Peptalyzer™ is a professional diagnostic peptide calculator built for rigorous physicochemical analysis and SPPS planning. It integrates classical biophysical constants with 3D topological mapping to identify aggregation risks, amphipathic domains, and purification challenges before you reach the bench.
Designed for Fmoc-SPPS strategy and analytical interpretation, Peptalyzer™ delivers real-time sequence evaluation so that every synthesis decision is grounded in validated mechanistic models.
Peptalyzer™
Residue Topology Graph
Peptide Sequence Identity
| Length | - |
| Mw (Average) | - |
| Mw (Monoisotopic) | - |
| pI (IPC 2.0) | - |
| Molecular Formula | - |
| Estimated Molecular Volume | - |
Molecular Characteristics
| Intramolecular SS Bonds | - |
| Intermolecular SS Bonds | - |
| Peptide State | - |
| Extinction Coefficient (ε280) | - |
| Extinction Coefficient (ε205) | - |
| Average Residue Volume | - |
| Aromaticity Index | - |
| └ Including Histidine (Neutral pH) | - |
Molecular Size
| Equivalent Sphere Radius (Compact) | - |
| Flexible-Chain Radius (Extended) | - |
| Expansion Ratio | - |
Amino Acids
| AA | Count | % | Nature | Residue Class |
|---|
Solubility & Polarity Matrix
Thermodynamic Aggregation Risk
| Helix | - |
| Sheet | - |
| Coil | - |
Bio-Predictive Metrics
| Boman Index | - |
| Aliphatic Index | - |
| Instability Index | - |
Z-Scale Descriptor
| Mean | Std | Range | |
|---|---|---|---|
| Z1 | - | - | - |
| Z2 | - | - | - |
| Z3 | - | - | - |
| Z4 | - | - | - |
| Z5 | - | - | - |
Peptide Charge Properties
| IPC 2.0 | - |
| └ Bjellqvist scale | - |
| └ EMBOSS scale | - |
| └ Lehninger scale | - |
| Method Agreement | - |
| Charge Density | - |
| Group | Group Count | % of Tracked Groups | Components Present |
|---|
Hydrophobicity Profiles
Structural Topology
alpha-Helical Structure
beta-Sheet Structure
MS Precursor Ions
Formula will appear here Observed m/z Check
| Observed m/z | Match | Isotope | Charge | Theoretical m/z | ppm error |
|---|---|---|---|---|---|
| No observed m/z entered. | |||||
Precursor Ion Table
| Ion | Mode | Charge | Peak | Neutral mass | Mass shift | Proton change | m/z | Relative intensity | Adducts |
|---|---|---|---|---|---|---|---|---|---|
| No precursor ions loaded. | |||||||||
MS/MS Fragment Ions
Fragment Ion Table
| Ion | Series | Start | End | Sequence | Charge | Neutral loss | Neutral mass | m/z |
|---|---|---|---|---|---|---|---|---|
| No fragment ions loaded. | ||||||||
Synthesis Difficulty Profile
Chemical Stability Audit
Side Reaction Audit
| Risk | Issue | Location | Action |
|---|
Aggregation Rescue
Synthesis Calculator
Scale & Resin
Coupling Protocol
Deprotection
Washes
Extra Coupling Passes
Cleavage Protocol
Recommended (primary)
Alternative
Why this cocktail (sequence-driven)
LC-MS adducts to monitor
For broader peak assignment, compare unexpected mass shifts against the peptide mass-shift reference.
Safety notes
Support Summary
Analysis Tools Support
| Tool | Status | Current Sequence Basis |
|---|
Detailed Feature Matrix
| Feature | Status | Current Sequence Basis |
|---|
Advanced Peptide Calcu for Synthetic Chemists
I. High-Precision Physical Constants
Reliable peptide physicochemical property analysis begins with absolute precision in mass and charge determination.
- Mass Spectrometry Support: High-precision calculation of Monoisotopic and Average Mass , fully accounting for N-terminal (e.g., Acetylation) and C-terminal (e.g., Amidation) modifications , as well as disulfide bond hydrogen-loss.
- Multi-Scale Isoelectric Point (pI): Determine the Isoelectric Point (pI) via an iterative bisection method using four simultaneous scales (IPC 2.0, Bjellqvist, EMBOSS, Lehninger). Calculate exact net charge at any user-selected pH (0.0–14.0).
- Molar Extinction Coefficients: Precise determination of ϵ280 (Trp/Tyr/SS bonds) and ϵ205 (peptide backbone) to facilitate accurate UV-based concentration assays.
II. Synthesis & Aggregation Diagnostics
Predicting the “difficult sequence” is a core objective of our peptide physicochemical property analysis.
- Sequence Chemical Stability Audit: Proactively scan your sequence for synthesis vulnerabilities, including aspartimide hotspots, oxidation-prone residues, and specific degradation motifs.
- Thermodynamic Aggregation Risk: A “Traffic Light” system utilizing a 6-residue sliding window to identify local beta-sheet hotspots and predict potential coupling failures during Fmoc-SPPS.
- Peptide Polarity Matrix: A proprietary classification mapping Total Hydrophobicity vs. Charge Fraction to predict solubility and the necessity of organic co-solvents (like DMSO).
III. Interactive Biophysical & Structural Mapping
Peptalyzer™ translates linear sequences into interactive, publication-ready visualizations to reveal hidden structural tendencies.
- 3D Structural Topology: Visualize amphipathic clusters and salt-bridges using the Spiral Helical Wheel (with 3D depth gradients) , or detect localized charge clusters via the Beta-Strand Zig-Zag projection.
- Hydropathy & Hydrophilicity Profiles: Interactive sliding-window charts (Kyte-Doolittle and Hopp-Woods) to pinpoint membrane-partitioning regions and surface-exposed antigenic epitopes.
IV. Bio-Predictive Indices
Peptalyzer™ calculator includes validated statistical descriptors for estimating in vivo behavior and handling.
- GRAVY & Boman Index: Assessment of overall hydropathy (Kyte-Doolittle) and protein-binding potential (kcal/mol) to evaluate solubility and interaction profiles. Assessment of overall hydropathy and protein-binding potential (kcal/mol) to evaluate interaction profiles.
- Instability & Aliphatic Index: Statistical estimates of in vivo half-life and thermostability based on dipeptide weight values and aliphatic side-chain volumes.
All calculations are grounded in peer-reviewed models widely used in peptide science. This makes Peptalyzer™ a reliable calculator for planning synthesis, evaluating stability, and interpreting biophysical data. To learn more about the math and algorithms behind these descriptors, visit our Peptalyzer™ Resources page.