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

N-terminus

C-terminus

⚛ Parameters

ProForma string

Ion types

Max charge

Generates 1..N charge states

Neutral losses

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?

Mode

② Parameters

Observed Δmass (Da) *

Observed peak − main peak (neutral)

Mass tolerance (Da)

Default 0.02 (HRMS recommend 0.005)

Max stacked mods

2 = allow two-step combinations (slower)

Max stacked mods

Keep at 1 in scan mode (combinatorial blowup)

Max candidates

Truncate beyond this

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.

🔤 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:

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
Aib	A[Formula:CH2]	Ala + CH2 = 103 Da
β-Ala	A[info:beta]	isomer of Ala (info tag only)
Sar (N-Me-Gly)	G[Formula:CH2]	Gly + CH2
Nle	L[info:nle]	isomer of Leu
Orn	K[Formula:-CH2]	Lys − CH2
Hyp	P[Oxidation]	hydroxyproline = Pro + O
Pyroglu	E[-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 ▶