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Echo-MS Method Onboarding

skills/ginkgo-cloud-lab/references/echo-ms-method-onboarding.md

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Echo-MS Method Onboarding

URL: https://cloud.ginkgo.bio/protocols/echo-ms-method-onboarding Status: Ginkgo Certified Price: $799/molecule Turnaround: up to 3 weeks

Overview

Echo-MS is an open-access, high-throughput mass spectrometry platform that eliminates the chromatography step. An acoustic liquid handler (Labcyte/Beckman Echo) ejects nanoliter droplets directly from a source plate into an open-port sampling interface connected to a mass spectrometer. Without a column to equilibrate, cycle times drop to 1-5 seconds per sample, enabling analysis of a full 384-well plate in ~2 hours (with replicates). Best suited for relative quantitation, screening, and titer assays where throughput matters more than chromatographic resolution.

This protocol onboards your analyte for future experiments: MS conditions (spray voltage, curtain gas, ion source settings) and ejection parameters (volume, interval, carrier solvent) are optimized, and a simple sample-prep protocol is established. Onboard a method here before running echo-ms-cfps-detection.md.

Input

(Download Template)

  • Molecule CAS ID
  • Expected reaction and conversion amount
  • Expected concentrations of substrates
  • Reaction conditions (time sensitivities, buffers, pure/lysate)

Output

For each molecule of interest:

  • Echo-MS method and calibration curve in the Cell Free Protein Expression Matrix
  • LOD + LOQ in the Cell Free Protein Expression Matrix
  • Validation run and report
  • Recommended next steps (e.g., sample-prep optimization) if method development was not successful

Automated Workflow

Phase 1 - In Silico Triage & Procurement

  1. Intake and triage (Nebula Core)
  2. Standard procurement (Nebula Core)

Phase 2 - Method Development with CFPS Matrix

  1. Establish standard solutions (Nebula Core)
  2. Optimize MRM transitions (SciEx TripleQuad 6500+ / EchoMS)
  3. Optimize EchoMS parameters (SciEx TripleQuad 6500+ / EchoMS)
  4. Matrix validation (SciEx TripleQuad 6500+ / EchoMS)

Ordering

  • Number of Molecules: configurable ($799/molecule)
  • File Upload: CSV, Excel, FASTA, TXT, PDF, ZIP
  • Additional Details: free-text field for special requirements

Use Cases

  • Onboarding a small molecule/analyte for high-throughput Echo-MS screening
  • Establishing calibration curves, LOD/LOQ in the CFPS matrix
  • Prerequisite for Echo-MS enzymatic detection runs