Evaluation of mass spectrometric data using principal component analysis for determination of the effects of organic lakes on protein binder identification

Abstract

Matrix-assisted laser desorption/ionisation-time of flight (MALDI-TOF) mass spectrometry is commonly used for the identification of proteinaceous binders and their mixtures in artworks. The determination of protein binders is based on a comparison between the m/z values of tryptic peptides in the unknown sample and a reference one (egg, casein, animal glues etc.), but this method has greater potential to study changes due to ageing and the influence of organic/inorganic components on protein identification. However, it is necessary to then carry out statistical evaluation on the obtained data. Before now, it has been complicated to routinely convert the mass spectrometric data into a statistical programme, to extract and match the appropriate peaks. Only several 'homemade' computer programmes without user-friendly interfaces are available for these purposes. In this paper, we would like to present our completely new, publically available, non-commercial software, ms-alone and multiMS-toolbox, for principal component analyses of MALDI-TOF MS data for R software, and their application to the study of the influence of heterogeneous matrices (organic lakes) for protein identification. Using this new software, we determined the main factors that influence the protein analyses of artificially aged model mixtures of organic lakes and fish glue, prepared according to historical recipes that were used for book illumination, using MALDI-TOF peptide mass mapping.

Data on low-molecular weight proteins of Escherichia coli treated by essential oils components, tetracycline, chlorine and peroxide by MALDI-TOF MS

“…Public statistical R software, multiMS-toolbox and Mass Spectrum Analysis and Data Conversion Tool [4] , [5] were used. Mass spectra of each sample treated by the tested agent from all three replications and measured dots were exported using FlexAnalysis 3.4 Compass 1.4 (Bruker Daltonics, Bremen, Germany).…”

A computer program to simplify analysis of mass scan data of organometallic compounds from high‐resolution mass spectrometers

“…Our survey of analytical mass spectrometry‐related software found many easily and often freely available programs but most were skewed toward proteomics analysis. A few, such as mMass, multiMS‐toolbox and Universal Mass Calculator, claim to perform calculations similar to those presented here, such as isotopologue mass, mass differences and abundances, but none is capable of searching output data sets for isotopic mass differences specific to organometallic compounds.…”

Stress response of Escherichia coli to essential oil components – insights on low-molecular-weight proteins from MALDI-TOF

“…Due to its limitations, MALDI Biotyper Version 3.1 could not be used to analyse the stress response. Instead, the public package R-project multiMS-toolbox and Mass Spectrum Analysis and Data Conversion Tool 78 , 79 were used.…”