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Peptide Analysis Suite

Side reactions ⚗️ SMILES → seq 🧬 API ↗ Contact ✉

① Sequence

Natural amino acids as single letters, joined with -. Express non-natural AAs as a natural analog plus a modification. e.g. Aib → A[Formula:CH2]

② Residues

③ Modifications

Bracket contents, separated by ;. e.g. Oxidation, +15.9949, Formula:CH2

# AA Modification Mass (Da)

④ N / C Terminal

⚛ Parameters

Generates 1..N charge states

Neutral mass
Precursor m/z
ProForma:

Theoretical spectrum (by m/z)

Fragment list ()

Ion Type Position Charge Neutral loss m/z Neutral mass
⚛

Enter a ProForma string and click Generate.

① API sequence

Already built one in the Builder?

② Parameters

Observed peak − main peak (neutral)

Default 0.02 (HRMS recommend 0.005)

2 = allow two-step combinations (slower)

Keep at 1 in scan mode (combinatorial blowup)

Truncate beyond this

API neutral mass
Total candidates
Category breakdown

Δmass scatter (color by category · hover · click to send to Fragments tab)

Candidate impurities

# Category Steps ΔM (Da) ProForma Path m/z 1+ m/z 2+ m/z 3+ Action

Note: isobaric candidates (e.g. +15.99 from M/W/H/Y/C oxidation) cannot be distinguished by MS1 alone. Use → Fragments to verify against an MS/MS spectrum.

🧪

Enter an API peptide sequence to predict synthesis impurities.

14 categories: deletion / insertion / substitution / truncation / chemical mods / protecting-group residue / coupling byproducts / …

🤔

No matches — try a wider tolerance, more steps, or more categories.

① Sequence

From the Builder?

Cys presence is auto-detected from sequence; this only controls protection.

Detected:

② Aspartimide risk

Each Asp/Asn scored from neighbour residue, position from C-terminus (= remaining Fmoc cycles), and side-chain protection.

References: Subirós-Funosas et al. Tetrahedron Lett. 2009 · Mergler et al. (Mpe, Bno) J. Pept. Sci. 2003 / 2015 · Liu et al. (hydrazide) Org. Lett. 2024. → side-reaction details

③ Recommended cleavage cocktail

Rule-based decision from sequence + protecting groups. Each component's role is shown.

🧫

🔤 3-letter → 1-letter

Separate codes with -. e.g. Ala-Asn-Glu

Unknown: — replaced with X

🧪 SMILES → formula

RDKit-based, includes a 2D structure preview.

Formula:
Monoisotopic mass:

🧬 SMILES → ProForma + monoisotopic mass browser-side · RDKit.js

Paste a peptide SMILES — get a fully-qualified ProForma string and the monoisotopic mass. 20 natural amino acids as letters; side-chain mods as [Formula:Δ]; Aib / N-methyl backbones as X[Formula:…]; N/C-terminal caps detected ([Acetyl]-…-[Amide]); cyclic peptides + disulfide bridges supported. Runs locally — no upload.

Examples (click to load):
3-letter ↔ 1-letter table ▶
Non-natural amino-acid notation ▶

Express non-natural AAs as a natural analog plus a modification:

Non-natural ProForma Note
AibA[Formula:CH2]Ala + CH2 = 103 Da
β-AlaA[info:beta]isomer of Ala (info tag only)
Sar (N-Me-Gly)G[Formula:CH2]Gly + CH2
NleL[info:nle]isomer of Leu
OrnK[Formula:-CH2]Lys − CH2
HypP[Oxidation]hydroxyproline = Pro + O
PyrogluE[-18.0106]N-term cyclized dehydration
ProForma cheatsheet ▶

ProForma is a PSI-MS standard string notation for one or more peptide/protein primary structures.

  • PTM (Unimod / PSI-MOD / RESID)
    EM[Oxidation]EVEES[UNIMOD:21]PEK
EM[L-methionine sulfoxide]EVEES[MOD:00046]PEK
  • Mass shift
    EM[+15.9949]EVEES[-79.9663]PEK
  • Element formula
    SEQUEN[Formula:C12H20O2]CE
  • Termini
    [iTRAQ4plex]-EMEVNESPEK-[Methyl]
  • Glycan (GNO)
    YPVLN[GNO:G62765YT]VTMPN[GNO:G02815KT]NSNGKFDK
  • Crosslink (XL-MOD)
    EMEVTK[XLMOD:02001#XL1]SESPEK[#XL1]
  • Isotope label
    <13C>ATPEILTVNSIGQLK
  • Charge
    VAEINPSNGGTT/2
Supported neutral losses ▶