Dr. Sc. Marko Haramija. (Biokemija, Molekularna medicina, Masena spektroskopija, Biomedicinske znanosti)

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1 Dr. Sc. Marko Haramija (Biokemija, Molekularna medicina, Masena spektroskopija, Biomedicinske znanosti) Obrazovanje OŠ Čavle OŠ Nikola Tesla Gimnazija Andrije Mohorovičića Prirodoslovno-matematički fakultet, Zagreb, Dipl. inž. Kemije, smjer Biokemija Diplomski rad: "Pročišćavanje seryl-trna sintetaze kukuruza dobivene heterolognom ekspresijom u bakteriji Escherichia coli mentor: prof. Ivana Weygand-Đurašević, Institut Ruđer Bošković Sveučilište u Muensteru, NJemačka, znanstveni suradnik, Bioanalitička masena spektrometrija Institut za medicinsku fiziku i biofiziku Medical College of Georgia, Georgia, SAD, 2002 Exchange student visitor, Institute for Molecular Medicine and Genetics Uspostavljanje Mass Spectrometry Core Facility od Jasne Peter-Katalinić Medical College of Georgia, Georgia, SAD, Ph.D. iz Biomedicinskih znanosti, smjer Molekularna medicina Doktorski rad: Influence of DNA Ends on Structure and Function of the DNA-dependent Protein Kinase Major Advisor: William S Dynan, Prof., Institute for Molecular Medicine and Genetics Medical College of Georgia, Georgia, SAD, 2007 Postdok -Popravak dvolančanih lomova u DNK pomoću Non-Homologous End-Joining mehanizma

2 Položeni Ispiti - Diplomski studij Opća kemija, Matematika I, Fizika I, Mineralogija, Biologija, Matematika II, Fizika II, Anorganska kemija, Organska kemija, Analitička kemija I, Fizikalna kemija, Matematičke metode u kemiji, Analitička kemija II, Opća biokemija, Kemijska termodinamika, Kvantna kemija, Instrumentalne metode analize I, Kemija prirodnih organskih spojeva, Elektrokemija, Fizikalno-organska kemija, Kemijska kinetika, Kemija čvrstog stanja, Stanična biokemija, Enzimska kataliza u organskoj sintezi, Molekularna biofizika, Fotokemija, Molekularna genetika, Fizikalna biokemija, Bioanorganska kemija, Kristalografija makromolekula, Praktikum iz opće kemije, Praktikum iz analitičke kemije I, Praktikum iz analitičke kemije II, Praktikum iz organske kemije I, Praktikum iz organske kemije II, Praktikum iz fizikalne kemije I, Praktikum iz organske kemije II, Praktikum iz fizikalne kemije II, Praktikum iz anorganske kemije, Praktikum iz biokemije Položeni Ispiti - Doktorski studij Biokemija i genska regulacija, Molekularna stanična biologija, Integrirana sistemska biologija, Neuroznanost, Imunologija i mikrobiologija, Osnove onkologije I, Moderan razvoj lijekova, Neuroznanost I, Odgovorno istraživanje u znanosti, Napredni seminari iz Molekularne medicine I, Napredni seminari iz Molekularne medicine II Cjeloživotno obrazovanje ASMS Short Courses: FTMS: Principles and Applications, ASMS, May 26-27, 2001 Practical LC/MS, ASMS, June 1-2, 2002, 2002 FEBS Advanced Courses: Diplome: Ostalo obrazovanje: FEBS Advanced Course: Ligand-binding Theory and Practice, Nove Hrady, Češka republika, 2016 FEBS Advanced Course: Glycoconjugates, Versatile structuresintriguing functions, Lovran-Opatija, Hrvatska, 1999 AB Applied Biosystems: Qstar with omaldi Option Training Class, Foster City, CA, SAD, 2002 Ciphergen: Ciphergen ProteinChip Technology Basic Course, CA, SAD, st Summer School in Mass Spectrometry in Biotechnology & Medicine, Dubrovnik, Hrvatska, th International Summer School on Biophysics, Rovinj, 2000

3 State-of-the-art vještine i iskustvo iz Masene spektroskopije Administrator: AB Sciex MALDI/ESI Q-TOF, QStar Pulsar i Micromass MALDI TOF, TofSpec 2E Ciphergen SELDI TOF, ProteinChip Operator: AB Sciex MALDI/ESI Q-TOF, QStar Pulsar i Micromass ESI Q-TOF, Q-Tof Micromass MALDI TOF, TofSpec 2E Ciphergen SELDI TOF, ProteinChip AB Sciex MALDI TOF, Voyager Iskustvo: Razvijanje MS metoda: razvoj nanoesi Q-TOF Affinity mass spectrometry metoda za analizu nekovalentnih kompleksa proteina i ugljikohidrata razvoj pripreme uzoraka za MALDI MS razvoj bioinformatičkih metoda za analizu glikomskih MS podataka Analiziranje MS rezultata: Afinitetna masena spektrometrija Glikomika Proteomika Optimizacija instrumentalnih parametara: na nivou administratora na nivou operatora Optimizacija pripreme uzoraka za MALDI MS QA za AB Sciex MALDI/ESI Q-TOF, QStar Pulsar i QA za Micromass MALDI TOF, TofSpec 2E Obrazovanje postdoktoranada i ostalih gostujućih znanstvenika

4 Radovi 1. Marko Haramija: Software Ion Scan Functions in Analysis of Glycomic and Lipidomic MS/MS Datasets, Journal of Mass Spectrometry, 2018, 53, Marko Haramija: Challenges in Separations of Proteins and Small Biomolecules and the Role of Modern Mass Spectroscopy Tools for Solving Them, as Well as Bypassing Them, in Structural Analytical Studies of Complex Biomolecular Mixtures, Separations, 2018, 5, 11: 3. Haramija M., Peter-Katalinić J.: Quantitative Characterization of Galectin-3-C Affinity Mass Spectrometry Measurements: Comprehensive Data Analysis, Obstacles, Shortcuts and Robustness, Rapid Communications in Mass Spectrometry, 2017, 31, Haramija M., Tyldesley-Worster R.: Analysis of matrix-assisted laser desorption/ionization quadrupole time-of-flight collision-induced dissociation spectra of simple precursor ions and isobaric oligosaccharide ion mixtures based on product ion intensities and pattern recognition, Rapid Communications in Mass Spectrometry, 2017, 31, Haramija M., Peter-Katalinić J.: Preliminary mass spectrometry characterization studies of galectin-3 samples, prior to carbohydrate-binding studies using Affinity mass spectrometry, Rapid Communications in Mass Spectrometry, 2017, 31, , doi: /rcm Haramija M., Peter-Katalinić J.: Negative ion MALDI-TOF MS, ISD and PSD of neutral underivatized oligosaccharides without anionic dopant strategies, using 2,5-DHAP as a matrix", Journal of Mass Spectrometry, 2016, 51, , doi: /jms Haramija M., Tyldesley-Worster R, Pohlentz G, Peter-Katalinić J, "MALDI Q-TOF CID MS for Diagnostic Ion Screening of Human Milk Oligosaccharide Samples", International Journal of Molecular Sciences, 2014, 15, , doi: /ijms , 8. Haramija M., Dynan WS: Terminal DNA structure and ATP influence binding parameters of the DNA-dependent protein kinase at an early step prior to DNA synapsis, Nucleic Acids Research, 34, , 2006, doi: /nar/gkj504,

5 Ostali radovi 9. Lee KJ, Haramija M., Udayakumar D, Bladen CL, Dynan WS: "Identification of DNA-PKcs phosphorylation sites in XRCC4 and effects of mutations at these sites on DNA end joining in a cellfree system", DNA Repair, 3, , 2004, doi: /j.dnarep Hanisch FG, Haramija M., Peter-Katalinić J: "Glycoprotein Identification and Localization of O- Glycosylation Sites by Mass Spectrometric Analysis of Deglycosylated/Alkylaminylated Peptide Fragments", Analytical Biochemistry, 290, 47-59, 2001, doi: /abio Područja znanstvenog djelovanja State-of-the-art temeljna znanstvena istraživanja iz: Biokemije - 10 radova Masene spektroskopije - 9 radova Glikobiokemije - 7 radova Nanobiokemije - 1 rad Interdisciplinarna istraživanja - 7 radova Molekularne medicine - 10 radova Glikomike - 5 radova Proteomike posttranslacijskih modifikacija - 3 rada Bioinformatike - 3 rada State-of-the-art temeljna znanstvena istraživanja nekovalentnih kompleksa proteina: Protein ugljikohidrat - 2 rada Protein DNK - 1 rad Protein protein - 1 rad

6 State-of-the-art temeljna znanstvena istraživanja iz Masene spektroskopije: MALDI MS - 6 radova nanoesi MS - 3 rada Q-TOF MS - 7 radova TOF MS - 3 rada MS/MS sequencing - 7 radova Affinity Mass Spectrometry - 2 rada Glikomika - 5 radova Proteomika PTM-a - 3 rada State-of-the-art temeljna znanstvena istraživanja proteina: ljudski galektin-3 (lektin) - 2 rada ljudska DNA-PKcs (proteinska kinaza, protein u popravku DNK) - 2 rada ljudski Ku (protein u popravku DNK) - 1 rad ljudski XRCC4 (protein u popravku DNK) - 1 rad ljudski glikoforin A (glikoprotein) - 1 rad State-of-the-art interdisciplinarna znanstvena istraživanja u glikomici: razvoj MALDI MS metoda u glikomici - 3 rada razvoj bioinformatičkih metoda za analizu MS podataka u glikomici - 2 rada oligosaharidi ljudskog mlijeka - 3 rada Proteomika posttranslacijskih modifikacija: Glikoproteomika - 2 rada Fosfoproteomika - 1 rad

7 Knjige 1. Haramija M.: "Introduction to Mass Spectrometry of Biomolecules: Theory and Principles", Nova Science Publishers, Inc., Editor:, ISBN: , 2016, New York, USA, ISBN-10: Haramija M.: "Introduction to Mass Spectrometry of Biomolecules: Problems and Practical Aspects", Nova Science Publishers, Inc., Editor: ISBN: , 2016, New York, USA, ISBN- 10: X

8 Poglavlja u knjigama 1. Haramija M. (2016): Introduction to mass spectrometers. In: Introduction to Mass Spectrometry of Biomolecules: Theory and Principles, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 2. Haramija M. (2016): Basic terms in analysis of mass spectra. In: Introduction to Mass Spectrometry of Biomolecules: Theory and Principles, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 3. Haramija M. (2016): Overview of basic classes of biomolecules. In: Introduction to Mass Spectrometry of Biomolecules: Theory and Principles, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 4. Haramija M. (2016): MS/MS Structural Analysis Basic Principles. In: Introduction to Mass Spectrometry of Biomolecules: Theory and Principles, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 5. Haramija M. (2016): MS/MS structural analysis of biomolecules. In: Introduction to Mass Spectrometry of Biomolecules: Theory and Principles, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 6. Haramija M. (2016): Mass spectrometry data acquisition techniques In: Introduction to Mass Spectrometry of Biomolecules: Theory and Principles, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 7. Haramija M. (2016): Advanced MS/MS data acquisition techniques. In: Introduction to Mass Spectrometry of Biomolecules: Theory and Principles, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 8. Haramija M. (2016): Basic calculation problems related to analyses of MS spectra. In: Introduction to Mass Spectrometry of Biomolecules: Problems and Practical Aspects, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 9. Haramija M. (2016): MS/MS analysis of peptides. In: Introduction to Mass Spectrometry of Biomolecules: Problems and Practical Aspects, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 10. Haramija M. (2016): MS/MS analysis of oligosaccharides and glycoconjugates. In: Introduction to Mass Spectrometry of Biomolecules: Problems and Practical Aspects, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 11. Haramija M. (2016): MS/MA analysis of lipids and polyphenols. In: Introduction to Mass Spectrometry of Biomolecules: Problems and Practical Aspects, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA

9 12. Haramija M. (2016): Overview of selected modern MS instruments. In: Introduction to Mass Spectrometry of Biomolecules: Problems and Practical Aspects, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 13. Haramija M. (2016): Sample preparation for MS analyses and related accessories. In: Introduction to Mass Spectrometry of Biomolecules: Problems and Practical Aspects, Nova Science Publishers, Inc., Editor: Haramija M., ISBN: , 2016, New York, USA 14. Haramija M.: Advances and challenges in structural analysis of milk biomolecules using modern mass spectrometry techniques, In: Bernhardt LV, editor. Advances in Medicine and Biology, Vol 94. New York: Nova Science Publishers, Inc.; p Haramija M., Peter-Katalinić J, "Advances and challenges in structural analysis of human milk oligosaccharides using modern mass spectrometry", In: Bernhardt LV, editor. Advances in Medicine and Biology, Vol 86. New York: Nova Science Publishers, Inc.; p

10 Sudjelovanje na većim kongresima th ASMS Conference on Mass Spectrometry and Allied Topics, Long Beach, CA, USA, th ASMS Conference on Mass Spectrometry and Allied Topics, Chicago, IL, USA, th ASMS Conference on Mass Spectrometry and Allied Topics, Orlando, FL, USA, XVI th International Symposium on Glycoconjugates, The Hague, Netherlands, XXIII rd International Symposium on Glycoconjugates, Split, Hrvatska, 2015 Pozvana predavanja 1. Haramija M., Svensson I., Leffler H. and Peter-Katalinić J: "Interactions of Intact Human Galectin-3 and its C-terminal Fragment with Oligosaccharides: an Electrospray Ionization Mass Spectrometry Study", (Galectins Session), XVIth International Symposium on Glycoconjugates, The Hague, Netherlands, Haramija M., Willets M, Tyldesley R, Brown J and Peter-Katalinić J: "Fragmentation of native and peracetylated oligosaccharides in PSD MALDI-TOF and CID MALDI-Q-TOF MS", MODpm (Carbohydrate Sequencing session), 49th ASMS Conference on Mass Spectrometry and Allied Topics, Chicago, IL, USA, 2001

11 Poster prezentacije 1. Marko Haramija, Ulf Nilsson, Hakon Leffler, Jasna Peter-Katalinić: Applicability of ESI MS for screening of galectin-3c affinity data for carbohydrates, GLYCO 23 XXIII International Symposium on Glycoconjugates, Split, Hrvatska, Marko Haramija, Ulf Nilsson, Hakon Leffler, Jasna Peter-Katalinić: Applicability of tandem MS experiments for study of galectin carbohydrate non-covalent complexes, GLYCO 23 XXIII International Symposium on Glycoconjugates, Split, Hrvatska, 2015

12 3. Marko Haramija, Jasna Peter-Katalinić: Fragmentation patterns of oligosaccharides in MALDI MS based on ion mode selection and the nature of precursor ion, GLYCO 23 XXIII International Symposium on Glycoconjugates, Split, Hrvatska, 2015

13 4. Marko Haramija: Novel bioinformatic tools needed for high-throughput data analysis and visualization of oligosaccharide MS/MS spectra, GLYCO 23 XXIII International Symposium on Glycoconjugates, Split, Hrvatska, Marko Haramija, Franz-Georg Hanisch, Jasna Peter-Katalinić: Applicability of MALDI MS for mapping and sequencing of oligosaccharides and glycoconjugates, GLYCO 23 XXIII International Symposium on Glycoconjugates, Split, Hrvatska, Marko Haramija, Nenad Ocelić, Jasna Peter-Katalinić: Bioinformatics-assisted survey of branching patterns in complex oligosaccharide mixtures, 50 th ASMS Conference on Mass Spectrometry and Allied Topics, Orlando, FL, SAD, Marko Haramija, Koenig, Simone; Peter-Katalinić, Jasna: Applicability of MALDI-PSD in Negative Mode for Analysis of Oligosaccharides, N-Glycans and O-Glycosylated Amino Acids, 48 th ASMS Conference on Mass Spectrometry and Allied Topics, Long Beach, SAD, Marko Haramija, Inge Svensson, Hakon Leffler and Peter-Katalinić J.: "Interactions of Intact Human Galectin-3 and its C-terminal Fragment with Oligosaccharides: an Electrospray Ionization Mass Spectrometry Study", (Galectins Session), XVIth International Symposium on Glycoconjugates, The Hague, Netherlands, 2001

14 Ispunjeni kriteriji znanstveno-stručnog doprinosa za znanstevno-nastavno zvanje Izvanredni profesor: 1. Uvjet prezentiranja radova na znanstvenim ili stručnim skupovima: 1. Marko Haramija, Ulf Nilsson, Hakon Leffler, Jasna Peter-Katalinić: Applicability of ESI MS for screening of galectin-3c affinity data for carbohydrates, GLYCO 23 XXIII International Symposium on Glycoconjugates, Split, Hrvatska, Marko Haramija, Ulf Nilsson, Hakon Leffler, Jasna Peter-Katalinić: Applicability of tandem MS experiments for study of galectin carbohydrate non-covalent complexes, GLYCO 23 XXIII International Symposium on Glycoconjugates, Split, Hrvatska, Marko Haramija, Jasna Peter-Katalinić: Fragmentation patterns of oligosaccharides in MALDI MS based on ion mode selection and the nature of precursor ion, GLYCO 23 XXIII International Symposium on Glycoconjugates, Split, Hrvatska, Marko Haramija: Novel bioinformatic tools needed for high-throughput data analysis and visualization of oligosaccharide MS/MS spectra, GLYCO 23 XXIII International Symposium on Glycoconjugates, Split, Hrvatska, Marko Haramija, Franz-Georg Hanisch, Jasna Peter-Katalinić: Applicability of MALDI MS for mapping and sequencing of oligosaccharides and glycoconjugates, GLYCO 23 XXIII International Symposium on Glycoconjugates, Split, Hrvatska, Uvjet pozvanog predavanja na međunarodnom znanstvenom skupu: 1. Marko Haramija, Svensson I., Leffler H. and Peter-Katalinić J: "Interactions of Intact Human Galectin-3 and its C-terminal Fragment with Oligosaccharides: an Electrospray Ionization Mass Spectrometry Study", (Galectins Session), XVIth International Symposium on Glycoconjugates, The Hague, Netherlands, Marko Haramija, Willets M, Tyldesley R, Brown J and Peter-Katalinić J: "Fragmentation of native and peracetylated oligosaccharides in PSD MALDI-TOF and CID MALDI-Q-TOF MS", MODpm (Carbohydrate Sequencing session), 49th ASMS Conference on Mass Spectrometry and Allied Topics, Chicago, IL, USA, 2001

15 3. Uvjet sudjelovanja u realizaciji znanstvenog programa znanstvenih centara izvrsnosti, europskih i međunarodnih kompetitivnih projekata i projekata Hrvatske zaklade za znanost. a) NIH projekt 5RO1CA098239, voditelj W.S.D. (SAD) b) IZKF projekt Molecular analysis ZP6, voditelj J.P.K. (Njemačka) 4. Uvjet objavljivanja stručnih radova nakon izbora u prethodno znanstveno-nastavno zvanje: 1. Marko Haramija: Software Ion Scan Functions in Analysis of Glycomic and Lipidomic MS/MS Datasets, Journal of Mass Spectrometry, doi: /jms Marko Haramija: Challenges in Separations of Proteins and Small Biomolecules and the Role of Modern Mass Spectroscopy Tools for Solving Them, as Well as Bypassing Them, in Structural Analytical Studies of Complex Biomolecular Mixtures, Separations, 5, 11, 2018, doi: /separations Marko Haramija, Jasna Peter-Katalinić: Quantitative Characterization of Galectin-3-C Affinity Mass Spectrometry Measurements: Comprehensive Data Analysis, Obstacles, Shortcuts and Robustness, Rapid Communications in Mass Spectrometry, 31, , 2017, /rcm Marko Haramija, Richard Tyldesley-Worster: Analysis of matrix-assisted laser desorption/ionization quadrupole time-of-flight collision-induced dissociation spectra of simple precursor ions and isobaric oligosaccharide ion mixtures based on product ion intensities and pattern recognition, Rapid Communications in Mass Spectrometry, 31, , 2017, doi: /rcm Marko Haramija, Jasna Peter-Katalinić: Preliminary mass spectrometry characterization studies of galectin-3 samples, prior to carbohydrate-binding studies using Affinity mass spectrometry, Rapid Communications in Mass Spectrometry, 31, , 2017, doi: /rcm.7775

16 6. Marko Haramija, Jasna Peter-Katalinić: Negative ion MALDI-TOF MS, ISD and PSD of neutral underivatized oligosaccharides without anionic dopant strategies, using 2,5-DHAP as a matrix", Journal of Mass Spectrometry, 51, , 2016, doi: /jms Marko Haramija, R. Tyldesley-Worster, G. Pohlentz, J. Peter-Katalinić, "MALDI Q-TOF CID MS for Diagnostic Ion Screening of Human Milk Oligosaccharide Samples", International Journal of Molecular Sciences, 15, , 2014, doi: /ijms

17 Ispunjeni kriteriji nastavnog doprinosa za znanstevno-nastavno zvanje Izvanredni profesor: 1. Uvjet usavršavanja nakon diplomiranja u svom znanstvenom području na sveučilišnim ili znanstvenim institucijama u zemlji ili inozemstvu, uključujući i boravak u inozemstvu u sklopu programa poslijediplomskog studija od najmanje 6 mjeseci: a) Sveučilište u Münsteru, Njemačka: Boehringer Ingelheim travel award: 5 mjeseci b) Sveučilište u Münsteru, Njemačka: Znanstveni suradnik, Laboratorij za masenu spektrometriju prof. J. Peter-Katalinić: 2 godine i 2 mjeseca c) Medical College of Georgia, SAD: Exchange student visitor, Laboratorij za masenu spektrometriju prof. J. Peter-Katalinić: 8 mjeseci d) Medical College of Georgia, SAD: Doktorski studij iz Biomedicinskih znanosti, smjer Molekularna medicina: 4 godine i 4 mjeseca e) Medical College of Georgia, SAD: Postdok iz DNA double strand break repair via non-homologous end joining pathway - 6 mjeseci Ukupno: 8 godina i 1 mjesec 2. Uvjet objavljivanja znanstvene knjige u autorstvu: Nakoon izbora u prethodno znanstveno-nastavno zvanje, objavio sam samostalno dvije znanstvene knjige: 1. Marko Haramija: "Introduction to Mass Spectrometry of Biomolecules: Theory and Principles", Nova Science Publishers, Inc., Editor:, ISBN: , 2016, New York, USA, ISBN-10: Marko Haramija: "Introduction to Mass Spectrometry of Biomolecules: Problems and Practical Aspects", Nova Science Publishers, Inc., Editor: ISBN: , 2016, New York, USA, ISBN- 10: X

18 3. Uvjet inoviranja znanstvenog sadržaja: Uveo sam dva nova kolegija koji su prihvaćeni od nadležnog stručnog tijela visokog učilišta: Masena spektrometrija u biomedicini Osnove masene spektrometrije 4. Uvjet recenziranja znanstvene knjige: Recenzirane znanstvene knjige: 1. Marko Haramija: "Introduction to Mass Spectrometry of Biomolecules: Theory and Principles", Nova Science Publishers, Inc., Editor:, ISBN: , 2016, New York, USA, ISBN-10: Marko Haramija: "Introduction to Mass Spectrometry of Biomolecules: Problems and Practical Aspects", Nova Science Publishers, Inc., Editor: ISBN: , 2016, New York, USA, ISBN- 10: X