Proteomics, 6 credits

Proteomik, 6 hp


Main field of study

Chemical Biology

Course level

Second cycle

Course type

Programme course


Karin Enander

Director of studies or equivalent

Magdalena Svensson

Education components

Preliminary scheduled hours: 36 h
Recommended self-study hours: 124 h

Available for exchange students

Course offered for Semester Period Timetable module Language Campus ECV
6CKEB Chemical Biology, Master of Science in Engineering (Protein Science and Technology) 7 (Autumn 2022) 1 3 English Linköping C
6MPRO Protein Science, Master's Programme (External) 3 (Autumn 2022) 1 3 English Linköping C
6MPRO Protein Science, Master's Programme (Internal) 1 (Autumn 2022) 1 3 English Linköping C
ECV = Elective / Compulsory / Voluntary

Main field of study

Chemical Biology

Course level

Second cycle

Advancement level


Course offered for

  • Master of Science in Chemical Biology
  • Master's Programme in Protein Science


Admission to advanced level studies in Chemical Biology. Protein chemistry, gene technology and biological measurements. Basic knowledge of analytical chemistry and bioinformatics is also recommended.

Intended learning outcomes

The aim of the course is to provide a broad knowledge of methods and applications within proteomics. Many of the basic methodological principles (genetic, biochemical, analytical chemical and bioinformatic) have been introduced in earlier courses, but here the student learns how these principles are used within a currently very expansive research area: Global characterisation of the proteome with regard to protein abundance, function, regulation, interactions and localisation in different cell types. Transcriptomics is also discussed. To pass the course, the student should be able to

  • describe the relevance and distinctive character of proteomics
  • describe and discuss principles and applications of modern methods and strategies to analyse the transcriptome and the proteome
  • identify proteins and peptides using mass spectra and genome databases
  • summarise the contents of selected original proteomics literature, interpret its message and review it critically


Course content

Quantitative mRNA-analysis with DNA microarrays and methods based on Next Generation Sequencing. Multi-dimensional protein separation methods (2DGE, 2DLC). Gel staining. Identification of cellular protein contents using enzymatic cleavage, MS- and MS/MS analysis and genome databases. Label-based and label-free protein quantification based on MS and MS/MS. Analysis of post-translational modifications. Analysis of protein interactions using affinity chromatography, Y2H methodology and protein microarrays. Characterisation of changes of the cellular protein contents following changes in the environment, for e. g. identification of disease biomarkers. Metaproteomics. Human Proteome Atlas.

Teaching and working methods

The course consists of lectures, seminars, demonstrations, and two home assignments.


TEN1Written examination4 creditsU, 3, 4, 5
UPG1Hand-in assignments1 creditsU, G
UPG2Presentation1 creditsU, G


Four-grade scale, LiU, U, 3, 4, 5

Other information

About teaching and examination language

The teaching language is presented in the Overview tab for each course. The examination language relates to the teaching language as follows: 

  • If teaching language is “Swedish”, the course as a whole could be given in Swedish, or partly in English. Examination language is Swedish, but parts of the examination can be in English.
  • If teaching language is “English”, the course as a whole is taught in English. Examination language is English.
  • If teaching language is “Swedish/English”, the course as a whole will be taught in English if students without prior knowledge of the Swedish language participate. Examination language is Swedish or English depending on teaching language.


The course is conducted in a manner where both men's and women's experience and knowledge are made visible and developed. 

The planning and implementation of a course should correspond to the course syllabus. The course evaluation should therefore be conducted with the course syllabus as a starting point.  

If special circumstances prevail, the vice-chancellor may in a special decision specify the preconditions for temporary deviations from this course syllabus, and delegate the right to take such decisions.


Institutionen för fysik, kemi och biologi

Course literature

Twyman, R. M.; ”Principles of Proteomics” 2nd edition. Originalartiklar.
Code Name Scope Grading scale
TEN1 Written examination 4 credits U, 3, 4, 5
UPG1 Hand-in assignments 1 credits U, G
UPG2 Presentation 1 credits U, G

Course syllabus

A syllabus must be established for each course. The syllabus specifies the aim and contents of the course, and the prior knowledge that a student must have in order to be able to benefit from the course.


Courses are timetabled after a decision has been made for this course concerning its assignment to a timetable module. 

Interruption in and deregistration from a course

The LiU decision, Guidelines concerning confirmation of participation in education (Dnr LiU-2020-02256), states that interruptions in study are to be recorded in Ladok. Thus, all students who do not participate in a course for which they have registered must record the interruption, such that the registration on the course can be removed. Deregistration from or interrupting a course is carried out using a web-based form:

Cancelled courses and changes to the course syllabus

Courses with few participants (fewer than 10) may be cancelled or organised in a manner that differs from that stated in the course syllabus. The Dean is to deliberate and decide whether a course is to be cancelled or changed from the course syllabus. 

Guidelines relating to examinations and examiners 

For details, see Guidelines for education and examination for first-cycle and second-cycle education at Linköping University, Dnr LiU-2020-04501  (

An examiner must be employed as a teacher at LiU according to the LiU Regulations for Appointments, Dnr LiU-2021-01204 ( For courses in second-cycle, the following teachers can be appointed as examiner: Professor (including Adjunct and Visiting Professor), Associate Professor (including Adjunct), Senior Lecturer (including Adjunct and Visiting Senior Lecturer), Research Fellow, or Postdoc. For courses in first-cycle, Assistant Lecturer (including Adjunct and Visiting Assistant Lecturer) can also be appointed as examiner in addition to those listed for second-cycle courses. In exceptional cases, a Part-time Lecturer can also be appointed as an examiner at both first- and second cycle, see Delegation of authority for the Board of Faculty of Science and Engineering.

Forms of examination

Principles for examination

Written and oral examinations and digital and computer-based examinations are held at least three times a year: once immediately after the end of the course, once in August, and once (usually) in one of the re-examination periods. Examinations held at other times are to follow a decision of the board of studies.

Principles for examination scheduling for courses that follow the study periods:

  • courses given in VT1 are examined for the first time in March, with re-examination in June and August
  • courses given in VT2 are examined for the first time in May, with re-examination in August and October
  • courses given in HT1 are examined for the first time in October, with re-examination in January and August
  • courses given in HT2 are examined for the first time in January, with re-examination in March and in August.

The examination schedule is based on the structure of timetable modules, but there may be deviations from this, mainly in the case of courses that are studied and examined for several programmes and in lower grades (i.e. 1 and 2). 

Examinations for courses that the board of studies has decided are to be held in alternate years are held three times during the school year in which the course is given according to the principles stated above.

Examinations for courses that are cancelled or rescheduled such that they are not given in one or several years are held three times during the year that immediately follows the course, with examination scheduling that corresponds to the scheduling that was in force before the course was cancelled or rescheduled.

When a course is given for the last time, the regular examination and two re-examinations will be offered. Thereafter, examinations are phased out by offering three examinations during the following academic year at the same times as the examinations in any substitute course. If there is no substitute course, three examinations will be offered during re-examination periods during the following academic year. Other examination times are decided by the board of studies. In all cases above, the examination is also offered one more time during the academic year after the following, unless the board of studies decides otherwise. In total, 6 re-examinations are offered, of which 2 are regular re-examinations. In the examination registration system, the examinations given for the penultimate time and the last time are denoted. 

If a course is given during several periods of the year (for programmes, or on different occasions for different programmes) the board or boards of studies determine together the scheduling and frequency of re-examination occasions.

Retakes of other forms of examination

Regulations concerning retakes of other forms of examination than written examinations and digital and computer-based examinations are given in the LiU guidelines for examinations and examiners,

Registration for examination

In order to take an written, digital or computer-based examination, registration in advance is mandatory, see decision in the university’s rule book An unregistered student can thus not be offered a place. The registration is done at the Student Portal or in the LiU-app during the registration period. The registration period opens 30 days before the date of the examination and closes 10 days before the date of the examination. Candidates are informed of the location of the examination by email, four days in advance. 

Code of conduct for students during examinations

Details are given in a decision in the university’s rule book:

Retakes for higher grade

Students at the Institute of Technology at LiU have the right to retake written examinations and digital and computer-based examinations in an attempt to achieve a higher grade. This is valid for all examination components with code “TEN”, “DIT” and "DAT". The same right may not be exercised for other examination components, unless otherwise specified in the course syllabus.

A retake is not possible on courses that are included in an issued degree diploma. 


The grades that are preferably to be used are Fail (U), Pass (3), Pass not without distinction (4) and Pass with distinction (5). 

  • Grades U, 3, 4, 5 are to be awarded for courses that have written or digital examinations.
  • Grades Fail (U) and Pass (G) may be awarded for courses with a large degree of practical components such as laboratory work, project work and group work.
  • Grades Fail (U) and Pass (G) are to be used for degree projects and other independent work.

Examination components

The following examination components and associated module codes are used at the Faculty of Science and Engineering:

  • Grades U, 3, 4, 5 are to be awarded for written examinations (TEN) and digital examinations (DIT).
  • Examination components for which the grades Fail (U) and Pass (G) may be awarded are laboratory work (LAB), project work (PRA), preparatory written examination (KTR), digital preparatory written examination (DIK), oral examination (MUN), computer-based examination (DAT), home assignment (HEM), and assignment (UPG).
  • Students receive grades either Fail (U) or Pass (G) for other examination components in which the examination criteria are satisfied principally through active attendance such as tutorial group (BAS) or examination item (MOM).
  • Grades Fail (U) and Pass (G) are to be used for the examination components Opposition (OPPO) and Attendance at thesis presentation (AUSK) (i.e. part of the degree project).

In general, the following applies:

  • Mandatory course components must be scored and given a module code.
  • Examination components that are not scored, cannot be mandatory. Hence, it is voluntary to participate in these examinations, and the voluntariness must be clearly stated. Additionally, if there are any associated conditions to the examination component, these must be clearly stated as well.
  • For courses with more than one examination component with grades U,3,4,5, it shall be clearly stated how the final grade is weighted.

For mandatory components, the following applies (in accordance with the LiU Guidelines for education and examination for first-cycle and second-cycle education at Linköping University, 

  • If special circumstances prevail, and if it is possible with consideration of the nature of the compulsory component, the examiner may decide to replace the compulsory component with another equivalent component.

For possibilities to alternative forms of examinations, the following applies (in accordance with the LiU Guidelines for education and examination for first-cycle and second-cycle education at Linköping University, 

  • If the LiU coordinator for students with disabilities has granted a student the right to an adapted examination for a written examination in an examination hall, the student has the right to it.
  • If the coordinator has recommended for the student an adapted examination or alternative form of examination, the examiner may grant this if the examiner assesses that it is possible, based on consideration of the course objectives.
  • An examiner may also decide that an adapted examination or alternative form of examination if the examiner assessed that special circumstances prevail, and the examiner assesses that it is possible while maintaing the objectives of the course.

Reporting of examination results

The examination results for a student are reported at the relevant department.


For examinations that involve the writing of reports, in cases in which it can be assumed that the student has had access to other sources (such as during project work, writing essays, etc.), the material submitted must be prepared in accordance with principles for acceptable practice when referring to sources (references or quotations for which the source is specified) when the text, images, ideas, data, etc. of other people are used. It is also to be made clear whether the author has reused his or her own text, images, ideas, data, etc. from previous examinations, such as degree projects, project reports, etc. (this is sometimes known as “self-plagiarism”).

A failure to specify such sources may be regarded as attempted deception during examination.

Attempts to cheat

In the event of a suspected attempt by a student to cheat during an examination, or when study performance is to be assessed as specified in Chapter 10 of the Higher Education Ordinance, the examiner is to report this to the disciplinary board of the university. Possible consequences for the student are suspension from study and a formal warning. More information is available at

Regulations (apply to LiU in its entirety)

The university is a government agency whose operations are regulated by legislation and ordinances, which include the Higher Education Act and the Higher Education Ordinance. In addition to legislation and ordinances, operations are subject to several policy documents. The Linköping University rule book collects currently valid decisions of a regulatory nature taken by the university board, the vice-chancellor and faculty/department boards.

LiU’s rule book for education at first-cycle and second-cycle levels is available at

Twyman, R. M.; ”Principles of Proteomics” 2nd edition. Originalartiklar.

Note: The course matrix is not fully translated to English.

I U A Modules Comment
1.1 Kunskaper i grundläggande matematiska och naturvetenskapliga ämnen
Kemi (speciellt proteinkemi och bioanalytisk kemi), biologi (speciellt molekylärbiologi).
Chemistry (especially protein chemistry and bioanalytical chemistry) and biology (especially molecular biology).
1.2 Kunskaper i grundläggande (motsvarande G1X) teknikvetenskapliga ämnen
1.3 Fördjupade kunskaper (motsvarande G2X), metoder och verktyg inom något/några teknik- och naturvetenskapliga ämnen
Genteknik, biomätteknik.
Gene technology, Biological measurements
1.4 Väsentligt fördjupade kunskaper (motsvarande A1X), metoder och verktyg inom något/några teknik- och naturvetenskapliga ämnen
Strategier och metoder inom proteomik, främst baserade på gelseparation, vätskekromatografi, masspektrometri och immunoassays.
Strategies and methods for proteomics, mainly based on gel separation, liquid chromatography, mass spectrometry and immunoassays.
1.5 Insikt i aktuellt forsknings- och utvecklingsarbete
Aktuellt forskningsläge inom proteomikområdet.
Current research in proteomics.
2.1 Analytiskt tänkande och problemlösning
Problemlösning inom proteomik.
Problem solving in proteomics.
2.2 Experimenterande och undersökande arbetssätt samt kunskapsbildning
2.3 Systemtänkande
2.4 Förhållningssätt, tänkande och lärande
Kreativt och kritiskt tänkande, tidsplanering
Creative and critical thinking, time management.
2.5 Etik, likabehandling och ansvarstagande
Hålla sig à jour med professionens utveckling
Keeping up-to-date with the professional development.
3.1 Arbete i grupp
Presentation/hemuppgifter i grupper om 2-3
Presentation and home assignments in groups of 2-3.
3.2 Kommunikation
Muntlig och skriftlig framställning
Oral and written communication.
3.3 Kommunikation på främmande språk
Muntlig redovisning på engelska. Engelskspråkig kurslitteratur.
Oral presentation in English. Course literature in English.
4.1 Samhälleliga villkor, inklusive ekonomiskt, socialt och ekologiskt hållbar utveckling för kunskapsutveckling
Teknikens inverkan på samhället och miljön.
Technology impact on society and environment.
4.2 Företags- och affärsmässiga villkor
4.3 Att identifiera behov samt strukturera och planera utveckling av produkter och system
4.4 Att konstruera produkter och system
4.5 Att realisera produkter och system
4.6 Att ta i drift och använda produkter och system
5.1 Samhälleliga villkor, inklusive ekonomiskt, socialt och ekologiskt hållbar utveckling
5.2 Ekonomiska villkor för kunskapsutveckling
5.3 Att identifiera behov samt strukturera och planera forsknings- eller utvecklingsprojekt
5.4 Att genomföra forsknings- eller utvecklingsprojekt
5.5 Att redovisa och utvärdera forsknings- eller utvecklingsprojekt

This tab contains public material from the course room in Lisam. The information published here is not legally binding, such material can be found under the other tabs on this page.

There are no files available for this course.