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Peptide molecular weight calculator

Paste a peptide sequence in one-letter code to get its molecular formula, average and monoisotopic mass, and the protonated ions a mass-spec report lists.

Load a known peptide

PeptideSequenceModificationsFormulaAvg. mass
BPC-157GEPPPGKPADDAGLV—C62H98N16O221419.54
GHK (GHK-Cu without copper)GHK—C14H24N6O4340.38
EpitalonAEDG—C14H22N4O9390.35
KPVKPV—C16H30N4O4342.43
SelankTKPRPGP—C33H57N11O9751.87
SemaxMEHFPGP—C37H51N9O10S813.92
DSIPWAGGDASGE—C35H48N10O15848.81
CartalaxAED—C12H19N3O8333.29
Thymosin Alpha-1SDAAVDTSSEITTKDLKEKKEVVEEAENN-acetylC129H215N33O553108.28
OxytocinCYIQNCPLGC-amide, 1 disulfideC43H66N12O12S21007.19
Kisspeptin-10YNWNSFGLRFC-amideC63H83N17O141302.44
SermorelinYADAIFTNSYRKVLGQLSARKLLQDIMSRC-amideC149H246N44O42S3357.88
AOD-9604YLRIVQCRSVEGSCGF1 disulfideC78H123N23O23S21815.08
MOTS-cMRWQEMGYIFYPRKLR—C101H152N28O22S22174.59
VIPHSDAVFTDNYTRLRKQMAVKKYLNSILNC-amideC147H238N44O42S3325.80
LL-37LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES—C205H340N60O534493.26
TB-500 fragment (Ac-LKKTETQ)LKKTETQN-acetylC38H68N10O14889.01

How the calculation works

A peptide's mass is the sum of its residue masses plus one water for the free termini. The calculator builds the exact molecular formula first, then prices each element at its average atomic weight (for weighing and molarity) and at its most abundant isotope (for mass spectrometry). Every known peptide in the table above reproduces the formula PubChem lists for it.

To check a lot, compare the [M+H]+ or multiply-charged ions here with the observed ions on its certificate of analysis. The COA guide walks through a report line by line, and the molecular weight reference covers compounds with non-standard residues.

Amino acid residue masses

Code3-letterAmino acidResidue formulaAverageMonoisotopic
GGlyGlycineC2H3NO57.051357.0215
AAlaAlanineC3H5NO71.077971.0371
SSerSerineC3H5NO287.077387.0320
PProProlineC5H7NO97.115297.0528
VValValineC5H9NO99.131199.0684
TThrThreonineC4H7NO2101.1039101.0477
CCysCysteineC3H5NOS103.1429103.0092
LLeuLeucineC6H11NO113.1576113.0841
IIleIsoleucineC6H11NO113.1576113.0841
NAsnAsparagineC4H6N2O2114.1026114.0429
DAspAspartic acidC4H5NO3115.0874115.0269
QGlnGlutamineC5H8N2O2128.1292128.0586
KLysLysineC6H12N2O128.1723128.0950
EGluGlutamic acidC5H7NO3129.1140129.0426
MMetMethionineC5H9NOS131.1961131.0405
HHisHistidineC6H7N3O137.1393137.0589
FPhePhenylalanineC9H9NO147.1739147.0684
RArgArginineC6H12N4O156.1857156.1011
YTyrTyrosineC9H9NO2163.1733163.0633
WTrpTryptophanC11H10N2O186.2099186.0793

pKa, charge, hydropathy and modification mass shifts for every residue are in the amino acid table.

Questions

How do you calculate the molecular weight of a peptide?

Add the residue masses of every amino acid in the chain, then add one water (18.02 g/mol average) for the free N- and C-termini. Adjust for modifications: N-terminal acetylation adds C2H2O (42.04), C-terminal amidation swaps OH for NH2 (−0.98), and each disulfide bond removes two hydrogens (−2.02).

What is the difference between average and monoisotopic mass?

Average mass uses natural isotope abundance and is the figure for weighing and molarity. Monoisotopic mass uses only the most abundant isotope of each element (12C, 1H, 14N, 16O, 32S) and is what a high-resolution mass spectrometer reports as the first peak of the isotope pattern.

Why does the mass on a COA differ from the calculated value?

Mass-spec results are usually reported as protonated ions ([M+H]+, [M+2H]2+), so the number is the molecule's mass plus one or more protons, divided by the charge. Salt forms such as acetate or TFA, and metal complexes such as GHK-Cu, change the weighed mass but not the peptide's own ion.

Does the calculator handle D-amino acids and unusual residues?

D-amino acids have the same mass as their L-forms, so enter them with the normal letter. Non-standard residues such as Aib, norleucine, 2-naphthylalanine or Dmt are not in the 20-letter code, so peptides that contain them (ipamorelin, PT-141, SS-31 and others) need their formula from PubChem; see the molecular weight reference.

A reference tool for laboratory research. Not for human or animal use.