ASCARIS LUMBRICOIDES AND ASCARIS SUUM PROTEIN PROFILE ANALYSIS WITH R SOFTWARE ENVIRONMENT (MALDIQUANT)

Abstract

Intro: In parasitology, the use of Mass spectrometric analysis is limited by the lack of databases of protein profiles for most parasitic pathogens. Aim: to study the feasibility of using the R software environment (MALDIquant) to identify differences in the protein profiles of ascaris by the example of Ascaris lumbricoides and Ascaris suum. Methods: For the experiment we used 10 species of A. lumbricoides and 10 A. suum. Head ends of specimens up to 20 mm were used.Ascaris was washed in 0.9% NaCl, exposure for 24 hours in a solution of 2 antibiotics. The biological material was homogenized mechanically, sonicated (70 kHz for 30 seconds five times in 3 cycles in an alcohol bath (–30 C). Protein profiles were obtained using the Sepsityper Kit 50, in accordance with the instructions based on Microflex LT MALDI–TOF MS (Bruker Daltonics) with FlexControl software (Bruker Daltonics).The result was visualized using Flex analysis 3.3 software (Bruker Daltonics).Preliminary processing of spectra using the R-MALDIquant package included the following steps: import of the raw spectra into the R environment; smoothing of spectra; baseline subtraction; spectrum normalization; averaging of repeated spectra; peak detection and peak equalization; creating a matrix of peak intensities; statistical analysis. Findings: Common patterns for both species ranged from 3100 to 8200 kDa. Differences were noted in the range from 13450 to 14655 kDa.For the A.suum cluster, the coincidence of the mass / charge index with the reference profile was recorded at 100%, and for A.lumbricoides - 95-99%. Discussion: The averaging of the repeated spectra made it possible to obtain reference spectrograms of Ascaris and construct dendrograms with two clusters. Conclusion: Processing mass spectra of Ascaris in the software environment R (MALDI quant) made it possible to obtain reference library profiles for species identification