Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint=true, destructiveHint=false and closed-world, so the safety profile is covered. The description adds genuinely useful behavioral context beyond that: the output is validated against pyteomics and cross-checked against OpenMS, signalling a deterministic, trusted computation rather than an approximate one.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Is the description appropriately sized, front-loaded, and free of redundancy?

Two sentences, front-loaded with the core capability before the parenthetical provenance note. It is dense but every clause carries information; the validation parenthetical is slightly long but justified.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema exists, so return values need not be explained, and the description covers the fragmentation model, ionization scope and modification syntax. It leaves maxCharge and the required-peptide input handling to the schema, which is acceptable given the 100% schema coverage.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so the baseline is 3; the description goes further by spelling out the three accepted modification-tag forms (signed mass, Unimod name, UNIMOD:accession) and the modification can sit on residues or termini. It adds mild value over the schema's own examples, though ionTypes and maxCharge semantics are left to the schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb+resource: the theoretical MS/MS fragment ion ladder of a peptide, enumerating the ion series (a/b/c N-term, x/y/z C-term) and the neutral-loss/radical variants. This is far more specific than sibling tools like peptide_mass or score_spectrum, so an agent can distinguish it without opening the schema.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description makes the tool's scope inferable (theoretical fragmentation, not experimental scoring), which implies when it applies. However, it never names a sibling alternative such as peptide_mass, score_spectrum, or protein_digest, nor states exclusions, so the agent must infer routing from the topic alone.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.