Peptide Analysis Glossary: COA and Lab Terms Explained

Published September 28, 2026 · ROVIQ Research

Plain definitions of the terms that appear on a peptide Certificate of Analysis and in laboratory handling, in alphabetical order. Each entry links to a longer guide where one exists.

Terms: Area-percent purity · Batch · Certificate of Analysis · Chromatogram · Counter-ion · Deamidation · Deletion sequence · Diastereomer · Electrospray ionization · HPLC · Identity confirmation · LC-MS · Lyophilization · m/z · Mass spectrometry · Monoisotopic and average mass · Net peptide content · Oxidation · Peptide · Related impurities · Research use only · Retention time · Solid-state stability · UV detection

Area-percent purity

The purity figure most COAs report: the area of the main HPLC peak divided by the total area of all integrated peaks, as a percentage. It describes how much of the UV-absorbing material the method detected came out as the main peak. It is not the amount of peptide in the vial. See: How to Read an HPLC Chromatogram.

Batch (lot) number

The identifier that ties a COA to one production run. The number on the COA should match the number on the vial it describes. See: How to Read a Peptide COA.

Certificate of Analysis (COA)

A laboratory document reporting test results for a specific batch: typically identity, purity and, on some COAs, content. See: How to Read a Peptide COA.

Chromatogram

The trace an HPLC run produces: detector response plotted against retention time. Each peak is a component the method separated. See: How to Read an HPLC Chromatogram.

Counter-ion

An oppositely charged ion paired with a peptide's charged groups in the solid. Peptides purified by reversed-phase HPLC are often isolated as trifluoroacetate (TFA) salts (Cornish et al., 1999), and residual counter-ions are a recognized component of synthetic peptide products (D'Hondt et al., 2014). Counter-ions add weight but do not appear as HPLC peaks.

Deamidation

A chemical change in which an asparagine residue loses its side-chain amide through a cyclic imide intermediate; aspartate can isomerize by a similar route. How readily it happens depends on the peptide's sequence and structure (Wakankar & Borchardt, 2006). See: Lyophilized Peptide Stability.

Deletion sequence

A synthesis-related impurity: a copy of the target peptide missing one amino acid (D'Hondt et al., 2014). Because it closely resembles the target, it often elutes close to the main HPLC peak.

Diastereomer

A form of the peptide with the same composition but a different spatial arrangement at one or more amino acids, which can arise from racemization during synthesis (D'Hondt et al., 2014). It has the same mass as the target, so mass spectrometry alone cannot tell them apart.

Electrospray ionization (ESI)

The ionization method used in most LC-MS systems. It produces intact ions from molecules in solution and, for larger molecules, a series of multiply charged ions (Fenn et al., 1989).

HPLC (high-performance liquid chromatography)

A technique that separates a sample's components by passing it through a packed column; components leave at different times and are measured by a detector. Reversed-phase HPLC is the most widely used mode for peptide separations (Mant et al., 2007). See: How to Read an HPLC Chromatogram.

Identity confirmation

Evidence that a sample is the compound it is labelled as, usually by mass spectrometry. An HPLC purity figure alone does not establish identity. See: How to Read a Peptide COA.

LC-MS

Liquid chromatography coupled to mass spectrometry: components separated by the column pass directly into a mass spectrometer, so one run reports both separation and mass.

Lyophilization (freeze-drying)

Removing water from a frozen sample under vacuum to leave a dry solid. It is the most common way proteins and peptides are made into solids for shelf life, although dry solids can still degrade slowly (Wang, 2000). See: Lyophilized Peptide Stability.

m/z (mass-to-charge ratio)

What a mass spectrometer measures: an ion's mass divided by its charge. A molecule carrying several charges appears at a lower m/z than its mass, which is why one compound can produce several peaks in a spectrum.

Mass spectrometry (MS)

A technique that ionizes molecules and measures their mass-to-charge ratios, used on COAs to confirm identity. Tandem mass spectrometry (MS/MS) breaks a peptide into fragments to read its sequence (Steen & Mann, 2004).

Monoisotopic and average mass

Two ways of quoting a molecule's mass. Monoisotopic mass uses only the lightest isotope of each element; average mass reflects the natural isotope mix. They differ, so a comparison is only meaningful when both sides use the same convention.

Net peptide content

The share of a powder's weight that is actually peptide, as opposed to counter-ions, water and other salts. It is a different measurement from purity. Methods include HPLC assay against a reference standard, amino acid analysis and quantitative NMR, and results can differ between methods and laboratories (Li et al., 2019).

Oxidation (of residues)

Chemical modification of susceptible amino acids; methionine, cysteine, histidine, tryptophan and tyrosine are the most susceptible. It can be triggered by contaminating oxidants, catalysed by trace metal ions and induced by light (Li et al., 1995). See: Lyophilized Peptide Stability.

Peptide

A short chain of amino acids joined by peptide bonds.

Related impurities

Impurities structurally related to the target peptide: from synthesis (deletions, insertions, incompletely removed protecting groups) or from degradation (such as oxidation and deamidation products) (D'Hondt et al., 2014). See: How to Read an HPLC Chromatogram.

Research use only (RUO)

A labelling designation for materials intended for laboratory research, not for human or animal use, and not for diagnostic or therapeutic purposes.

Retention time

The time a component takes to pass through the HPLC column, read on the chromatogram's horizontal axis. The same compound on the same method should appear at a consistent retention time. See: How to Read an HPLC Chromatogram.

Solid-state stability

How well a compound resists chemical change as a dry solid. Temperature, moisture content, excipients and whether the solid is amorphous or crystalline all affect it (Lai & Topp, 1999). See: Lyophilized Peptide Stability.

UV detection

The detector most HPLC purity methods use. Peptide bonds absorb strongly in the far ultraviolet, so peptides are generally detected at 210–220 nm (Mant et al., 2007). See: How to Read an HPLC Chromatogram.