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Research Peptide Glossary and Guide

This research peptide guide explains what Pepta Labs publishes, what the analytical report can establish, and what it cannot. A glossary of research peptide terms, from lyophilized and HPLC purity to amidate, m/z and UNII, and the compound classes in the catalog follow the overview.

Chemical identity

Review the compound name, CAS Registry Number, molecular formula, molecular weight, and amino-acid sequence when applicable. These fields describe chemical identity; they do not establish safety, efficacy, sterility, or suitability for a human or animal use.

HPLC and mass spectrometry

HPLC separates components and is the basis of the reported purity percentage for the analyzed sample. Mass spectrometry compares an observed mass with the expected molecular mass and is the basis of identity confirmation. Neither result alone establishes vial fill quantity, sterility, endotoxin level, pharmaceutical grade, or clinical suitability.

Analytical-report limitations

Testing is commissioned through a cooperative purchasing group. Reports may name the group or source as the client and have supplier-identifying fields redacted. Vials do not carry lot or batch numbers.

Request an available analytical report with the form on any product page or by emailing support@peptalabs.com.

Shipping and storage

Lyophilized powder ships at ambient temperature without cold packs or insulated packaging. Dry powder is substantially more thermally stable than the same compound in solution; short-term ambient transit is not expected to meaningfully affect purity. Refrigerate at 2–8°C on arrival or store at -20°C long term.

Research use only

Products are intended and offered solely for laboratory research. They are not for human or animal use, consumption, administration, clinical use, diagnosis, or treatment. Pepta Labs does not provide dosage, injection, administration, or reconstitution instructions.

Glossary of research peptide terms

Definitions of the analytical and chemistry terms used on listings, analytical reports and registry records, each linked to the guide that goes deeper.

Lyophilized
Lyophilization, or freeze-drying, removes water from a frozen solution by sublimation under vacuum and leaves the compound as a dry powder or cake inside the vial. A lyophilized peptide is therefore supplied as a dry solid rather than as a solution. The dry form is the state in which the material is shipped and stored. The labelled quantity is the stated fill of the compound; the counter-ion and any residual water also contribute to the total mass of the solid, and vial fill quantity is not independently tested.
CAS Registry Number
A CAS Registry Number is a unique numeric identifier assigned by the Chemical Abstracts Service to a specific chemical substance. It has up to ten digits in three hyphen-separated groups, for example 137525-51-0, and ends with a check digit. A salt form and its free base can carry different CAS numbers, so the number on a listing identifies the registered substance rather than a supplier or lot. Pepta Labs publishes the CAS number on each product page so the listed substance can be cross-referenced in chemical databases such as PubChem.
Molecular weight (average vs monoisotopic)
Molecular weight is the mass of one molecule, expressed in daltons (Da) or grams per mole. The average molecular weight is calculated from the natural isotopic abundance of each element and is the figure normally printed on a listing. The monoisotopic mass uses the most abundant isotope of each element, such as carbon-12 and hydrogen-1, and is the value compared against a high-resolution mass spectrum. For peptides the two values differ by a fraction of a dalton to several daltons, and the gap grows with molecular size, so a reported mass should be compared with the matching figure.
RP-HPLC
Reversed-phase high-performance liquid chromatography separates the components of a dissolved sample by pumping it under pressure through a column packed with a non-polar stationary phase, commonly C18-bonded silica, using a polar mobile phase such as water and acetonitrile with a small amount of acid. Components leave the column at different retention times and are detected by UV absorbance, typically at 214 or 220 nm for peptides. The area of the main peak relative to the total peak area is the basis of the reported purity percentage.
Purity vs assay
Purity, as reported from HPLC, is the percentage of the total detected peak area that belongs to the main compound. It describes how much of the UV-absorbing material is the target compound relative to related impurities. Assay, or content, is a different measurement: the absolute amount of compound present, usually determined against a reference standard or by amino-acid analysis. A sample can show high chromatographic purity while its content by mass is lower because of counter-ions and water. The figures on Pepta Labs listings are HPLC purity values, not assay values.
Net peptide content
Net peptide content is the fraction of a lyophilized solid's mass that is peptide, excluding the counter-ion (for example trifluoroacetate or acetate), residual water and other non-peptide solids. For synthetic peptides it commonly falls between about 70 % and 90 % and is determined by elemental nitrogen analysis or amino-acid analysis rather than by HPLC. Chromatographic purity and net peptide content are independent numbers: a material that is 99 % pure by HPLC can still have a net peptide content well below 100 %. Net peptide content is not part of the HPLC and mass-spectrometry reporting available for Pepta Labs listings.
Counter-ion: TFA vs acetate
Peptides purified by RP-HPLC are usually isolated as salts because the acid in the mobile phase pairs with basic residues. Trifluoroacetic acid (TFA) gives a trifluoroacetate salt; a further ion-exchange step can replace it with acetate or hydrochloride. The counter-ion form changes the total mass of the solid, and therefore the net peptide content, without changing the peptide sequence. Where the salt form is known it is stated on the product page; where it is not stated, the form should be confirmed from the analytical report.
ESI and MALDI
Electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) are the two ionization techniques most often used for peptide mass spectrometry. ESI produces ions from a solution and typically yields multiply charged species, so the instrument reports mass-to-charge (m/z) values that are deconvoluted to a neutral mass. MALDI ionizes the sample from a solid matrix and usually gives singly charged [M+H]+ ions, so the observed m/z is close to the molecular mass plus one proton. Either technique serves for identity confirmation by comparing the observed mass with the theoretical value.
Observed vs theoretical mass
The theoretical mass is calculated from the molecular formula, either as an average or a monoisotopic value. The observed mass is the value measured by the mass spectrometer after accounting for charge state and adducts such as H+, Na+ or K+. Identity confirmation compares the two: agreement within the instrument's tolerance, commonly a fraction of a dalton on high-resolution instruments or about one dalton on lower-resolution ones, indicates that the compound has the expected mass. A mass match confirms composition rather than sequence order, and it does not measure purity or quantity.
Analytical report (COA)
A certificate of analysis (COA) is the document issued by the testing laboratory that records the results for an analysed sample: typically the compound name, the HPLC purity percentage with its chromatogram, the mass-spectrometry result with the observed mass, and the method conditions. For Pepta Labs listings the testing is commissioned by a cooperative purchasing group, so the client field may name that group or the source rather than Pepta Labs, and supplier-identifying fields are redacted. Reports are provided by email request and are not posted as downloads.
Lot number
A lot, or batch, number identifies a specific production run of a compound so that a sample can be traced to the analytical report for that run. On a COA the lot number links the recorded results to the material that was tested. Pepta Labs vials carry the compound name, quantity and research-use designation but do not carry a lot or batch number. Because vials are not lot-marked, a report is matched to a purchase by compound name and order rather than by a printed lot.
Endotoxin and sterility (not tested)
Endotoxin testing, for example the limulus amebocyte lysate (LAL) assay, quantifies bacterial endotoxin, and sterility testing checks for viable microorganisms. Both are microbiological analyses that are separate from chemical purity and identity work. The HPLC and mass-spectrometry reporting for Pepta Labs listings does not include sterility, endotoxin or LAL, potency, pharmaceutical-grade, cGMP, contaminant-panel or vial fill-quantity testing, and none of these is claimed. Listings should therefore be read as chemical reference materials characterised for purity and identity only.
Research use only
Research use only is the designation under which Pepta Labs supplies every product. The compounds are chemical reference materials intended solely for laboratory research and are not for human or animal use, consumption, diagnosis or treatment. They are not drugs, dietary supplements, cosmetics or medical devices, and no use-related instructions are provided. Purchasers confirm the research-use designation at checkout, and orders are accepted only for delivery to addresses in the United States. The full policy is published on the research use and compliance page.
Storage
Lyophilized peptides are shipped at ambient temperature as dry powder. On arrival, sealed vials are refrigerated at 2–8 °C, or stored at −20 °C for longer periods, and kept dry and protected from light. The dry solid is considerably more stable than a solution, which is why cold-chain shipping is not required for the powder. Storage guidance for each compound is printed on its product page, and the storage-conditions section of an analytical report gives the laboratory's own recommendation.
Amidate / amidated peptide (C-terminal amide, -NH2)
Amidate in a peptide product name means that the C-terminus is a primary amide rather than a free carboxylic acid; chemists usually write amide, and the sequence ends in -NH2 instead of -OH. Replacing OH with NH2 changes the molecular formula and lowers the mass by 0.98 Da, so an amidated peptide is a distinct compound with its own formula, molecular weight and, where registered, its own CAS number, not a salt or a grade of the parent peptide. The residue sequence itself is unchanged. A low-resolution mass-spectrometry window of about ±0.1% is wider than 0.98 Da for any peptide above about 1,000 Da, so the formula on the listing, not the mass alone, states which form is meant. See peptide sequence notation for the terminal marks and their mass changes.
N-acetyl (Ac-) vs acetate salt
N-acetyl means that the N-terminal amine carries an acetyl group, written Ac- at the start of a sequence. The group is covalently bonded to the peptide, adds C2H2O to the molecular formula (+42.01 Da monoisotopic, +42.04 Da average) and leaves no free N-terminal amine. Acetate is different: it is the counter-ion of an acetate salt, paired with the peptide's basic groups but not part of its formula, and it dissociates from the peptide on ionization in the mass spectrometer. A name of the form "N-acetyl [peptide] amidate acetate" therefore describes an acetylated, amidated peptide isolated as its acetate salt. The formula and molecular weight on a listing are those of the peptide; the counter-ion adds to the solid mass in the vial. The sequence notation guide works through the arithmetic.
Sequence notation (one-letter and three-letter codes)
A peptide sequence is written from the N-terminus on the left to the C-terminus on the right, in three-letter codes (Gly-Glu-Pro) or one-letter codes (GEP). Both abbreviate the same twenty standard amino acids; the three-letter form leaves room for modified residues. Several one-letter codes are not the initial of the name: D is aspartic acid, E glutamic acid, N asparagine, Q glutamine, K lysine, R arginine, F phenylalanine, W tryptophan and Y tyrosine. Prefixes and suffixes state the terminal groups (H- and -OH for a free amine and acid, Ac- for an acetyl group, -NH2 for an amide), a D- prefix or lower-case letter marks a D-residue, and cyclo[...] marks a ring. Peptide sequence notation tabulates every element with its mass change.
N-terminus and C-terminus
The N-terminus (amino terminus) is the end of a peptide chain that carries the free alpha-amino group; the C-terminus (carboxyl terminus) is the end that carries the free carboxylic acid. Sequences are written, and residues numbered, from the N-terminus, so Lys7 is the lysine at position 7 counted from that end, and reversing the order describes a different molecule with the same formula and mass. Each hyphen between residue codes stands for a peptide bond, and each bond forms with the loss of one water molecule (18.02 Da average). Either end can be modified: an acetyl or other acyl cap on the N-terminus, an amide (-NH2) in place of the acid at the C-terminus, or a pyroglutamate residue cyclized onto its own amine. Solid-phase synthesis assembles the chain from the C-terminus toward the N-terminus. See peptide sequence notation.
Residue (amino-acid residue)
A residue is an amino acid as it exists inside a peptide chain: the free amino acid minus the water lost when its peptide bond formed. Residue masses are therefore lower than free amino-acid masses; glycine, C2H3NO, is 57.02 Da monoisotopic and 57.05 Da average, and arginine, C6H12N4O, 156.10 and 156.19 Da. A linear peptide with free termini weighs the sum of its residue masses plus one water (18.02 Da average). The residue count names the chain: tripeptide, pentadecapeptide. A rule of thumb of about 110 Da per residue is only an order-of-magnitude estimate: a glycine- or proline-rich sequence weighs less per residue, an arginine-rich one more. Residues outside the twenty standard amino acids, such as Aib, Nle or Dmt, are written by abbreviation. The sequence notation guide lists all twenty residue masses.
D-amino acid (D-configured residue)
A D-amino acid is the mirror-image form of the usual L-amino acid at its alpha carbon. In three-letter notation it carries a D- prefix (D-Arg, D-Phe); in one-letter notation it is written as a lower-case letter. Residues without a prefix are L, and glycine, which has no stereocentre, never carries either. A D-residue has exactly the same molecular formula and mass as its L-form, so the notation records configuration only, and an intact-mass measurement cannot distinguish the two; telling them apart takes a chiral chromatographic method or a chiral amino-acid analysis. A residue inverted from L to D during synthesis is an epimer and shows, if at all, as a separate or shoulder peak on the chromatogram at 0 Da mass difference. See peptide sequence notation.
Cyclic peptide and disulfide bridge
A cyclic peptide contains a ring closed by a covalent bond between two residues; the ring is written with cyclo and brackets around the residues it contains, as in cyclo[Asp-...-Lys]. A side-chain lactam, an amide bond between a carboxyl side chain such as Asp and an amine side chain such as Lys, closes the ring with the loss of one water (18.01 Da monoisotopic), so the cyclic formula has one H2O less than the open chain. A disulfide bridge is a different ring closure: a covalent S-S bond between two cysteine residues, written as a note such as "disulfide Cys7-Cys14", which removes two hydrogens (2.02 Da) instead of a water. An open-ring form of the same residues is heavier by that amount and appears as a separate mass. See peptide sequence notation.
Retention time
Retention time is the time, in minutes, at which a component leaves the HPLC column and reaches the detector, recorded for each peak in the report's peak table. On a reversed-phase column peptides elute broadly in order of increasing hydrophobicity, so a chain missing one residue usually forms its own peak at a slightly different retention time. The value depends on the gradient, flow rate, column dimensions and chemistry, column temperature and the instrument's dwell volume, so it is comparable only between runs made under the same stated conditions: a main peak at 14.2 minutes on one report and 17.8 minutes on another is not a discrepancy unless both state the same column, gradient, flow and temperature. It locates the target; identity needs mass spectrometry. HPLC purity of research peptides explains each report line.
Area percent (peak area)
Area percent is the HPLC purity calculation: the area of the main peak divided by the sum of all integrated peak areas, multiplied by 100. The data system detects each peak above the reporting threshold stated in the method, draws a baseline under it, integrates the area between trace and baseline in units such as mAU·s, and sums the areas; peaks that also appear in a blank run, such as the solvent front, are excluded when the method says so. With illustrative numbers, a main peak of 9,920 mAU·s beside minor peaks of 38, 25 and 17 mAU·s gives 9,920 / 10,000 × 100 = 99.2%. The detection threshold, baseline type and whether a shoulder is split from the main peak all change the result and belong on the report. See how the HPLC purity percentage is determined.
m/z and charge state
A mass spectrometer measures the mass-to-charge ratio, m/z, of ions rather than the mass of neutral molecules. In positive-ion electrospray a peptide picks up one or more protons, and the number it carries is its charge state, z; for an ion with z protons, m/z = (M + z × 1.007276) / z, where M is the neutral mass and 1.007276 Da the proton mass. One peptide therefore appears as a series of peaks, one per charge state. A 1,420 Da peptide gives [M+H]+ near m/z 1421.0 and [M+2H]2+ near m/z 711.0; MALDI mostly forms singly charged [M+H]+ ions. Deconvolution converts the series back to one neutral mass, the figure compared with the calculated mass; on the m/z scale every difference is divided by the charge. See mass spectrometry identity confirmation.
PubChem CID and UNII
A PubChem CID is the compound identifier that the PubChem database assigns to one chemical structure, and a UNII is the alphanumeric code that the FDA Global Substance Registration System (GSRS) assigns to one substance. Each registry records a salt and its free peptide as separate entries with separate numbers, and the CID, UNII and molecular weight on a listing normally describe the free peptide while the vial holds a salt. GSRS holds a much narrower set of substances than PubChem, so a valid CAS number with no GSRS record is common, and a PubChem name search can resolve to a different entity, such as a short fragment. Product pages cite the CID and, where one exists, the UNII for compounds with a verified identity record. Peptide registry records lists the known disagreements.
Reference material vs certified reference material
A laboratory reference material, in the sense used on Pepta Labs listings, is a characterized chemical sold for laboratory research, analytical method work and chemical characterization, identified by name, CAS number, formula and molecular weight and documented by an independent report on a sampled production run. It is not a certified reference material (CRM) or a pharmacopeial reference standard: a CRM comes with a certificate that states a property value for the lot with an uncertainty and a traceability statement, and its vial is tied to that certificate by a lot number, while a reference standard is a material of known content against which an assay is measured. The Pepta Labs Terms state that products are not certified reference materials or pharmaceutical reference standards. What research peptides are sets out what each document establishes.
Certificate of analysis (COA) vs certificate of testing
A certificate of testing is a laboratory's report of the results it measured on the sample it received. A certificate of analysis, in its traditional sense, is a producer's document for a numbered lot that lists specifications beside each result and carries a conformance statement, a declaration that the lot meets those limits; its lot number appears on the certificate and on the product label. The names are not standardized, and in the research-peptide market COA is used for both, so the useful questions are who issued the document and what it is tied to. Pepta Labs documentation is a laboratory report on a sampled production run, and vials carry no lot number. How to read and verify a peptide COA compares the two.
Deletion sequence and other synthesis impurities
A deletion sequence is a peptide chain missing one residue because a coupling step in solid-phase synthesis was incomplete; its mass is lower than the target by that residue's mass, for example −57.02 Da for glycine, −97.05 Da for proline or −128.09 Da for lysine. Related species appear as the minor peaks on a chromatogram: truncated chains capped with an acetyl group (+42.01 Da), oxidized methionine (+15.99 Da), deamidated asparagine or glutamine (+0.98 Da), residual protecting groups left after cleavage (tert-butyl +56.06, Boc +100.05 Da, eluting after the main peak) and diastereomers, which have exactly the target mass and separate only by chromatography. An HPLC-UV report lists each minor peak's retention time and area but does not identify it; that takes LC-MS of the peak. HPLC purity of research peptides gives the mass shift of each species.

Compound classes

Catalog listings grouped by structural class. Each class page shows the CAS number, molecular weight and reported purity of its compounds.

More reading: what research peptides are · how to read a peptide COA · HPLC vs mass spectrometry · peptide storage guide · CAS numbers and molecular weights reference · research peptide articles and guides · browse all compounds · testing and documentation.