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Targeted LC/GC-MS,
analysed end to end.

MRMpipe reads your raw vendor files, picks every analyte peak, scores it and returns validated results. A human sees only what the model is unsure about.

Start your free 100-sample pilot How it works

The problem

Manual peak review does not scale.

Tedious review, analyte mispicks, and one integration mode for every analyte. MRMpipe removes the review, minimizes the mispicks and applies analyte-specific integration.

Manual workflow · peak integration is done once per compound, per injection
One peak integrated by hand on the left; on the right a grid of every compound in every injection, each a small trace, with the wrong picks highlighted in red and a few peaks absent.

MRMpipe replaces error-prone and tedious manual peak integration with robust automated workflows.

How it works

From raw file to reported concentration, on every injection.

Read raw data, any vendor, and start processing

Vendor raw files go in as they are, no conversion step. Every injection of a compound is picked together: one consensus retention time, one integration window, set from the whole batch rather than re-guessed per sample.

Peak detection · thyroxine · 46 injections
One patient sample of thyroxine with its integration window, next to the same compound across 46 injections stacked behind each other, all sharing one consensus retention time.

Internal standards paired automatically

Native and labelled standard are integrated on the same boundaries and the ratio is taken per sample. Here a deuterated GC standard that co-elutes with the native peak.

Native / internal-standard ratio · glycine and glycine-d2 · GC-MS/MS
Glycine native peak in green above the axis and its deuterated internal standard mirrored below, both with integration boundaries, a related compound proline in blue beside them, and the native to IS ratio taken.

Heavy-labelled peptides, the same way

For targeted proteomics the stable-isotope-labelled peptide is the internal standard. Native and heavy are integrated together, the ratio is calibrated across the standards, and the QCs are back-calculated against their nominal value.

Peptide · native and heavy-labelled internal standard · MRM
Left: one QC injection with the native peptide above the axis and its heavy-labelled internal standard mirrored below, both integrated on the same boundaries, and the native to IS ratio taken. Right: the calibration of that ratio over eight standards with the QCs back-calculated onto the curve.

Calibration levels, QCs and samples in one sequence

Standards, blanks, QCs and samples are picked on one common scale. The curve is fitted with settable gates and weak levels are dropped by rule.

Bromopropylate · pesticide panel · acquisition order
Bromopropylate quantifier traces for every injection of a pesticide batch stacked in acquisition order: two calibration ladders with shaded integrated areas, flat blanks and samples, and the QCs.
Calibration curve
Log-log calibration curve for bromopropylate: ten standards from two ladders on a linear fit with 1 over x squared weighting.

Methods stored per compound, not per analyst

Integration settings, retention-time windows, ion-ratio rules and calibration gates live with the compound. The same rule applies to every batch that follows, and every override goes to an audit trail.

Integration parameters · stored with the compound
One method, stored with the compound, feeding batch n, n plus 1, n plus 2 and n plus 3.

Questions

The ones we get asked first.

Do I need to convert my files?

No. Send vendor raw files or mzML. Conversion is part of processing.

Can I see why a peak was flagged?

Yes. Each flagged peak lists its score, the tier threshold it crossed and the features that contributed most.

Where is my data processed?

Trial data is processed on our cloud. Going forward you process on the cloud, or on your own workstation with the desktop app.

Who uses it

Labs that run the same assay again and again.

Bioanalytical and clinical LC/GC-MS labs
Steroid, drug and metabolite panels in plasma, urine and tissue, batch after batch.
Targeted proteomics groups
MRM and PRM peptide panels where hundreds of transitions per sample make manual review impractical.
CROs
Volume that exceeds in-house review capacity, with an audit trail on every decision.
Core facilities
Overflow capacity, independent second-opinion QC, or a consistent standard across user groups.

Free pilot

Try it on your own batch first.

Send one batch of up to 100 samples. We return the full report, at no cost.

Start your free pilot
  1. 1Tell us about your assay. Instrument, analytes, how many samples. One short form.
  2. 2Create your account and upload. Raw files and your transition list, straight into MRMpipe. Up to 100 samples on us.
  3. 3Review the results in your browser. Concentrations, ion ratios and QC flags per peak, with the chromatograms. We check the flagged peaks with you.
  4. 4Keep going. Upload the next batch yourself on the cloud or the desktop app, or send data for us to process as a service.

Questions about MRMpipe?

We answer within two working days.

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