COURSE UNIT TITLE

: PROTEOMICS

DEGREE PROGRAMMES

Description of Individual Course Units

Course Unit Code Course Unit Title Type Of Course D U L ECTS
ONK 6084 PROTEOMICS ELECTIVE 1 0 0 3

Offered By

Basic Oncology

Level of Course Unit

Third Cycle Programmes (Doctorate Degree)

Course Coordinator

ASSOCIATE PROFESSOR YASEMIN BASKIN

Offered to

Basic Oncology

Course Objective

The purpose of this course is to introduce proteomics field,
Understand the importance of proteomic analysis and proteomic techniques to provide knowledge about.

Learning Outcomes of the Course Unit

1   Knowledgeable about cancer proteomics.
2   Be able to know Proteomics methods
3   Be able to critically evaluate the published literature in the field of cancer proteomics methods.
4   Be able to know bioinformatics on proteomics
5   Be able to understand the diagnostic importance of cancer proteomics

Mode of Delivery

Face -to- Face

Prerequisites and Co-requisites

None

Recomended Optional Programme Components

None

Course Contents

Week Subject Description
1 Course description and general concepts
2 Proteom discription and significance
3 2D-gel electrophoresis: SDS-PAGE and isoelectric focusing (IEF)
4 Visualtization of proteins
5 Sample preparation in MS
6 In-gel digestion
7 Mass spectrometric (MS) analysis of proteins
8 Electrospray ionization (ESI)-MS , Tandem MS
9 Isotope coded affinity tags (ICAT); HPLC-MS
10 Matrix assisted laser desorption ionization-time off flight (Maldi-tof)-MS
11 Surface-enhanced laser desorption/ionization time off flight -MS (SELDI-Tof-MS)
12 Determination of post-translational modifications, Amino acid sequencing: Edman degredation)
13 Antibody based proteomics
14 Applications of proteomics-Tissue Microarray ,Proteomics databanks
15 Bioinformatics on proteomics

Recomended or Required Reading

Textbook(s):
1. The Protein Protocols Handbook, J. M. Walker Ed, Humana Press, 2002
2.Proteins and Proteomics: A Laboratory Manuel, R.J. Simpson, Cold Spring Harbor, 2003
3.Cell Biology: A Laboratory Handbook,. Ed. E J Celis, 1994, Academic Press,California.
Supplementary Book(s):
References: 4.The human keratinocyte two-dimensional protein database (update 1994): Towards an integrated approach to the study of cell proliferation, differantiation and skin diseases Celis J.E., Rasmussen H.H., Olsen E., Madsen P., Leffers H., Honore B., Dejgaard K., Gromov P., Vorum H., Vassilev A., Baskın Y., et all. Electrophoresis 1994 nov.; 15,1349-1458.
5. Clinical Proteomics of Breast Cancer Yasemin Baskın, Türkan Yiğitbaşı. Current Genomics, 2010, 11,528-536.
Materials:

Planned Learning Activities and Teaching Methods

Theoretical Lectures, the topics in-class activities (presentations and assignments) to consolidate and discussion and homeworks

Assessment Methods

SORTING NUMBER SHORT CODE LONG CODE FORMULA
1 PRF PERFORMANCE
2 FIN FINAL EXAM
3 FCG FINAL COURSE GRADE PO * 0.40 + FN*0.60
4 RST RESIT
5 FCGR FINAL COURSE GRADE (RESIT) PO * 0.40 + BUT*0.60

Further Notes About Assessment Methods

None

Assessment Criteria

Learning outcomes, intermediate and long-answer questions will be evaluated with classical written final exam. Strengthened by homework

Language of Instruction

Turkish

Course Policies and Rules

To be announced.

Contact Details for the Lecturer(s)

yasemin.baskin@deu.edu.tr 0 232 4125890/5801

Office Hours

Monday 12.30-13.30

Work Placement(s)

None

Workload Calculation

Activities Number Time (hours) Total Work Load (hours)
Lectures 15 1 15
Preparation for midterm exam 1 15 15
Preparation for final exam 1 30 30
Preparing assignments 1 13 13
Final 1 1 1
Midterm 1 1 1
TOTAL WORKLOAD (hours) 75

Contribution of Learning Outcomes to Programme Outcomes

PO/LOPO.1PO.2PO.3PO.4PO.5PO.6PO.7PO.8PO.9PO.10PO.11
LO.15
LO.25555
LO.35
LO.455
LO.5555

CONTACT INFORMATION
Dokuz Eylül Üniversitesi Cumhuriyet Bulvarı No: 144 35210 Alsancak / İZMİR
Phone: +90(232) 412 12 12 - Fax: +90 (232) 464 81 35

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