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

Annotations already cover the safety profile (readOnlyHint=true, destructiveHint=false, openWorldHint=false), so the bar is lower, and the description still adds useful context: results are 'validated against pyteomics', ion type applies only to plain sequences, and ProForma input is monoisotopic-only. It does not mention limits, cost, or failure modes, but that is minor given the annotation coverage.

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 primary output (mass and m/z), then the input-form rules. Dense but every clause carries information; the example list is slightly over-packed but directly serves disambiguation of the sequence format.

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?

With an output schema present, the description needn't explain return values, and it covers both accepted input forms plus the ion-type constraint. The only real gap is routing guidance relative to sibling mass/ion tools, which is not strictly required for correct invocation.

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 baseline is 3, but the description goes beyond it: it enumerates the ion series (b, y, c, z, a, x plus neutral-loss forms), explains the accepted modification syntaxes (signed mass, Unimod name, UNIMOD:accession) and gives concrete ProForma examples such as [TMT6plex]-PEPTM[Oxidation]IDE. It says nothing extra about the charges parameter, but the schema covers that.

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 computation (monoisotopic/average mass and m/z per charge state) on a specific resource (peptide), and names the validation basis (pyteomics). It is clear what the tool does, but it never distinguishes itself from nearby siblings such as fragment_ions, isotope_envelope, isotopic_composition, or protein_properties.

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?

Usage is implied rather than stated: the description differentiates the two input regimes (plain one-letter sequences take an ion type; ProForma peptidoforms are weighed monoisotopically with modifications), which helps an agent pick the right input form. However, there is no explicit when-to-use guidance, no statement of when another tool is preferable, and no prerequisite notes.

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