Peptide Calculator

How to use Peptide Calculator

Peptide Calculator is a peptide chemical formula and molecular weight calculator and MS peak assignment tool.

Peptide sequences are entered using the standard capitalized single-letter codes. Various nonstandard multiple-letter amino acid codes are also supported and should be enclosed in parentheses, for example:

GVLYVG(pS)K(pT)KEGVVHGVA

N- and C-termini can be selected from the predefined lists. Peptide Calculator also accepts custom termini entered as chemical formulae.

MS peaks for assignment can be provided in the form of a comma-separated list and Peptide Calculator will attempt to assign them to deletion sequences and/or adducts.

A ChemDraw file is automatically generated for each peptide sequence entered, and can be downloaded via a link on the results page. It may be necessary to increase the document size in order to view the complete structure.

Where possible, Peptide Calculator will also provide estimated isoelectric point and molar extinction coefficient values for your sequence, as well as a calculated sequence difficulty profile.

Predefined termini and residues currently supported are given below (with chemical formulae). Hovering over underlined residue codes will display molecular structures.

The calculation functions of Peptide Calculator can also be used in Microsoft Excel, see the add-in page for more information.

Please send comments, questions, residue requests and bug reports to:

Theoretical isoelectric points are calculated using the bisection method algorithm described by Lukasz Kozlowski (http://isoelectric.ovh.org/).

Molar absorption coefficients are estimated using the equation described by Pace et al. (Protein Sci., 1995, 4, 2411).

Beta-strand propensity scores are calculated using an implementation of the SALSA algorithm described by Zibaee et al. (Protein Sci., 2007, 16, 906), which uses Chou-Fasman parameters (P. Y. Chou and G. D. Fasman, Biochemistry, 1974, 13, 211). Nonstandard residues are not included in sequence difficulty calculations.

Residue letter codes

1NalStructureC13H11NO
2NalStructureC13H11NO
2PalStructureC8H8N2O
3PalStructureC8H8N2O
4BipStructureC15H13NO
4BpaStructureC16H13NO2
AStructureC3H5NO
AadStructureC6H9NO3
AbuStructureC4H7NO
AglStructureC2H4N2O
AhxStructureC6H11NO
AibStructureC4H7NO
AspOAllStructureC7H9NO3
AsuStructureC8H13NO3
AzeStructureC4H5NO
CStructureC3H5NOS
ChaStructureC9H15NO
ChgStructureC8H13NO
CitStructureC6H11N3O2
DStructureC4H5NO3
DabStructureC4H8N2O
DapStructureC3H6N2O
DhaStructureC3H3NO
DhpStructureC5H5NO
DprStructureC3H6N2O
EStructureC5H7NO3
FStructureC9H9NO
GStructureC2H3NO
GlaStructureC6H7NO5
GluOAllStructureC8H11NO3
HStructureC6H7N3O
HarStructureC7H14N4O
HciStructureC7H13N3O2
HcyStructureC4H7NOS
hCysStructureC4H7NOS
HphStructureC10H11NO
HprStructureC6H9NO
HylStructureC6H12N2O2
HypStructureC5H7NO2
IStructureC6H11NO
KStructureC6H12N2O
LStructureC6H11NO
LysAllocStructureC10H16N2O3
MStructureC5H9NOS
NStructureC4H6N2O2
NleStructureC6H11NO
NvaStructureC5H9NO
OicStructureC9H13NO
OrnStructureC5H10N2O
PStructureC5H7NO
PalStructureC8H8N2O
PenStructureC5H9NOS
PhgStructureC8H7NO
PipStructureC6H10N2O
PraStructureC5H5NO
pSStructureC3H6NO5P
pTStructureC4H8NO5P
pYStructureC9H10NO5P
PyrStructureC5H5NO2
QStructureC5H8N2O2
RStructureC6H12N4O
SStructureC3H5NO2
TStructureC4H7NO2
ThiStructureC7H7NOS
TicStructureC10H9NO
TleStructureC6H11NO
TpiStructureC12H10N2O
UStructureC3H5NOSe
VStructureC5H9NO
WStructureC11H10N2O
YStructureC9H9NO2

Predefined N-termini

AcetylCH3CO
BenzylC8H9
FmocC15H11O2
MethylCH3

Predefined C-termini

Alloc DbzC11H12N3O3
AmideNH2
Benzyl esterC7H7O
DbzC7H8N3O
Ethyl 3-mercaptopropionateC5H9O2S
Methyl esterOCH3
N-acylureaC8H6N3O2
Sulfamyl RinkC4H9N2O3S
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