title: The application of fuzzy statistics and linear discriminant analysis as criteria for optimizing the preparation of plasma for matrix-assisted laser desorption/ionization mass spectrometry peptide profiling.
abstract: An alternative bioinformatics approach based on fuzzy theory statistics and linear discriminant analysis is proposed for the interpretation of MALDI MS spectra in peptide profiling. When applied, the methodology enables the establishment of a reproducible plasma preparation protocol appropriate for the evaluation of small data sets. The samples were collected from pregnant women affected by gestational diabetes mellitus (GDM), n=18 and control group, n=13. The following pre-treatment sets were tested: pipette tips with C18 stationary phase (ZipTip, Millipore and Omix, Agilent) and magnetic bead-based weak cation exchange chromatography kit (MB WCX, Bruker Daltonics). The spectra were recorded using a MALDI TOF mass spectrometer (UltrafleXtreme, Bruker Daltonics) for a mass range of m/z from 1000 to 10,000. The significant features were selected using the wrapper selection method, and two classification systems were tested: discriminant analysis (DA) and fuzzy inference system (FIS). ClinProTools software was employed to compare the usefulness of the proposed methodology. The study showed that the optimum results for MS spectra were obtained after the use of the ZipTip as pre-treatment method in plasma preparation. Chemometric analysis allowed the differentiation of the GDM group from the control with a high degree of accuracy: 0.7333 (DA) and 0.8065 (FIS).
authors.affiliation: Department of Inorganic & Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznań, Poland.
authors.forename: Joanna
authors.initials: J
authors.lastname: Hajduk
authors.affiliation: Department of Inorganic & Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznań, Poland.
authors.forename: Jan
authors.initials: J
authors.lastname: Matysiak
authors.affiliation: Obstetrics and Gynecology Ward, Mielec District Hospital, 22a Żeromskiego Street, 39-300 Mielec, Poland.
authors.forename: Piotr
authors.initials: P
authors.lastname: Kokot
authors.affiliation: Department of Inorganic & Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznań, Poland.
authors.forename: Piotr
authors.initials: P
authors.lastname: Nowicki
authors.affiliation: Department of Inorganic & Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznań, Poland.
authors.forename: Paweł
authors.initials: P
authors.lastname: Dereziński
authors.affiliation: Department of Inorganic & Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznań, Poland. Electronic address: zkokot@ump.edu.pl.
authors.forename: Zenon J
authors.initials: ZJ
authors.lastname: Kokot
mesh_terms: D000328:Adult; D053000:Analytic Sample Preparation Methods / Q000379:methods* / Q000592:standards; D019295:Computational Biology; D016640:Diabetes, Gestational / Q000097:blood* / Q000175:diagnosis; D016002:Discriminant Analysis; D005260:Female; D017143:Fuzzy Logic; D006801:Humans; D011247:Pregnancy; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D055815:Young Adult
keywords: Diabetes mellitus; Discriminant analysis; Fuzzy inference system; Mass spectrometry; Matrix-assisted laser desorption/ionization; Peptide profiling