Digging deeper - A new data mining workflow for improved processing and interpretation of high resolution GC-Q-TOF MS data in archaeological research

Abstract

Gas chromatography-mass spectrometry profiling is the most established method for the analysis of organic residues, particularly lipids, from archaeological contexts. This technique allows the decryption of hidden chemical information associated with archaeological artefacts, such as ceramic pottery fragments. The molecular and isotopic compositions of such residues can be used to reconstruct past resource use, and hence address major questions relating to patterns of subsistence, diet and ritual practices in the past. A targeted data analysis approach, based on previous findings reported in the literature is common but greatly depends on the investigator's prior knowledge of specific compound classes and their mass spectrometric behaviour, and poses the risk of missing unknown, potentially diagnostic compounds. Organic residues from post-prehistoric archaeological samples often lead to highly complex chromatograms, which makes manual chromatogram inspection very tedious and time consuming, especially for large datasets. This poses a significant limitation regarding the scale and interpretative scopes of such projects. Therefore, we have developed a non-targeted data mining workflow to extract a higher number of known and unknown compounds from the raw data to reduce investigator's bias and to vastly accelerate overall analysis time. The workflow covers all steps from raw data handling, feature selection, and compound identification up to statistical interpretation.

Tattoo Pigment Identification in Inks and Skin Biopsies of Adverse Reactions by Complementary Elemental and Molecular Bioimaging with Mass Spectral Library Matching

“…Focusing on the development of computational methods to streamline the data handling, compound annotation, and reporting for large (multi GB) datasets, the open-source mass spectrometry data processing software MZmine was extended. The changes include support for importing the open data format for mass spectrometry imaging (imzML), spectral clustering as a data reduction strategy, and methods to generate and match against mass spectral libraries . Library matching algorithms with comprehensive options are presented to provide optimal results when comparing experimental spectra with those from reference pigments.…”

Neolithic culinary traditions revealed by cereal, milk and meat lipids in pottery from Scottish crannogs

“…Importantly, this approach provides the superb sensitivity to target biomarkers present at levels of only few ppb in the ceramics without, in contrast to Selected Ion Monitoring or Multiple Reaction Monitoring, losing information on the other compounds present in the sample. In addition to now enabling the detection of this important commodity, the application of this approach more widely in archaeological science offers vast opportunities in terms of wealth of information that can be gained from each individual sample and even allows completely new angles of interpretation to be considered 38 .…”

Contrasting Volatilomes of Livestock Dung Drive Preference of the Dung Beetle Bubas bison (Coleoptera: Scarabaeidae)

“…MZmine version 2.53 [53,54] and Metaboanalyst 5.0 were used to process high-resolution molecular profile data for further analysis. The data analysis workflow consisted of sequential peak detection, deconvolution, alignment, gap-filling, and statistical analysis [53,55,56]. First, raw GC-MS/QToF data files were converted from Agilent proprietary ".d" format to "mzData" format using Agilent Mass Hunter Qualitative Analysis 7.0 and then imported into MZmine for pre-processing.…”