A certificate of analysis for a synthetic peptide uses a small, fairly standard vocabulary: a few analytical methods (HPLC, mass spectrometry, Karl Fischer titration, the LAL test), the quantities they report (area percent, net peptide content, endotoxin units), and the terms that tie a result to a lot and a limit (specification, acceptance criteria, conforms). This glossary defines 31 of those terms, alphabetically, with the standard or source behind each definition.
Definitions describe what a term means on a document. They are not claims about any product. For how the terms fit together, start with our guide to reading a certificate of analysis and our explainer on HPLC purity versus net peptide content.
Terms, A to Z
Acceptance criteria
The numerical limits, ranges or other conditions a test result must meet, such as "not less than 98.0 percent" for purity. The ICH Q6A guideline defines them as part of a specification. A result printed without its acceptance criterion cannot be judged as a pass or a fail.
Amino acid analysis
A method that breaks a peptide down with strong acid into its individual amino acids, then separates and quantifies them, according to Bachem's quality-control guide. It is used to estimate peptide content and to check composition, but it gives no sequence information.
Area percent
The way HPLC purity is calculated: the area of the main peak divided by the total area of all detected peaks, expressed as a percentage. It is a relative figure that only counts material the detector responds to. Our explainer on what an HPLC trace shows covers why that matters.
Bacterial endotoxins test
The compendial test for endotoxin, described in United States Pharmacopeia chapter <85> and often called the LAL test after its reagent. The FDA's inspection guide lists gel-clot, turbidimetric and chromogenic methods among those used.
Batch or lot
A defined quantity of material made in one production run and identified by a single number. Every result on a certificate applies only to the lot named on it, which is why the lot number on a document has to match the container.
Certificate of analysis (COA)
A document reporting the tests performed on a specific lot, with the method, result and acceptance criterion for each. A certificate reports only what was tested: a test that is not listed was not reported.
Chain of custody
A documented record of who handled a sample, when, and why, from collection through analysis. NIST defines it as a process that tracks the movement of evidence through its collection, safeguarding and analysis lifecycle. For third-party peptide testing, it is what connects a lab result to a particular vial from a particular seller.
Chromatogram
The graph an HPLC instrument produces: detector signal on the vertical axis against time on the horizontal axis, with each peak representing material leaving the column. A certificate that includes the chromatogram lets a reader check the number it reports.
Conforms
A one-word result meaning the test met its acceptance criterion. ICH Q6A describes conformance to specifications as meeting the listed acceptance criteria when tested by the listed procedures. On its own, "conforms" shows neither the measured value nor the limit it was measured against.
Counter-ion
An ion of opposite charge paired with a peptide in its salt form, most often trifluoroacetate, acetate or chloride. Counter-ions add weight to the powder without adding peptide, which is one reason net peptide content runs below HPLC purity.
Detection limit (LOD)
The lowest amount of a substance a method can detect, though not necessarily measure as an exact value, as defined in the ICH Q2(R2) guideline. "Not detected" on a certificate means below this limit, not zero, so the limit itself should be stated.
Elemental impurities
Metals and other elements that can enter a product from catalysts, equipment or raw materials, tested under USP chapters <232> and <233> and the ICH Q3D guideline. Class 1 under ICH Q3D covers arsenic, cadmium, mercury and lead. The older term is heavy metals.
Endotoxin
A lipopolysaccharide from the outer membrane of gram-negative bacteria that can cause fever, according to the FDA. It is not removed by sterilizing filters, so a product can be sterile and still contain it.
Endotoxin unit (EU)
The FDA's inspection guide describes the EU as the unit of measurement for endotoxin activity. Results and limits are reported in EU per unit of weight or volume of product.
Fill or quantity
How much material a specific container holds compared with its label claim. It describes one vial, not a batch, and should state whether it refers to gross powder or to peptide content.
High-performance liquid chromatography (HPLC)
A separation method that pushes a dissolved sample through a packed column and records components as they come off. For peptides, reversed-phase HPLC with ultraviolet detection is the standard purity method; Bachem describes detection at 210 to 220 nanometers.
Identity
The test that establishes what a substance is, as distinct from how pure it is. ICH Q6A states that identification by a single chromatographic retention time alone is not regarded as specific, while combinations such as HPLC with mass spectrometry are generally acceptable.
ISO/IEC 17025 accreditation
ISO/IEC 17025 is the international standard for the competence of testing and calibration laboratories. Accreditation to it is granted by an accreditation body for a defined scope: an A2LA scope document, for example, lists each test and method the lab is accredited to perform. A test outside the scope is not covered, so the scope is worth checking, not just the word "accredited."
Karl Fischer titration
A chemical titration specific to water, used to report the water content of a freeze-dried peptide. ICH Q6A names it as preferred over the less specific loss-on-drying test.
LAL (Limulus amebocyte lysate)
The reagent at the center of the bacterial endotoxins test, which reacts in the presence of endotoxin. The FDA requires LAL reagents to come from an FDA-licensed manufacturer.
LC-MS
Liquid chromatography coupled to mass spectrometry: the chromatograph separates the components and the mass spectrometer measures each one's mass. It combines a purity picture with identity confirmation in a single run, the kind of combined procedure ICH Q6A describes as generally acceptable for identification.
Mass spectrometry and m/z
Mass spectrometry measures ions by their mass-to-charge ratio, written m/z. IUPAC defines m/z as the mass number of an ion divided by its charge number, so the same peptide carrying different numbers of charges appears at different m/z values. A certificate should compare the observed mass with the sequence's theoretical mass.
Net peptide content (NPC)
The share of a powder's weight that is peptidic material, after counter-ions and water. Bachem notes it can be measured by nitrogen elemental analysis or amino acid analysis, and it is a different figure from HPLC purity.
Quantitation limit (LOQ)
The lowest amount of a substance a method can measure with suitable precision and accuracy, per ICH Q2(R2). It sits above the detection limit: below it, a method may see something without being able to put a reliable number on it.
Related substances
Impurities that are structurally related to the target peptide, such as sequences missing a residue or carrying a modified one. Bachem describes these peptidic by-products as varying in proportion and structure. They are what HPLC purity is designed to separate, though very similar ones can co-elute with the main peak.
Residual solvents
Traces of organic solvents left over from synthesis and purification, usually measured by gas chromatography. The ICH Q3C guideline groups solvents into classes by toxicity and sets limits for each.
Retention time
How long a component takes to pass through the HPLC column. Compared against a reference standard run under identical conditions, it is suggestive of identity but not proof, because different compounds can elute at the same time.
Specification
The ICH Q6A definition: a list of tests, references to analytical procedures, and acceptance criteria that a substance should conform to be considered acceptable for its intended use. A certificate is a report against a specification, and the specification sets how strict the pass is.
Sterility test
A test for living bacteria and fungi, described in USP chapter <71>, in which samples are incubated in growth media for not less than 14 days, according to the FDA's Pharmaceutical Microbiology Manual. Because only a sample of a lot is tested, a pass is evidence about the units tested rather than proof about every vial.
TFA (trifluoroacetate)
The counter-ion left when trifluoroacetic acid is used in reversed-phase purification, as described by Cornish and colleagues (American Journal of Physiology, 1999). In that study, trifluoroacetate at nanomolar concentrations reduced cell numbers in rat osteoblast cultures, which is why salt form matters for cell experiments.
Water content
The percentage of a sample's weight that is water, usually by Karl Fischer titration. Freeze-dried peptides absorb moisture, and water adds to the gap between gross weight and net peptide content.
Frequently asked questions
What is the most important term on a peptide certificate of analysis?
There is no single one. Identity (usually mass spectrometry) says what the material is, HPLC purity says how much of the detected material is the target, and net peptide content says how much of the powder is peptide. A certificate needs all three to describe a lot.
What does "conforms" mean on a COA?
That the result met its acceptance criterion. Without the measured value and the limit beside it, the word is a conclusion with the evidence removed.
What is the difference between LOD and LOQ?
The detection limit is the lowest amount a method can detect. The quantitation limit is the lowest amount it can measure reliably. Both come from the ICH Q2(R2) guideline.
Does ISO 17025 accreditation cover every test a lab runs?
No. Accreditation applies to a defined scope of tests and methods. A result from a test outside that scope was not produced under the accreditation.
Sources:
- ICH Q2(R2), Validation of analytical procedures, 2023 (glossary: detection limit, quantitation limit)
- ICH Q6A, Specifications (specification, acceptance criteria, identification, water content)
- ICH Q3C(R9), Impurities: guideline for residual solvents, 2024
- ICH Q3D(R2), Guideline for elemental impurities, 2022
- FDA, Inspection Technical Guide: Bacterial Endotoxins/Pyrogens
- FDA, Pyrogen and Endotoxins Testing: Questions and Answers
- FDA, Pharmaceutical Microbiology Manual (sterility testing)
- FDA, Elemental Impurities in Drug Products: Guidance for Industry, August 2018
- Bachem, Quality control of amino acids and peptides: a guide, January 29, 2025
- Bachem, What does net peptide content mean?
- IUPAC Gold Book, mass-to-charge ratio
- NIST Computer Security Resource Center glossary, chain of custody
- ANSI, Changes to ISO/IEC 17025:2017 for laboratories
- A2LA scope of accreditation to ISO/IEC 17025, Office of the Texas State Chemist (example of a scope listing specific tests and methods)
- Cornish et al., Am J Physiol, 1999 (trifluoroacetate in rat osteoblast cultures)
Definitions only. Nothing here is guidance on preparing or using any compound. Research use only.
For research use only · Not for human or veterinary use · No research compound discussed here is FDA-approved for any indication