MRMpipe
Automated LC-MS Review and Quantification for Targeted Workflows
MRMpipe helps targeted LC‑MS labs process batches faster by automating peak detection, handling overlapping signals, and flagging uncertain results for review.
One batch, up to 100 samples free
Send us your test data — we'll process a batch and return a full report so you can evaluate the results.
Review interactively — explore peaks, chromatograms, and QC reports in our cloud platform.
Start processing your own batches — upload data and get results directly. Sign up for free trial
Who It's For
What You Get
Core Technology
Built for Real-World Chromatography
BEMG Peak Deconvolution
Co-eluting compounds produce merged chromatographic signals that standard integration tools treat as a single peak. MRMpipe fits Bi-Exponentially Modified Gaussian curves to mathematically separate overlapping peaks and extract accurate areas for each analyte.
- Resolves peaks with valley depth < 5% of maximum
- Asymmetry-aware model captures real peak shapes
- Accurate ion ratios from deconvolved areas
DTW Cross-Sample Consistency
Dynamic Time Warping aligns and compares peak shapes across every sample in your batch. This catches retention time drift, integration outliers, and false positives that single-sample analysis would miss.
- Automatic RT drift correction across samples
- Shape-based outlier detection flags anomalies
- Batch-level reproducibility metrics at a glance
ML-Powered Quality Scoring
Every detected peak is scored by a model trained on thousands of expert-curated reference chromatograms. Peaks are classified as green (accepted), blue (review), or red (rejected) -- giving you audit-ready confidence tiers.
- Trained on curated reference library of peak shapes
- Three-tier confidence system (green / blue / red)
- Continuous learning from analyst feedback
Full Batch Processing
Upload an entire batch of mzML files with your compound list and walk away. MRMpipe processes every sample, validates ion ratios, calculates SNR, and exports publication-ready CSV results.
- Simpson's rule numerical integration for accuracy
- ALS baseline correction removes background noise
- CSV export, interactive HTML reports, JSON data
sample_001.mzML
48 molecules • 2.1s
sample_002.mzML
48 molecules • 1.8s
sample_003.mzML
Processing molecule 32/48...
sample_004.mzML
Queued
sample_005.mzML
Queued
Under the Hood
Technical Specifications
Input
- mzML or vendor files
- CSV compound / transition lists
- Triple quad MRM / PRM data
Signal Processing
- ALS baseline correction
- Savitzky-Golay smoothing
- Adaptive FWHM estimation
Detection
- Derivative-based peak finding
- Dynamic noise level (DNL)
- RT-guided candidate selection
Integration
- Simpson's rule (numerical)
- BEMG deconvolution
- Ion ratio calculation
Quality Control
- ML confidence scoring
- DTW shape matching
- SNR & peak shape metrics
Output
- CSV / JSON results
- Interactive HTML reports
- JSON structured export
Just want your data analyzed?
You don't need to install anything. Send us your targeted LC‑MS/MS files and we'll run MRMpipe for you — with expert review and publication-ready deliverables.
See MRMpipe in Action
Send us a batch of mzML files and we'll run MRMpipe on your data. We'll run MRMpipe on your data and send back the full results report -- free, no strings attached.