SS-31 is a laboratory code, not a chemical name. This reference covers the identity of SS-31: what the structure is, what mass to expect, how it behaves under reverse-phase HPLC, and how a buyer can confirm that the material in a vial is what the label says. It does not describe what SS-31 does, and preparation, handling and dosing are not covered.
The structure behind the name
SS-31 is a tetrapeptide amide with the sequence D-Arg-Dmt-Lys-Phe-NH2. Two of its four residues are not the standard L-amino acids found in most catalogue peptides:
- D-Arg at position one is the D-enantiomer of arginine, the mirror image of the natural L-form.
- Dmt at position two is 2′,6′-dimethyl-L-tyrosine, a tyrosine carrying two methyl groups on the aromatic ring either side of the side-chain attachment point.
- Lys and Phe at positions three and four are ordinary L-lysine and L-phenylalanine.
- The C-terminus is a primary amide (-NH2) rather than a free carboxylic acid.
The molecular formula is C32H49N9O5 and the average molecular mass of the free base is approximately 639.8 g/mol. Because this is a very small molecule, the salt form makes up a large share of what is actually weighed, which is discussed below.
What the name SS-31 refers to
The letters SS come from the surnames of the two researchers in whose laboratory the series of aromatic-cationic tetrapeptides was developed (Szeto and Schiller), and 31 is the compound’s number within that series. Other members of the series carry different numbers and differ in one or more residues. Elamipretide is the International Nonproprietary Name for the same structure.
That numbering is the reason the sequence matters so much. Sibling compounds in the same series use the same building blocks in a different order or with one substitution, and they can have the same or very similar mass. A label that says “SS-31” without printing D-Arg-Dmt-Lys-Phe-NH2, including the D-configuration and the C-terminal amide, is not a complete identity statement.
How SS-31 behaves on reverse-phase HPLC
SS-31 alternates cationic and aromatic residues. Arginine and lysine side chains plus the free N-terminal amine give it three positive charges under the acidic conditions of a trifluoroacetic acid mobile phase, and the C-terminal amide removes the negative charge a free acid would carry. The Dmt and Phe side chains provide two aromatic rings and most of the hydrophobic surface.
For a molecule this small and this highly charged, retention on a C18 column is modest and it elutes relatively early in a standard water/acetonitrile gradient, though later than a purely polar tripeptide because of the two aromatic rings. A shallow gradient improves separation from closely related species. Ion-pairing strength also matters: with three basic groups, retention time shifts noticeably if the TFA concentration in the mobile phase changes, so a certificate should state it.
On detection, SS-31 absorbs at 214 nm on its peptide bonds, and its phenolic Dmt ring gives it measurable absorbance around 280 nm as well, though weaker than a tryptophan-containing peptide. Purity is normally reported at 214 nm or 220 nm, where all peptide species are seen.
What an analysis for SS-31 should show
A useful certificate reports the column chemistry and dimensions, mobile phases and gradient, detection wavelength, retention time, the integrated main peak with its integration window visible, and a mass confirmation at or near 639.8 for the free base (or the corresponding protonated ions). Our guide on how to read an HPLC chromatogram covers what each element tells you.
Two identity questions are specific to this structure. The first is stereochemistry. An L-Arg version of the peptide has exactly the same mass as the D-Arg version, so mass spectrometry alone cannot tell them apart, and on an ordinary achiral column the two may elute very close together. The second is the C-terminus: a free-acid variant differs from the amide by about 1 Da, which a low-resolution mass spectrum can miss. Both points are covered in our article on peptide synthesis impurities.
Net peptide content for SS-31 belongs on the certificate as its own figure, apart from chromatographic purity, together with the named counter-ion. SS-31 is a textbook case of why this matters. With three basic sites on a molecule of under 640 g/mol, a tris-trifluoroacetate salt adds roughly 340 g/mol of counter-ion, so a substantial fraction of the powder by weight is not peptide at all. SS-31 is also commonly prepared as an acetate or hydrochloride salt, and each gives a different conversion from weighed mass to peptide mass. Our comparison of TFA vs acetate counter-ions explains the arithmetic.
Confirming identity independently
For SS-31, the structure is a better search key than the name. Public chemical databases index this compound under its full systematic name and under elamipretide, and those records show the D-configuration at arginine, the dimethyltyrosine and the C-terminal amide explicitly. Checking a vendor’s stated formula and mass against those records takes a minute. Database links for SS-31 are on its product page.
How SS-31 is supplied here
SS-31 10mg is supplied as a lyophilised powder in a sealed vial. An independent reverse-phase HPLC analysis of SS-31 is published with the product. Both the vial size and the published HPLC purity of SS-31 appear on the product page. There is no lot number on a SS-31 vial; the crimp and cap color identify which published analysis it belongs to.
Frequently asked questions
What is the structure of SS-31?
D-Arg-Dmt-Lys-Phe-NH2: D-arginine, 2′,6′-dimethyl-L-tyrosine, L-lysine and L-phenylalanine, with a C-terminal amide.
Are SS-31 and elamipretide the same compound?
Yes. SS-31 is the laboratory series code and elamipretide is the International Nonproprietary Name for the same tetrapeptide amide.
What molecular weight should I expect for SS-31?
Approximately 639.8 g/mol for the free base, formula C32H49N9O5. Salt forms read considerably higher, which is why the counter-ion has to be declared with the mass.
Can mass spectrometry confirm the D-arginine?
No. D- and L-arginine have identical masses. Confirming stereochemistry needs a chiral method or amino acid analysis with chiral derivatisation; mass spectrometry confirms composition, not configuration.
Research use only. All products supplied by Battle Born Peptides are laboratory reference materials for in-vitro research and analytical use by qualified professionals. They are not drugs, foods, dietary supplements, cosmetics or medical devices; they are not approved by the FDA or any other regulator for use in humans or animals; and they are not intended to diagnose, treat, cure, mitigate or prevent any disease, or to affect the structure or any function of the body of humans or animals. Nothing in this article is preparation, handling or dosing guidance. See our full research-use terms.