TEXPRESS v1.0: A MATLAB toolbox for efficient processing of GDGT LC–MS data

•User-friendly software environment for processing LC–MS data.•Automated peak integration of branched and isoprenoid GDGTs.•Chemometric based backend for complex baseline correction and peak deconvolution. Liquid chromatography–mass spectrometry (LC–MS) analysis of glycerol dialkyl glycerol tetraethers (GDGTs) from sediment and soil samples has become a widely adopted approach for reconstructing past ocean and continental climate variables such as temperature and pH. The LC–MS data used for constructing these GDGT climate proxies are taken directly from the peak area values of individual GDGT [M+H]+ ions, often determined from manual peak integration due to unreliable computer integrators in commercial software, particularly in cases of complex baselines, asymmetric peak shapes and peak coelution. Manual integration is not only time consuming, but also prone to user induced inconsistency when individuals utilize different criteria for peak/baseline definition. To overcome these problems, we have developed a user friendly, graphical user interface (GUI) programmed in the MATLAB environment, allowing users to efficiently and reproducibly perform batch processing and peak integration of LC–MS data. The program, “TEXPRESS” v1.0 (“tetraether index express”), incorporates modern chemometric based techniques for baseline definition and deconvolution of complex chromatographic peaks and we show that LC–MS data processed using the TEXPRESS toolbox are in strong agreement with results obtained from manual peak integration. We provide a general overview of the concepts and architecture of the TEXPRESS toolbox and discuss the advantages of chemometric based peak integration methods for processing branched and isoprenoid GDGT LC–MS data.