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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 |