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Peptide Analysis Suite

API β†— Contact βœ‰

β‘  Sequence

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

β‘‘ Residues

β‘’ Modifications

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

# AA Modification Mass (Da)

β‘£ N / C Terminal

βš› 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
βš›

Enter a ProForma string and click Generate.

β‘  API sequence

Already built one in the Builder?

β‘‘ Parameters

Observed peak βˆ’ 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

Ξ”mass scatter (color by category Β· hover Β· click to send to Fragments tab)

Candidate impurities

# Category Steps Ξ”M (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 β†’ Fragments to verify against an MS/MS spectrum.

πŸ§ͺ

Enter an API peptide sequence to predict synthesis impurities.

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

πŸ€”

No matches β€” try a wider tolerance, more steps, or more categories.

πŸ”€ 3-letter β†’ 1-letter

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

Unknown: β€” replaced with X

πŸ§ͺ SMILES β†’ formula

RDKit-based, includes a 2D structure preview.

Formula:
Monoisotopic mass:
3-letter ↔ 1-letter table β–Ά
Non-natural amino-acid notation β–Ά

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

Non-natural ProForma Note
AibA[Formula:CH2]Ala + CH2 = 103 Da
Ξ²-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 βˆ’ CH2
HypP[Oxidation]hydroxyproline = Pro + O
PyrogluE[-18.0106]N-term cyclized dehydration
ProForma cheatsheet β–Ά

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 β–Ά