The identification of proteins by Peptide Mass Fingerprinting (PMF). Part I – properties of the identification experiment

Journal : Acta Bio-Optica et Informatica Medica. Inżynieria Biomedyczna
Article : Identyfikacja białek z wykorzystaniem techniki Peptide Mass. Część I – charakterystyka eksperymentu identyfikacji

Authors :
Giemza, Cz.
Wydział Fizjoterapii, Akademia Wychowania Fizycznego we Wrocławiu, Wrocław tel. +48 (71) 347-30-86, czeslaw.giemza@awf.wroc.pl,
Łukowicz, M.
Katedra Podstaw Teoretycznych Nuk Biomedycznych i Informatyki Medycznej, Collegium Medicum im. Ludwika Rydygiera w Bydgoszczy, Uniwersytet Mikołaja Kopernika w Toruniu, ul. M. Skłodowskiej-Curie 9, 85-094 Bydgoszcz, kizterfiz@cm.umk.pl,
Soroko, M.
Zakład Hodowli Koni i Jeździectwa, Wydział Biologii i Hodowli Zwierząt, Uniwersytet Przyrodniczy we Wrocławiu, ul. Kożuchowska 5A, 51-631 Wrocław, tel. +48 507 495 109, marysia@cieplej.pl,
Stelengowska, M.
Instytut Techniki i Aparatury Medycznej ITAM, ul. Roosevelta 118, 41-800 Zabrze, tel. +48 (32) 271 60 13, miroslawa.stelengowska@itam.zabrze.pl,
Orzechowska, S.
Instytut Fizyki, Katedra Fizyki Medycznej i Biofizyki, Uniwersytet Jagielloński, ul. Reymonta 4, 30-059 Kraków, tel. +48 (12) 633-56- 97, sylwia.orzechowska@uj.edu.pl,
Jeka, S.
Szpital Uniwersytecki nr 2 im. dr. Jana Biziela w Bydgoszczy, Oddział Reumatologii i Układowych Chorób Tkanki Łącznej, ul. Ujejskiego 75, 85-168 Bydgoszcz, s.jeka@wp.pl,
Bliźniuk, G.
Instytut Systemów Informatycznych, Wydział Cybernetyki, Wojskowa Akademia Techniczna, 00-908 Warszawa, ul. gen. S. Kaliskiego 2, tel. +48 (22) 683 95 04, grzegorz.blizniuk@wat.edu.pl,
Małecka-Massalska, T.
Physiology Department, Medical University of Lublin, Radziwiłłowska 11 Str., 20-080 Lublin, Poland, tel.: +48 (81) 528 84 05, 609 304 934, tmalecka@gmail.com,
Kamińska, H.
Instytut Inżynierii Biomedycznej i Pomiarowej, Wydział Podstawowych Problemów Techniki, Politechnika Wrocławska, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, tel. +48 71 320 28 25, hanna.kaminska@pwr.wroc.pl,
Abstract : Wprowadzenie w spektrometrach jonizacji typu MALDI zrewolucjonizowało proces identyfikacji białek. Automatyzacja procesu identyfikacji oraz bezpośrednie połączenie analizy spektrometrem masowym z separacją białek dwuwymiarową elektroforezą żelową (2D-GE) pociągnęły za sobą znaczny rozwój proteomiki. Późniejszy rozrost proteomicznych baz danych pozwolił na zwiększenie dokładności identyfikacji, z wykorzystaniem pierwszej w historii techniki wydajnej identyfikacji białek – peptide mass fingerprinting, w skrócie: PMF. Metoda peptide mass fingerprinting pozwala identyfikować białka z widm masowych uzyskanych w wyniku analizy próbki spektrometrem masowym. Przez wzgląd na powszechność stosowania metody, jak i ciągle obserwowane jej ulepszenia, autorzy postanowili podsumować obecny stan wiedzy w tym zakresie. Praca została podzielona na dwie części: w pierwszej znajduje się opis historii powstania metody PMF wraz z charakterystyką części eksperymentalnej i opisem najpopularniejszych baz danych stosowanych przy identyfikacji, natomiast druga część pracy jest poświęcona zagadnieniom algorytmicznym, związanym z wyszukiwaniem w bazie danych protein najlepiej odzwierciedlających białko analizowane w próbce. Specyfikacja eksperymentu w pierwszej części pracy uwzględnia zarówno opis metody separacji, trawienia białek w próbce, jak i późniejszej ich analizy z wykorzystaniem spektrometru masowego. Eksperymentalne fazy metody PMF są opisane z uwzględnieniem ich cech biochemicznych, mających wpływ na dalsze etapy schematu identyfikacji.

The development of MALDI ionization method in mass spectrometers, had revolutionized the protein identification procedure. The automation of an identification procedure and the mass spectrometry direct connection to the protein separation with the two-dimensional gel electrophoresis (2D-GE) implicated the significant proteomics development. The later growth of the proteomics databases contributed to the enhancement of the identification accuracy, by using the first method of effective protein identification in the history: the peptide mass fingerprinting (PMF). The peptide mass fingerprinting enabled the protein identification from the mass spectra acquired by the mass spectrometry sample analysis. Due to the common use of method and its continuous improvements, the authors decided to summarize the current state of the knowledge in this field of science. The publication is divided into two parts. The first one is devoted to the origins of PMF scheme, the characteristics of its experimental part and a description of the most popular databases used in the identification procedure. The second part relates to the algorithmic issues of searching the database protein, which reflects the sample content in the best way. The experiment specification in the first part takes into the consideration the description of separation and sample digestion methods, as well as the later protein sample analysis by the mass spectrometer. The experimental steps of the PMF method are described according to their biochemical properties, having an impact for the later stages of the identification procedure.

Keywords : proteomika, identyfikacja protein, spektrometria masowa, schematy scoringu, proteomics, identification of proteins, mass spectrometry, peptide mass fingerprinting, scoring schemes,
Publishing house : Indygo Zahir Media
Publication date : 2011
Number : Vol. 17, nr 2
Page : 153 – 160

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DOI :
Qute : Giemza, Cz. ,Łukowicz, M. ,Soroko, M. ,Stelengowska, M. ,Orzechowska, S. ,Jeka, S. ,Bliźniuk, G. ,Małecka-Massalska, T. ,Kamińska, H. ,Kamińska, H. , Identyfikacja białek z wykorzystaniem techniki Peptide Mass. Część I – charakterystyka eksperymentu identyfikacji. Acta Bio-Optica et Informatica Medica. Inżynieria Biomedyczna Vol. 17, nr 2/2011
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