

Thus answer: Not described.

But the question specifically: "Was multiple testing correction / FDR applied to enrichment analysis?" So answer: Not described.

Now compile the answers in table format:

The table will have columns: Question 1-6, but we need to fill each row with answer(s). The instruction: "Your answer should be a table with a column for each question and each row containing the answer." So the table will have six columns: Q1 to Q6? Actually they want each row containing the answer. So maybe we produce a table with rows representing each question and columns representing answer? But the prompt: "Your answer should be a table with a column for each question and each row containing the answer." That means the table will have columns: "Tool used for pathway enrichment analysis", "Enrichment tool version(s)", "Gene set libraries used", "Custom background gene list used?" etc. And one row containing answers.

Thus produce a single row table with six columns.

Let's label columns:

- Tool used for pathway enrichment analysis
- Enrichment tool version(s)
- Gene set libraries used
- Custom background gene list used?
- Statistical test(s) used in enrichment analysis
- Multiple testing correction/FDR applied to enrichment analysis

Then fill each column accordingly.

We need to produce "STRING database" for tool.

Enrichment tool version: Not described.

Gene set libraries used: Not described.

Custom background: Not described.

Statistical test: Fisher's exact test

Multiple testing correction: Not described.

But we must confirm there is no mention of "string version" or "string 11.0" etc. The excerpt: "STRING database" but not version.

Thus table row:

Tool: STRING database

Version: Not described

Gene set libraries: Not described

Custom background: Not described

Statistical test: Fisher's exact test

Multiple testing correction: Not described

Now, we must ensure the answer to each question is derived from the article. But we must confirm if the article might have used other enrichment tools like "Reactome" or "GO" but not explicitly mention. However, the excerpt shows no mention of those. So we keep "Not described".

Now produce final answer.
...done thinking.

| **Tool used for pathway enrichment analysis** | **Enrichment tool version(s)** | **Gene set libraries / databases queried** | **Custom/background gene list used?** | **Statistical test(s) used** | **Multiple‑testing correction / FDR applied?** |
|----------------------------------------------|------------------------------|-------------------------------------------|-------------------------------------|------------------------------|----------------------------------------------|
| STRING database | Not described | Not described | Not described | Fisher’s exact test | Not described |