Nevşehir Hacı Bektaş Veli University Course Catalogue
|
|||||
| Year/Semester of Study | 1 / Spring Semester | ||||
| Level of Course | 2nd Cycle Degree Programme | ||||
| Type of Course | Optional | ||||
| Department | BİYOLOJİ(DOKTORA) | ||||
| 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 an advanced level of knowledge about the recent and best practices in Biology, deepen and expand their knowledge on the expert level, conduct and assess the analyses by employing statistical methods PO-2 Plan experiments and carry out original researches in the field by making use of the theoretical and practical knowledge at the expert level that they have obtained in their field 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 Have the qualification and capability to gain admission to doctoral programs, R&D units or occupations related to the field with the knowledge they have gathered in the field PO-9 Transfer in a systematical way the latest developments in Biology and their field of study reinforcing with qualitative and quantitative data to the groups either concerned with the field or not by verbal, visual and written means |
Examination |
| LO-2 | can give information about the purposes of bioinformatics analyzes in proteomics. |
PO-1 Have an advanced level of knowledge about the recent and best practices in Biology, deepen and expand their knowledge on the expert level, conduct and assess the analyses by employing statistical methods PO-2 Plan experiments and carry out original researches in the field by making use of the theoretical and practical knowledge at the expert level that they have obtained in their field 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 Have the qualification and capability to gain admission to doctoral programs, R&D units or occupations related to the field with the knowledge they have gathered in the field PO-9 Transfer in a systematical way the latest developments in Biology and their field of study reinforcing with qualitative and quantitative data to the groups either concerned with the field or not by verbal, visual and written means |
Examination |
| LO-3 | can give information about the use of mass spectrometry in proteomics. |
PO-1 Have an advanced level of knowledge about the recent and best practices in Biology, deepen and expand their knowledge on the expert level, conduct and assess the analyses by employing statistical methods PO-2 Plan experiments and carry out original researches in the field by making use of the theoretical and practical knowledge at the expert level that they have obtained in their field 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 Have the qualification and capability to gain admission to doctoral programs, R&D units or occupations related to the field with the knowledge they have gathered in the field PO-9 Transfer in a systematical way the latest developments in Biology and their field of study reinforcing with qualitative and quantitative data to the groups either concerned with the field or not by verbal, visual and written means |
Examination |
| LO-4 | learn the basic approaches and experimental methods of mass spectrometry in proteomics studies. |
PO-1 Have an advanced level of knowledge about the recent and best practices in Biology, deepen and expand their knowledge on the expert level, conduct and assess the analyses by employing statistical methods PO-2 Plan experiments and carry out original researches in the field by making use of the theoretical and practical knowledge at the expert level that they have obtained in their field 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 Have the qualification and capability to gain admission to doctoral programs, R&D units or occupations related to the field with the knowledge they have gathered in the field PO-9 Transfer in a systematical way the latest developments in Biology and their field of study reinforcing with qualitative and quantitative data to the groups either concerned with the field or not by verbal, visual and written means |
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 inproteomics. | 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 (with exercise). | Lecture, Discussion, Question Answer, Literature Search |
| 10 | Protein identification by mass spectrometry II: Peptide Fragment Fingerprint Analysis (with exercise). | Lecture, Discussion, Question Answer, Literature Search |
| 11 | Mass spectrometry based de novo amino acid sequence and software used for this purpose (with exercise). | 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 | Hubbard SJ, Jones AR. 2010. Proteome Bioinformatics. Springer. | |
| 4 | Matthiesen R (Ed). 2007. Mass Spectrometry Data Analysis in Proteomics. Humana Press. | |
| 5 | Eyers CE, Gaskell S (Eds). 2014. Quantitative Proteomics. RSC Publishing. | |
| 6 | Hoffmann E, Stroobant V. 2007. Mass Spectrometry: Principles and Applications. Wiley. | |
| 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 | 3 | 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 | 4 | 14 | 56 |
| 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 | 2 | 7 | 14 |
| mid-term exam | 2 | 1 | 2 |
| Own study for final exam | 3 | 7 | 21 |
| final exam | 3 | 1 | 3 |
| 0 | |||
| 0 | |||
| Total work load; | 180 | ||