Journal of MASS SPECTROMETRY RESEARCH ARTICLE MALDI‐FT‐ICR‐MS for archaeological lipid residue analysis Ester Oras 1,2 | Signe Vahur 2 | Sven Isaksson 3 | Ivari Kaljurand 2 | Ivo Leito 2 1 Institute of History and Archaeology, Faculty of Arts and Humanities, University of Tartu, Jakobi 2, 51014 Tartu, Estonia 2 Institute of Chemistry, Faculty of Science and Technology, University of Tartu, Ravila 14A, 50411 Tartu, Estonia 3 The Archaeological Research Laboratory, Department of Archaeology and Classical Studies, SE‐106 91, Stockholm, Sweden Correspondence Ester Oras, Institute of History and Archaeology, Faculty of Arts and Humanities, University of Tartu, Jakobi 2, 51014, Tartu, Estonia. Email: ester.oras@ut.ee Funding information Estonian Ministry of Education and Research, Grant/Award Number: PUTJD64, IUT 20‐7, PUT1521 and IUT20‐14 Abstract Soft‐ionization methods are currently at the forefront of developing novel methods for analysing degraded archaeological organic residues. Here, we present little‐used soft ionization method of matrix assisted laser desorption/ionization‐Fourier transform‐ion cyclotron resonance‐mass spectrometry (MALDI‐FT‐ICR‐MS) for the identification of archaeological lipid residues. It is a high‐resolution and sensitive method with low limits of detection capable of identifying lipid com- pounds in small concentrations, thus providing a highly potential new technique for the analysis of degraded lipid components. A thorough methodology development for analysing cooked and degraded food remains from ceramic vessels was carried out, and the most efficient sample prep- aration protocol is described. The identified components, also controlled by independent parallel analysis by gas chromatography‐mass spectrometry (GC‐MS) and gas chromatography‐combus- tion‐isotope ratio mass spectrometry (GC‐C‐IRMS), demonstrate its capability of identifying very different food residues including dairy, adipose fats as well as lipids of aquatic origin. The results obtained from experimentally cooked and original archaeological samples prove the suitability of MALDI‐FT‐ICR‐MS for analysing archaeological organic residues. Sample preparation protocol and identification of compounds provide future reference for analysing various aged and degraded lipid residues in different organic and mineral matrices. KEYWORDS ancient food, lipids, MALDI‐FT‐ICR‐MS, organic residue analyses, soft ionization 1 | INTRODUCTION Organic residue analysis has become one of the major and rapidly developing fields in archaeological sciences. The analyses of lipid resi- dues have produced several fruitful studies allowing a better under- standing of past life‐ways and economy, pottery function, agricultural practices, etc. 1-5 Current routine analysis evolves around gas chromatography‐mass spectrometry (GC‐MS) and gas chromatography‐combustion‐isotope ratio mass spectrometry (GC‐C‐ IRMS), 6,7 sometimes combined with bulk isotopic analysis with elemen- tal analyser isotope ratio mass spectrometry (EA‐IRMS) of food crusts. These methods imply rather complicated and time‐consuming sample preparation, 8,9 which, depending on the extraction protocol, also include derivatization and/or breaking down complex lipid molecules. For example, acylglycerols do not preserve in the case of acid extraction and are broken into free fatty acids, whilst they can be detected in derivatized forms using solvent extraction protocol. However, data obtained on original and intact lipid molecules, ie, triacylglycerols (TAGs) highly depends on overall molecule preservation and is often not avail- able. The bulk isotope analysis, simpler in terms of sample preparation, provides only limited information about the origin of lipids relating to the larger food groups (plants, aquatic, and terrestrial animals), trophic levels, and wider metabolic systems of the organisms analysed. One potentially fruitful yet under‐utilized analytical method for the identification of archaeological lipid residues is matrix assisted laser desorption/ionization‐Fourier transform‐ion cyclotron resonance‐ mass spectrometry (MALDI‐FT‐ICR‐MS). MALDI is a soft ionization method which can produce ions directly from the solid state. Ionization of the analyte by the laser beam is assisted by matrix material which absorbs radiation at the laser wavelength, is in large excess compared with the substance analysed and helps to separate analyte molecules. Laser energy is absorbed by the matrix (not the analyte), and as a result the whole analyte molecules (not fragments) are ionized by adding a proton (from the matrix) or a single positively charged metal ion (available in all biological samples by nature), resulting mostly in H + or Na + adducts, although some other cations are possible as well. 10,11 MALDI has been mainly coupled with time‐of‐flight mass spectrom- eter (TOF‐MS) 11-16 or Fourier transform mass spectrometer (FTMS). 17,18 The combination with FT‐ICR‐MS makes it a sensitive method with low limit of detection. It affords high resolution (reaching hundreds of Received: 12 April 2017 Revised: 30 June 2017 Accepted: 19 July 2017 DOI: 10.1002/jms.3974 J Mass Spectrom. 2017;52:689–700. 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