The present invention is concerned with a method of identifying microbial strains (e.g. from a cell culture), the method comprising; i) a lipid extraction step, comprising extraction of phospholipids from the microbe, suitably with an extraction composition comprising more than 50 vol % MeOH; ii) a sample preparation step, comprising preparation of a MALDI sample incorporating the extracted lipids; iii) a data gathering step, comprising performing MALDI-based mass spectrometry on the MALDI sample, and iv) a microbe identification step, comprising analysis of the mass spectrometry data to characterise or identify the microbial strain. Suitably the method also includes extracting proteins from the microbes and analysing the extracted proteins using MALDI-based mass spectrometry so as to obtain not only lipid m/z data but also protein m/z data.