Skip to main content
Glama
Sign In

Jean — Molecular Biology & Genomics

by io.github.genmnz
OverviewDiscussionsAdmin

peptide_mass

Read-only

Monoisotopic and average mass of a peptide, and its m/z at each charge state (validated against pyteomics).

Input Schema

NameRequiredDescriptionDefault
_filesNoThe project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
chargesNocharge states to report m/z for (positive integers).
ionTypeNoweigh the peptide as this ion; M is the intact molecule. Plain sequences only.M
_subjectNoThe record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
sequenceYespeptide: one-letter residues, optionally ProForma tags on residues and termini (a signed mass, a Unimod name, or UNIMOD:accession).

Output Schema

NameRequiredDescriptionDefault
mzYesper charge: monoisotopic and average m/z
averageYesneutral average mass (Da); null for a peptidoform with modification tags
monoisotopicYesneutral monoisotopic mass (Da)

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changed
    • addedOutput schema / properties / average / x-unit
      Added value: +"Da"
    • addedOutput schema / properties / monoisotopic / x-unit
      Added value: +"Da"
  2. First observed

TDQS

B3.4/5.0
Behavior3/5

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

Annotations already establish that this is a non-destructive, read-only, non-open-world operation. The description adds that results are validated against pyteomics, which is useful context, but it does not describe error behavior, sequence limitations, or what happens with invalid input.

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

Conciseness5/5

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

The description is a single efficient sentence with the core function front-loaded. Every phrase contributes to explaining what is calculated and the validation basis.

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

Completeness4/5

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

An output schema exists, so the description need not explain return values. The tool's core computation is clear, though the nested _subject and _files parameters are left to the schema rather than summarized in the description.

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

Parameters3/5

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

Schema description coverage is 100%, so the input schema already documents sequence, charges, ionType, _subject, and _files in detail. The description does not add parameter-level meaning beyond the schema, making the baseline score appropriate.

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

Purpose4/5

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

The description states a specific calculation: monoisotopic and average mass of a peptide plus m/z at each charge state. It is clear what the tool returns, but it does not differentiate itself from sibling tools such as fragment_ions or isotope_envelope.

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

Usage Guidelines2/5

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

The description provides no explicit when-to-use guidance or alternatives. It implies mass calculation from the output described, but an agent must infer when this tool is preferable to fragment_ions, isotope_envelope, or protein_digest.

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

All Jean — Molecular Biology & Genomics toolsInspect
Try in Browser
One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

Glama MCP Gateway

Add one secure layer between your agents and this server.

Resources