{"id":457,"date":"2026-09-06T20:55:22","date_gmt":"2026-09-06T20:55:22","guid":{"rendered":"https:\/\/premiumpeptide.shop\/research\/lc-ms-peptide-analysis\/"},"modified":"2026-09-06T22:16:30","modified_gmt":"2026-09-06T22:16:30","slug":"lc-ms-peptide-analysis","status":"publish","type":"page","link":"https:\/\/premiumpeptide.shop\/en\/research\/lc-ms-peptide-analysis\/","title":{"rendered":"LC-MS in peptide analysis"},"content":{"rendered":"

A purity figure answers how uniform a sample is. It does not answer whether the correct compound is present at all. That second question belongs to mass spectrometry. This page explains how LC-MS works, what a mass spectrum states about a peptide and where the method reaches its limits.<\/p>\n

Two methods in one instrument<\/h2>\n

LC-MS is a coupling. The first part, liquid chromatography, separates the sample so that the components leave the column one after another. The second part, mass spectrometry, takes over the column outlet and determines the mass-to-charge ratio for each eluting component.<\/p>\n

The gain lies in the assignment: one obtains not only the information that something elutes at a particular point in time, but also which mass this something has. A peak in the chromatogram is thereby given a chemical assignment instead of merely a retention time.<\/p>\n

Ionisation: how a peptide enters the gas phase<\/h2>\n

Peptides are large, polar and non-volatile. In order to be recorded by mass spectrometry they must be ionised gently and transferred into the gas phase. In peptide analysis, electrospray ionisation (ESI) is the standard method: the liquid stream is nebulised at a capillary under high voltage, the solvent evaporates and charged molecular ions remain.<\/p>\n

A characteristic of ESI is multiple charging. Peptides frequently take up several protons and therefore appear not as a single signal but as a series of signals with different charge states. The actual molecular mass is reconstructed computationally from this series, a step referred to as deconvolution.<\/p>\n

A signal at m\/z 800 can be a singly charged molecule of about 799 Da or a triply charged one of about 2397 Da. Only consideration of the entire charge series and its spacings allows an unambiguous assignment. A mass spectrum without a stated charge number is therefore only interpretable to a limited extent.<\/p>\n

Comparison with the calculated mass<\/h2>\n

The theoretical molecular mass can be calculated exactly from the amino acid sequence. The comparison with the measured value is the actual proof of identity. Four terms must be distinguished for this:<\/p>\n