Adopt AI — but prove it
Leadership wants AI-accelerated discovery. Regulators (FDA Jan 2025, EMA reflection paper) want every AI-assisted claim reproducible, documented, and subordinate to human review. You need both at once.
Solution · Pharmaceutical R&DDiscovery → Development → Submission
Move faster on the molecule. Not on the evidence.
MolTrace gives pharmaceutical R&D teams one audit-grade evidence stack from the first hit spectrum to the IND dossier. Confirm structures, profile impurities, optimize routes, and compose submission-ready sections — without ever losing the trail back to the raw data.
Why pharma R&D
Four pressures, hitting at the same time.
Discovery teams are asked to go faster with AI, prove more to regulators, catch impurities earlier, and do it across a toolchain that was never designed to hold evidence together. MolTrace is built for exactly that intersection.
Reproducibility is now table stakes
ICH Q2(R2) raised the bar on analytical method validation. 'It looked similar when we re-ran it' no longer survives an inspection. Every processing step has to be replayable bit-for-bit.
Impurities decide timelines
A nitrosamine flag or an unresolved degradant can stall a program for months. The earlier in the lifecycle you catch and classify it, the cheaper the route change.
The toolchain is fragmented
NMR in one app, LC-MS in another, impurity tables in spreadsheets, the dossier in Word, the audit trail reconstructed from email. The handoffs are where evidence — and weeks — go missing.
Across the lifecycle
One evidence stack, five phases deep.
MolTrace isn't a point tool you bolt onto one step. The same audit-grade evidence object follows the molecule from the first hit spectrum to the submission — so what discovery learns is still legible to CMC and regulatory months later.
The lifecycle, at a glance
Discovery ──► Lead opt ──► Candidate ──► Process / CMC ──► IND / Submission
│ │ │ │ │
▼ ▼ ▼ ▼ ▼
confirm optimize definitive impurity + dossier +
hits the route elucidation method val. ALCOA+ ledger
(NMR+MS) (Repho) (DP4 + trail) (Q3x · Q2(R2)) (signoff gate)DSC
Discovery & hit identification
- Confirm hit structures from NMR + HRMS in one evidence stack
- Cross-modal contradiction warnings rule out mis-assignments early
- Artifact / solvent / impurity auto-classification on every peak
LO
Lead optimization
- Repho proposes the next experiment by Bayesian optimization
- Track analog series with traceable structure evidence per compound
- Surface process impurities while the route is still cheap to change
CS
Candidate selection
- Definitive elucidation with DP4 confidence + a full evidence trail
- Nominate a candidate with the data package already assembled
- Every numerical claim hyperlinked back to the spectrum it came from
CMC
Process & CMC development
- Impurity profiling against ICH Q3A / Q3B / Q3C / Q3D + M7
- Analytical method validation tracked across the Q2(R2) lifecycle
- Batch-to-batch comparison with recipe-hash-reproducible processing
IND
IND / submission
- CTD dossier-section drafts composed from the underlying evidence
- ALCOA+ audit ledger + human signoff gate before any release
- Regulatory surveillance routes guidance changes to affected items
Workflows we light up
Six R&D workflows, with their inputs and outputs.
Each of these is a typed pipeline available in the platform — not a bespoke build. Inputs come from your instruments or your data lake; outputs land in the evidence stack, the audit ledger, and the dossier composer.
Structure confirmation & elucidation
NMR, HRMS, and MS/MS scored together against candidate SMILES with DP4 confidence. Cross-modal disagreement surfaces as a first-class warning before you commit.
Inputs
Raw FID · mzML · candidate SMILES
Outputs
Ranked candidates · DP4 · evidence trail
Impurity & degradant profiling
Peaks auto-classified against curated impurity-shift tables and mapped onto ICH Q3A/Q3B (organic), Q3C (residual solvent), and Q3D (elemental) acceptance windows.
Inputs
Spectra · solvent_hit table · drug substance
Outputs
Classified impurities · ICH verdict · open items
Nitrosamine & genotoxic risk (M7)
Structural-alert detection plus literature priors flag candidate nitrosamines and mutagenic impurities, and recommend the confirmatory MS/MS acquisition to settle them.
Inputs
Structure · synthesis route · spectra
Outputs
M7 verdict · risk tier · recommended MS/MS
Reaction & route optimization
Repho runs multi-objective Bayesian optimization over yield, selectivity, and impurity limits — and accepts those limits as priors so the next route is cleaner by design.
Inputs
Reaction recipe · objectives · constraints
Outputs
Next experiment · Pareto front · rationale
Analytical method validation (Q2(R2))
Track specificity, linearity, accuracy, precision, range, and robustness across a validation campaign — every parameter recipe-hash-linked to the run that produced it.
Inputs
Method runs · acceptance criteria · campaigns
Outputs
Q2(R2) report · parameter coverage · gaps
Submission-ready reporting
Structure-elucidation and impurity reports compose into CTD dossier-section drafts, each numerical claim hyperlinked to source and gated behind explicit human signoff.
Inputs
Reviewed evidence · framework refs
Outputs
CTD drafts · ALCOA+ ledger · signoff record
Measured on our test corpus
What the platform is built to do.
Every number below is derived from our internal benchmark corpus and release notes — not a marketing estimate. The regression gate runs in CI on every detector change.
40
Evidence layers
Typed, additive evidence layers — NMR, HRMS, MS/MS, predicted shifts, fragmentation trees, reaction history, J-couplings — fused into one confidence score per candidate.
8.5×
Faster dense ¹³C
In our v0.5.0 benchmark on dense ¹³C FIDs, heavy raw files that previously took 5+ minutes process in under a minute — so confirmation keeps pace with synthesis.
94.4%
Solvent auto-detect
On our NMRShiftDB2 benchmark corpus, residual-solvent peaks are identified automatically, masked out of candidate scoring, and routed to ICH Q3C classification.
Bit-identical
Recipe-hash replay
Re-derive a processed spectrum or report and get byte-for-byte identical output for the same recipe and inputs. Reproducibility is structural, not aspirational.
The honest comparison
What changes for an R&D program.
Most teams today run discovery through a stack of disconnected apps, spreadsheets, and email. Here's exactly what flips when the evidence travels with the molecule.
| Dimension | Today | With MolTrace |
|---|---|---|
| Confirming a structure | today NMR app + MS app + manual reconciliation, judgement call recorded in a notebook | with MolTrace Cross-modal evidence stack with DP4 confidence and contradiction warnings in one view |
| Impurity audit trail | today Spreadsheet of shifts, hand-typed ICH class, limits looked up per project | with MolTrace Auto-classified peaks mapped to Q3A/B/C/D + M7 with cited reference shifts and deltas |
| Chem ↔ analytical ↔ regulatory handoff | today Files emailed between teams; context and provenance lost at each boundary | with MolTrace One evidence object flows through the modules; every handoff written to the audit ledger |
| Reproducing an analysis months later | today Re-run from scratch; 'looks close enough' is usually the verdict | with MolTrace Recipe-hash replay yields bit-identical output for the same recipe and inputs |
| Reaching a submission-ready section | today Dossier written in parallel in week 11, reconciled against raw data by hand | with MolTrace CTD draft composed from the evidence as a by-product of the science, claim-by-claim cited |
| AI evidence under inspection | today Hard to show how a model reached a call; documentation assembled retroactively | with MolTrace Model documentation designed to support FDA expectations + human signoff gate + ALCOA+ ledger, designed to support inspection readiness |
One worked example
An impurity, end-to-end — and back into the next batch.
The modules aren't separate apps you stitch together. Here is a single finding travelling across all three, with the audit ledger recording every handoff.
SpectraCheck detects
A peak at 2.10 ppm is auto-classified as acetic acid (residual), 93% confidence, and HRMS corroborates the implied formula. No mis-assignment slips through.
Regentry classifies
ICH Q3C: acetic acid is Class 3, no action below 5000 ppm. The finding lands in dossier section 3.2.S.3.2 as informational — no human review queued.
Repho constrains
The impurity limit propagates as a Bayesian prior on the next route. Workup and solvent are adjusted automatically so the following batch is cleaner by design.
The loop closes
The re-acquired spectrum confirms the impurity below threshold. The audit ledger records every step — FID hash → recipe → classification → route update → signoff.
Built for inspection
Speed designed to survive an audit.
Going faster only helps if the work holds up when an inspector arrives. Every acceleration in MolTrace is backed by the same provenance machinery — designed against ICH Q2(R2) ALCOA+, the FDA's January 2025 AI framework, and the EMA reflection paper from day one.
Immutable raw vault
Every FID is SHA-256 hashed, vault-path-policy enforced, and never overwritten. The original evidence survives every reprocess.
Recipe-hash provenance
Every processing run links a recipe hash to the unchanged raw archive. Bit-identical replay from any prior date.
Human signoff queue
No regulatory document is released without an explicit qualified-human attribution — the FDA Stage 4 oversight gate, in code.
ALCOA+ audit ledger
Attributable · Legible · Contemporaneous · Original · Accurate · Complete · Consistent · Enduring · Available — on every event.
Cross-modal contradiction warnings
HRMS exact mass disagreeing with the NMR-implied formula raises a first-class warning before signoff — every time.
Tenant isolation by default
Controls designed to support SOC 2 Type II, data residency designed to support GDPR, and a role-scoped audit-event ledger isolate each organization's data.
Bring a program you're stuck on.
Pick a compound where the structure, the impurity profile, or the submission section is eating weeks. We'll walk through how MolTrace would carry the evidence end-to-end.