SS-31 (elamipretide) CAS, molecular weight and sequence: analytical reference for lab procurement

For analytical procurement the durable identifiers are CAS 736992-21-5, formula C32H49N9O5 and an average mass of 639.8 g/mol. PubChem CID 11764719 is the public structure record behind those numbers. Vendor listings that print 640.8 g/mol are off by one mass unit; the PubChem value is 639.8.

Write the salt form on the order as well. SS-31 has three basic sites, so it is usually isolated as an acetate or trifluoroacetate salt, and the counter-ions add weight to the powder without adding peptide.

1. CAS 736992-21-5 and the name elamipretide / SS-31 on the PO and receiving log.
2. Formula C32H49N9O5 and MW 639.8 g/mol (free base) on the analytical worksheet.
3. Salt form (acetate or TFA) and the lot number printed on the vial.

The two unusual residues are what make SS-31 analytically interesting. The N-terminal arginine is the D-enantiomer, and Dmt is a tyrosine with two extra methyl groups on the ring. The Zhao et al. paper that introduced the series describes the design as alternating aromatic and basic residues with Dmt supplying the phenol.

A peptide made with L-arginine by mistake has exactly the same mass as SS-31, so mass spectrometry alone cannot exclude that diastereomer. Only a chromatographic method that separates the two (or a chiral amino-acid analysis) can. That is why a single LC-MS identity result is not a complete identity check for this compound.

SS-31 is small, very polar and carries about +3 charge, so on a reversed-phase C18 column it elutes early unless an ion-pairing acid such as 0.1% TFA is in the mobile phase. A useful HPLC report states the column, mobile phases, gradient, detection wavelength and the integration rule behind the area-percent purity number.

Expect [M+H]+ at m/z 640.39 and [M+2H]2+ at m/z 320.70 for the free peptide. A sodium adduct, if present, sits about 21.98 Da above the protonated ion. Counter-ions such as acetate or TFA are lost in the source and should not shift the peptide ion.

Two small mass shifts are worth knowing. Hydrolysis of the C-terminal amide to the free acid adds 0.984 Da, which is easy to miss at low resolution. A missing or extra residue changes the mass by a whole residue (for example 128.09 Da for lysine), which any LC-MS run will catch.

1. +0.984 Da: C-terminal acid instead of amide.
2. −128.09 Da: des-Lys deletion.
3. −147.07 Da: des-Phe deletion.
4. Same mass, different retention: L-Arg diastereomer (needs chromatography to resolve).

Gross powder weight is not peptide weight. As an illustration only, a tri-acetate salt of SS-31 adds three acetic acid equivalents (60.05 g/mol each) to the 639.8 g/mol peptide, so peptide would be roughly 78% of the roughly 820 g/mol salt formula weight before any water is counted. A real lot needs its own net peptide content or counter-ion result; do not use this illustration as a lot value.

For stock-solution arithmetic in an assay, use the net peptide content from the lot report when it exists, and record the salt form, solvent and date in the notebook.

No third-party lot report for SS-31 is published on this site yet. A lab report is available on request for the lot you would receive, and the batch number on the vial can be checked on the lot lookup page. Only some lots have a published COA.

Self-serve orders from the United States (Canada and Mexico are paused) use US fulfillment and usually ship within 5 business days of confirmed payment. Credentialed laboratories in other eligible countries can request an institutional export review through the international lab orders page. Self-serve shipping is not offered to Australia, New Zealand or OFAC-sanctioned destinations.