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echo-ms-cfps-detection.md

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1# Echo-MS Detection of Molecules from an Enzymatic Reaction (Cell Free)
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3**URL:** https://cloud.ginkgo.bio/protocols/echo-ms-cfps-detection
4**Service terms:** https://cloud.ginkgo.bio/terms/echo-ms-cfps-detection
5**Reviewed:** 2026-09-30; prices and turnaround below are catalog estimates.
6**Status:** Beta
7**Price:** $44/sample
8**Turnaround:** up to 13 days
9

Echo-MS Detection of Molecules from an Enzymatic Reaction (Cell Free)

URL: https://cloud.ginkgo.bio/protocols/echo-ms-cfps-detection Service terms: https://cloud.ginkgo.bio/terms/echo-ms-cfps-detection Reviewed: 2026-09-30; prices and turnaround below are catalog estimates. Status: Beta Price: $44/sample Turnaround: up to 13 days

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10## Overview
12Fastest path from a protein sequence to a functional, quantitative readout on enzyme activity. Using a proprietary reconstituted E. coli transcription-translation (CFPS) system, Ginkgo expresses your enzyme of interest in 4-16 hours. A substrate or product is then added directly to the well and substrate conversion is measured by acoustic ejection mass spectrometry (Echo-MS), delivering a go/no-go signal without protein purification. Enzyme expression and Echo-MS are performed using the baseline Cell Free Protein Synthesis Master Mix.
14To run this protocol, the relevant analyte/method must first be onboarded (see [echo-ms-method-onboarding.md](echo-ms-method-onboarding.md)).

Overview

Fastest path from a protein sequence to a functional, quantitative readout on enzyme activity. Using a proprietary reconstituted E. coli transcription-translation (CFPS) system, Ginkgo expresses your enzyme of interest in 4-16 hours. A substrate or product is then added directly to the well and substrate conversion is measured by acoustic ejection mass spectrometry (Echo-MS), delivering a go/no-go signal without protein purification. Enzyme expression and Echo-MS are performed using the baseline Cell Free Protein Synthesis Master Mix.

To run this protocol, the relevant analyte/method must first be onboarded (see echo-ms-method-onboarding.md).

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16## Input
18- Enzyme DNA or AA sequence; contact Ginkgo for DNA sequences longer than 1800 bp
19- Analyte CAS ID and expected substrate concentration
20- Reaction timing/temperature constraints and per-well buffer, substrate, and cofactor conditions

Input

  • Enzyme DNA or AA sequence; contact Ginkgo for DNA sequences longer than 1800 bp
  • Analyte CAS ID and expected substrate concentration
  • Reaction timing/temperature constraints and per-well buffer, substrate, and cofactor conditions
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22## Output
24- **Method summary**
25- **Peak table** (substrate depletion and/or product formation)

Output

  • Method summary
  • Peak table (substrate depletion and/or product formation)
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27## Automated Workflow

Automated Workflow

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29### Phase 1 - CFPS Expression
311. Express enzyme in CFPS master mix (4-16 h)

Phase 1 - CFPS Expression

  1. Express enzyme in CFPS master mix (4-16 h)
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33### Phase 2 - Enzymatic Reaction
351. Dispense molecule, buffers, reagents (Agilent Bravo 96)
362. Incubate under reaction conditions (Inheco)

Phase 2 - Enzymatic Reaction

  1. Dispense molecule, buffers, reagents (Agilent Bravo 96)
  2. Incubate under reaction conditions (Inheco)
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38### Phase 3 - Dilution and Echo-MS Detection
401. Prepare a standard curve in diluted CFPS matrix
412. Dilute reaction wells
423. Measure substrate/product by Echo-MS; interpret within the onboarded matrix and detection limits

Phase 3 - Dilution and Echo-MS Detection

  1. Prepare a standard curve in diluted CFPS matrix
  2. Dilute reaction wells
  3. Measure substrate/product by Echo-MS; interpret within the onboarded matrix and detection limits
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44## Ordering
46- **Number of Samples:** configurable ($44/sample)
47- **File Upload:** CSV, Excel, FASTA, TXT, PDF, ZIP
48- **Additional Details:** free-text field for special requirements

Ordering

  • Number of Samples: configurable ($44/sample)
  • File Upload: CSV, Excel, FASTA, TXT, PDF, ZIP
  • Additional Details: free-text field for special requirements
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50## Use Cases
52- Go/no-go enzyme activity screening without purification
53- Detecting substrate depletion / product formation for biocatalysis
54- High-throughput functional triage of enzyme variants

Use Cases

  • Go/no-go enzyme activity screening without purification
  • Detecting substrate depletion / product formation for biocatalysis
  • High-throughput functional triage of enzyme variants
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