Nevşehir Hacı Bektaş Veli University Course Catalogue

Information Of Programmes

INSTITUTE OF SCIENCE / MBG627 - MOLECULAR BIOLOGY AND GENETICS (PHD)

Code: MBG627 Course Title: ADVANCED PROTEOMIC METHODS Theoretical+Practice: 3+0 ECTS: 6
Year/Semester of Study 1 / Fall Semester
Level of Course 3rd Cycle Degree Programme
Type of Course Optional
Department MOLECULAR BIOLOGY AND GENETICS (PHD)
Pre-requisities and Co-requisites None
Mode of Delivery Face to Face
Teaching Period 14 Weeks
Name of Lecturer NAŞİT İĞCİ (nasitigci@nevsehir.edu.tr)
Name of Lecturer(s)
Language of Instruction Turkish
Work Placement(s) None
Objectives of the Course
The aim of this course is to provide information about the use of mass spectrometers in proteomics and mass spectrometry based analysis methods in proteomics.

Learning Outcomes PO MME
The students who succeeded in this course:
LO-1 can give information about current proteomic strategies. PO-1 Have information about current topics in molecular biology and genetics
PO-2 Obtain basic knowledge of Molecular Biology
PO-3 Scientific developments contribute to research and development
PO-4 To be able to transfer current developments and own studies in the field with quantitative and qualitative data to the groups in the field and outside the field in a systematic manner in written, oral and visual form
Examination
LO-2 can give information about the purposes of bioinformatics analyzes in proteomics. PO-1 Have information about current issues in molecular biology and genetics.
PO-3 Make use of the knowledge they have in order to find a solution to problems by analyzing, comparing and questioning them and can carry out original research in the related field on their own
PO-6 Ability to design a research project in the field of molecular biology and genetics and to evaluate and present the results related to it
Examination
LO-3 can give information about the use of mass spectrometry in proteomics. PO-1 Have information about current issues in molecular biology and genetics.
PO-3 Make use of the knowledge they have in order to find a solution to problems by analyzing, comparing and questioning them and can carry out original research in the related field on their own
PO-4 Evaluate the knowledge and skills in a critical way in every activity regarding the field, thereby guiding their learning
PO-6 Ability to design a research project in the field of molecular biology and genetics and to evaluate and present the results related to it
Examination
LO-4 can learn the basic approaches and experimental methods of mass spectrometry in proteomics studies. PO-1 Have information about current issues in molecular biology and genetics.
PO-3 Make use of the knowledge they have in order to find a solution to problems by analyzing, comparing and questioning them and can carry out original research in the related field on their own
PO-4 Evaluate the knowledge and skills in a critical way in every activity regarding the field, thereby guiding their learning
PO-6 Ability to design a research project in the field of molecular biology and genetics and to evaluate and present the results related to it
Examination
PO: Programme Outcomes
MME:Method of measurement & Evaluation

Course Contents
Current strategies and data sources in proteomics, mass spectrometry and their use in proteomics, sample preparation for peptide/protein analysis using mass spectrometry, measurement and spectrum analysis, protein identification with bioinformatic tools, de novo amino acid sequencing, labeled protemics, quantitative proteomics, cross-link mass spectrometer technique.
Weekly Course Content
Week Subject Learning Activities and Teaching Methods
1 Current strategies and data sources in proteomics. Lecture, Discussion, Question Answer, Literature Search
2 Mass spectrometers and their use in proteomics. Lecture, Discussion, Question Answer, Literature Search
3 “Top-down” and “bottom-up” proteomics strategies. Lecture, Discussion, Question Answer, Literature Search
4 Sample preparation for mass spectrometry. Lecture, Discussion, Question Answer, Literature Search
5 Methods used to measure the accurate mass of peptides and proteins by mass spectrometry. Lecture, Discussion, Question Answer, Literature Search
6 Structure and knowledge of the spectrum obtained by mass spectrometry. Lecture, Discussion, Question Answer, Literature Search
7 Peptide fragmentation methods and their use in mass spectrometry. Lecture, Discussion, Question Answer, Literature Search
8 mid-term exam
9 Protein identification by mass spectrometry I: Peptide Mass Fingerprint Analysis. Lecture, Discussion, Question Answer, Literature Search
10 Protein identification by mass spectrometry II: Peptide Fragment Fingerprint Analysis. Lecture, Discussion, Question Answer, Literature Search
11 Mass spectrometry based de novo amino acid sequence and software used for this purpose. Lecture, Discussion, Question Answer, Literature Search
12 Labeled proteomics approaches. Lecture, Discussion, Question Answer, Literature Search
13 Methods used in quantitative proteomics. Lecture, Discussion, Question Answer, Literature Search
14 Use of bioinformatics in quantitative proteomics. Lecture, Discussion, Question Answer, Literature Search
15 Determining the 3-dimensional protein structure by mass spectrometry based cross-linking approach. Lecture, Discussion, Question Answer, Literature Search
16 final exam
Recommend Course Book / Supplementary Book/Reading
1 Özel Demiralp F, İğci N, Peker S, Ayhan B. 2014. Temel Proteomik Stratejiler. Ankara Üniversitesi Yayınevi, Ankara.
2 Hamdan M, Righetti PG. 2005. Proteomics Today. John Wiley & Sons, New Jersey.
3 Matthiesen R (Ed). 2007. Mass Spectrometry Data Analysis in Proteomics. Humana Press.
4 Hoffmann E, Stroobant V. 2007. Mass Spectrometry: Principles and Applications. Wiley.
5 İğci, N. Ders Notları.
Required Course instruments and materials
Lecture notes, books, related articles, computer

Assessment Methods
Type of Assessment Week Hours Weight(%)
mid-term exam 8 2 40
Other assessment methods
1.Oral Examination
2.Quiz
3.Laboratory exam
4.Presentation
5.Report
6.Workshop
7.Performance Project
8.Term Paper
9.Project
final exam 16 2 60

Student Work Load
Type of Work Weekly Hours Number of Weeks Work Load
Weekly Course Hours (Theoretical+Practice) 3 14 42
Outside Class
       a) Reading 3 14 42
       b) Search in internet/Library 3 14 42
       c) Performance Project 0
       d) Prepare a workshop/Presentation/Report 0
       e) Term paper/Project 0
Oral Examination 0
Quiz 0
Laboratory exam 0
Own study for mid-term exam 3 7 21
mid-term exam 2 1 2
Own study for final exam 3 7 21
final exam 2 1 2
0
0
Total work load; 172