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AI agent for biochemists

Mass Spectrometry Run Quality and Reprocessing Agent

Catch and fix poor-quality runs while samples and instrument time are still available

Quality controlMonitoringScience and research
See how it worksGet access
Mass Spectrometry Run Quality and Reprocessing Agent: what goes in, what the agent does and what you get

What it does

A proteomics study runs for four days, and only when the full dataset is processed does the team see that some runs drifted and the signal fell. The samples are gone or the instrument time is spent. This agent watches as runs complete. It checks QC standards, retention time drift and signal intensity per run, flags drifting runs, tries reprocessing with adjusted alignment and rechecks the QC after each try. It queues reruns for samples that still fail while the sample is available. It keeps a running table of run quality. The scientist approves excluding any run. Edge case: a drift starts mid-batch. The agent suggests stopping the queue for maintenance.

How it works

Follow the arrows from top to bottom. The orange dashed arrow is the loop: when a check fails, the agent goes back and tries again.

Start and resultWhat it doesA check on its own workWaits for your OKGoes back and retries
Yes, continueYes, continueApprovedNoNo 1 STARTS WHEN A run completes 2 USES A TOOL Read the QC standards, retention times andintensities 3 DOES Compare the metrics with the acceptance limits andprevious runs 4 CHECKS THE RESULT Is the run within the limits? If not: Flag it and try reprocessing with adjustedalignment. Back to step 2. 5 USES A TOOL Reprocess the run with the new settings 6 CHECKS THE RESULT Does the reprocessed run meet QC? If not: Queue a rerun if the sample is available. Backto step 4. 7 DOES Check for drift patterns across the batch 8 DOES Recommend a pause for maintenance if drift passesthe stop limit 9 YOU APPROVE Scientist approves excluding any run or pausing thequeue 10 USES A TOOL Update the run quality table and the queue 11 RESULT Batch QC report with included, reprocessed and rerunsamples
Read the steps as a list
  1. A run completes
  2. Read the QC standards, retention times and intensities
  3. Compare the metrics with the acceptance limits and previous runs
  4. Is the run within the limits?If not: Flag it and try reprocessing with adjusted alignment. Back to step 2.
  5. Reprocess the run with the new settings
  6. Does the reprocessed run meet QC?If not: Queue a rerun if the sample is available. Back to step 4.
  7. Check for drift patterns across the batch
  8. Recommend a pause for maintenance if drift passes the stop limit
  9. Scientist approves excluding any run or pausing the queueThe agent waits here for your OK.
  10. Update the run quality table and the queue
  11. Batch QC report with included, reprocessed and rerun samples

How it decides

A run passes if the QC standards meet retention time and intensity limits. Reprocessing is tried before rerunning, because drift can often be corrected computationally.

  • Retention time drift over 0.5 minutes is flagged
  • Signal intensity below 50 percent of the QC median is flagged
  • Three consecutive drifting runs trigger a pause recommendation
  • Reprocess before rerunning

Make it yours

Every agent is a starting point. You choose these settings for your own situation.

  • QC limits
  • Number of drifting runs before a pause (default 3)
  • Processing settings to try
  • Report format
  • Who receives alerts

What keeps you in control

It always asks you first

  • Scientist approves excluding any run
  • Scientist approves pausing the queue

Hard limits

  • Never deletes raw data
  • Never excludes a run without approval

It stops when

  • Done: all samples pass QC or are excluded with approval
  • Stop: instrument fault, stop the queue and call the facility

Set it up

We guide you through the set-up, step by step

Members get the full set-up guide for this agent. No technical skills needed: you copy, paste and upload.

10 minto set it up in your AI
5 AIsChatGPT, Claude, Copilot, Gemini, Grok
  • One set of instructions to paste into your AI, with the clicks for ChatGPT, Claude, Microsoft 365 Copilot, Gemini and Grok
  • The agent then walks you through connecting your own data, one source at a time
  • A downloadable copy with the flow chart, the rules and the full guide
Get access to this agent

An example run

What happensOn day 2 of a 96-sample batch, run 41 shows a 0.8 minute retention drift and 40 percent signal. The agent reprocesses with a new alignment, and the retention error falls to 0.2 but signal stays low. Samples are available, so it queues a rerun. Runs 42 and 43 also drift, so it recommends cleaning the source. The scientist approves the pause.

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