Laboratory glossary
Amino acid sequences and structural notation
The residue order of a chain; a complete representation must state relevant modifications and termini.
Source editorial review:
The distinction that matters
A letter sequence without amidation or stereochemical information may leave the exact entity unresolved.
What a sequence records
Amino acid sequence is residue order, conventionally read from the amino N-terminus toward the carboxyl C-terminus. It is not merely the list of constituent residues. Rearranging the same residues creates a different compound with the same formula and theoretical mass. An HPLC method may separate such structures, but that separation is not guaranteed.
Three-letter notation uses an initial capital followed by lowercase letters and hyphen separators, as in Gly-His-Lys. One-letter notation uses adjacent capitals, as in GHK. Both represent the 20 standard amino acids. Noncanonical residues such as Aib, Nle and Orn require explicit notation rather than an assumed one-letter equivalent.
What residue letters cannot express alone
Residue order is only part of chemical identity. Additional modifications must be stated; omitting them can describe another formula and theoretical mass.
Capitalization and punctuation can change interpretation. Gly is glycine in three-letter notation, while GLY read as one-letter code means glycine–leucine–tyrosine. Preserve the notation when transcribing.
- An N-terminal acetyl group is commonly written Ac- before the first residue.
- C-terminal amidation is commonly written -NH2 after the last residue.
- D configuration can be marked with D- in three-letter notation or a defined lowercase convention in one-letter notation; check the source legend.
- Disulfide bridges and cyclization require additional connection annotations because a linear string cannot describe them fully.
Why sequence matters in quality assessment
The declared sequence and modifications provide the structure used to calculate theoretical mass for comparison with ESI-MS. Without that structural reference, a measured mass is an isolated number rather than a meaningful identity comparison.
HPLC does not fill that gap. It measures chromatographic responses and their relative areas, not the complete identity of the main peak. Identity and purity remain distinct determinations in batch documentation.
On receipt, compare the sequence information available in the certificate, vial labeling and catalog data sheet. Resolve discrepancies before opening or reconstituting the material; subsequent preparation changes the original sample condition.
Decisions in a research catalog
Analogs and fragments are defined in relation to a reference: a substituted residue, modified terminus or shortened interval. Abbreviations vary and recur across suppliers. Compare complete sequences and modifications rather than relying on a shared short name.
Sequence alone is not a complete handling protocol. Consult the individual data sheet and laboratory procedure for diluent selection, preparation volume and storage conditions.
Common confusion
A sequence determines a theoretical mass, but mass does not uniquely recover the sequence. Leucine and isoleucine have the same mass, as do permutations of the same residues. Agreement is compatible with the declared sequence rather than proof of residue order. A sequence string also does not necessarily define the entire supplied material: counterion, terminal chemistry and stereochemistry can distinguish products sharing the same basic residue letters.
How to record it
Notation convention, direction, nonstandard residues and modifications.