Reaction-aware candidates
Considers the expected product, starting materials, likely transformations, common side reactions, byproducts and relevant reagent-derived signals.
Founding Chemist private beta
Turn unexplained LCMS peaks into chemical hypotheses.
MolSage looks at the reaction context—not just the mass. Upload a reaction scheme, add observed m/z values, and investigate plausible products, side products, byproducts and reagent-derived signals in one focused workflow.
Built for synthetic, medicinal and process chemists. Assignments are hypotheses—not structural proof.
REACTION-AWARE ANALYSIS
catalyst
base · solvent
base · solvent
m/z 238
Expected product · [M+H]+
Strong
m/z 187
Plausible reaction side product
Moderate
m/z 171
Starting-material-derived species
Moderate
Reaction context matters.Mass fit + chemistry context + transparent evidence.
Designed for day-to-day synthetic chemistry
Medicinal chemistry
CRO / discovery
Process chemistry
Analytical support
MolSage LCMS
Less time staring at a peak. More time deciding what to do next.
Mass matching is useful, but it is not enough. MolSage brings reaction structures, conditions and observed masses into the same analysis so the candidate list reflects the chemistry you actually ran.
Mass precision handled properly
Distinguishes nominal and rounded entries from high-resolution values, so a typed integer is not incorrectly treated as an exact measurement.
Deeper review when needed
Routine cases stay fast. Difficult, ambiguous or unresolved peaks can trigger a broader chemistry review before candidates are re-checked and ranked.
Workflow
Three inputs. One focused analysis.
The interface is intentionally built around how a synthetic chemist reviews a reaction after an LCMS run.
Add the reaction
Upload the reaction scheme or paste editable structures and conditions. The chemistry remains reviewable before analysis.
Enter observed m/z
Paste one or many masses, choose ion mode, and retain the precision reported by the instrument.
Review ranked hypotheses
See candidate structures, formulas, adducts, calculated masses, evidence strength, rationale and unresolved or ambiguous peaks.
Why reaction-aware?
The same m/z can mean very different things in different reactions.
Mass-only workflow
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Generate formulas or database hits near the measured mass.
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Manually decide which structures are plausible under the actual conditions.
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Repeatedly check starting materials, adducts, protecting groups and known side reactions.
MolSage workflow
✓
Use reaction structures and conditions as part of candidate generation.
✓
Separate structural side products from ordinary ion/adduct explanations.
✓
Escalate only the hard cases and keep the final mass checks deterministic.
Scientific rigor
Useful hypotheses without pretending MS1 is proof.
MolSage is designed to help a chemist narrow the search space, not to overstate certainty. The interface explicitly separates mass agreement from structural confidence and surfaces ambiguity rather than hiding it.
Strong evidenceModerate evidenceTentative
01
Exact calculations are re-checked
Candidate structures are validated before formulas, neutral masses and common ion forms are calculated for matching.
02
Ambiguity is visible
When several structures fit the same peak, the result is marked as ambiguous rather than silently implying that the first candidate is uniquely identified.
03
Data quality affects evidence
Nominal and low-precision masses are prevented from receiving the same evidence level as high-resolution measurements.
04
Orthogonal confirmation is encouraged
Important assignments should still be checked with isotope pattern, MS/MS, retention behavior, authentic standards, isolation or NMR where appropriate.
Security & privacy
Built with confidential chemistry in mind.
Different organizations have different data policies. MolSage is being designed so the analysis workflow can support multiple privacy models without changing how the chemist works.
Clear data boundaries.
Routine calculations and structure checks run within the MolSage application. When deeper chemistry reasoning is enabled, relevant reaction context may be sent to the configured reasoning service.
✓
Encrypted browser-to-server traffic over HTTPS.
✓
Private beta access is restricted while the product is being validated.
✓
Enterprise architecture can support customer-controlled credentials or approved private endpoints.
Beta
MolSage-managed access
Simple for individual beta users. Advanced analysis can use a server-managed credential with usage controls.
Planned
Bring your own key
For users or teams that prefer to control their own approved reasoning-service account and spend.
Enterprise
Private deployment options
For organizations with stricter IP policies, the architecture can be adapted to customer-approved infrastructure and endpoints.
The MolSage platform
LCMS is the first module, not the final destination.
The long-term goal is one chemistry workspace where reaction context and analytical evidence can reinforce each other.
MolSage LCMS
Reaction-aware impurity and peak assignment for synthetic chemistry.
MolSage NMR
Structure-linked annotation and consistency checking for NMR workflows.
MolSage Workspace
Connected reaction, structure and analytical tools in a single chemist-focused environment.
Founding Chemist Program
Help shape the product on real chemistry.
The first beta is intentionally small. We are looking for synthetic chemists willing to test MolSage on historical or day-to-day LCMS problems and tell us where the assignments help—or fail.
✓Free private-beta access for early testers
✓Direct influence on reaction coverage and workflow
✓Early access to NMR and future chemistry modules
FAQ
Questions chemists usually ask first.
Does MolSage identify an impurity with certainty?
No. It generates and ranks plausible assignments from the available chemistry and mass evidence. MS1 alone often cannot distinguish constitutional or stereochemical isomers, so important assignments still require appropriate confirmation.
Do I need high-resolution MS?
No. MolSage can work with nominal or rounded masses, but the evidence level reflects the lower specificity. HRMS values allow tighter mass discrimination.
What if the reaction is unusual?
The standard analysis handles common patterns quickly. Difficult or weakly covered cases can use a broader chemistry review, after which proposed structures are checked again before they appear in the results.
Can my organization use its own approved AI/reasoning account?
That is part of the intended team and enterprise architecture. The beta is starting with a simpler hosted configuration, while customer-controlled credentials and private deployment paths are being prepared.
Is MolSage only for LCMS?
No. LCMS is the first live module. NMR annotation and a broader chemistry workspace are planned as separate modules under the same MolSage platform.