Academic management

The course “Qualitative and quantitative proteomics and biomarker analysis” is integrated in the first semester (module 2) within the block of optional courses offered in the programme of the “Master in Analytical and Bioanalytical Sciences”. The teaching language will be English.

The main objective of this course will be to give an introduction into a scientific field of high actual importance within life sciences: Mass spectrometry-based Proteomics.

Besides an introduction into this topic and its actual relevance, fundamentals on analytical methods (sample preparation, separation and mass spectrometric detection techniques) will be taught and put into the context of important scientific disciplines like biochemistry, biology or medicine. Proteomics workflows for protein identification and their most relevant post-translational modifications will be discussed in detail, and furthermore, relative and absolute quantification will be highlighted. Finally, biomarkers and their analytical control conclude the programme.

This course is very well linked to subjects of module 1 (e.g. mass spectrometry for elemental and molecular analysis, modern techniques in separation science) and other subjects of module 2 (e.g. clinical and pharmaceutical analysis, food analysis and toxicology). Especially, the analytical methods and techniques (like chromatography, mass spectrometry) have great importance and impact on other subjects within this master and can be, therefore, regarded as essential within the presented programme. Furthermore, some of the offered practical courses within the subject, such as “Experimental introduction to advanced analytical techniques in routine and research laboratories” (module 3) contain the analysis of proteins and peptides in biological materials.

This course will provide a specific formation, which is pivotal for the PhD students as well as for professionals working in private and public laboratories, in which mass spectrometric techniques play an important role in basic and applied proteomic studies.

The prerequisites of this course match up with the general ones of the master degree:

The prerequisite for entry the master will be a first cycle degree in one of the following disciplines:

-  Bachelor degree in chemistry

-  Bachelor degree in the related disciplines: Physics, Geology, Biology, Biochemistry, Pharmacy, Medicine, Environmental Sciences and Food technology

-  Bachelor degree in Engineering Chemistry

-  Other related Bachelor degrees in Sciences and Life Sciences.

In the case of students from other countries which could have studied different disciplines, every specific case will be evaluated to check if the student profile matches the prerequisites of this master.

More precisely, basic knowledge is recommended on the following topics: Bioanalysis, instrumental analysis, spectroscopic techniques and separation methods.

4. Competencies and learning results

The expected learning outcomes will be:

RA-1.- The student should demonstrate knowledge and understanding of essential facts, concepts, principles and theories relating to the subject areas studied during the Master program.

RA-2.- The student should be able to read and understand related scientific papers published in international journals.

RA-3.- The student should be able to write correctly a report about a specific research topic and present it in front of a specialized audience.

RA-4.-  The student should be able to apply knowledge in practice, in particular to solve specific and complex problems.

Basic competences:

CB6.-  Ability to understand the knowledge required to be original in the development and application of ideas, usually in a research context

CB8     Ability to integrate knowledge and handle complexity, and formulate judgments with incomplete or limited information, but that include reflecting on ethical responsibilities linked to the application of their knowledge and judgments

CB9     Ability to communicate their conclusions, and the knowledge and rationale underpinning these, to specialist and non-specialist audiences clearly and unambiguously.

CB10   Learning skills that will allow them to continue to study in a manner that may be largely self-directed or autonomous, and to take responsibility for their own professional development.

General Competences:

CG1    Ability to analyze material and synthesize concepts

CG4    Information-management competences, in relation to primary and secondary information sources and ability to manage adequately such obtained information.

Specific Competences:

CE1     Knowledge of the basis for the main analysis techniques, both already established and state-of-the-art techniques, and the related experimental methodologies.

CE2     Skills required for the conduct of advanced laboratory procedures and use of instrumentation in synthetic and analytical work both in a research and routine lab.

CE-5   Ability to choose the right analytical technique for the analysis and characterization of different materials and nanomaterials.

CE-6   Ability to choose the right analytical technique for the analysis, characterization and quantification of compounds of interest, both inorganics and organics, in complex samples.

CE-7   Ability to assimilate and evaluate laboratory results to solve problems efficiently

Unit 1:          Introduction. Definitions. Objectives.

Unit 2:          Separation techniques in proteomics. Sample preparation. Gel electrophoresis. Liquid chromatography. Peptide separation.

Unit 3:          Mass spectrometry. MALDI-TOFMS. ESI-MS. MS/MS techniques. Peptide sequencing.

Unit 4:          Proteomic workflows. “Top-down”, “bottom-up” y “shotgun” workflows. Bioinformatics. “de novo” sequencing.

Unit 5:          Post-translational modifications and their analysis. Introduction. Phosphorylation. Glycosylation.

Unit 6:          Quantitative proteomics. Problems. ICAT. iTRAQ. SILAC. AQUA. MRM. Elemental mass spectrometry in proteomics.

Unit 7:          Biomarkers. Definition. Examples.

Uni7 8:         Introduction to metallomics and metabolomics. Definitions. Importance. Strategies

The wide variety of learning and teaching approaches used is divided into 2 big groups:

On-site activities:

• 14.5 lectures (one hour each), supported by multimedia teaching techniques, where the basis of MS will be introduced to the students.
• 4 problem-solving classes (one hour each) where different topics and problems, previously worked out by the students, will be discussed and solved.
• Teaching in smaller groups (1 hour), where issues related to the theoretical classes will be discussed. Student participation will be promoted.
• 3 h in the laboratories of the Scientific Services of the University of Oviedo, in which the student will receive a first insight into a proteomic workflow.

Distance activities:

• Individual work: The student should devote time to assimilate the concepts and background introduced by the teacher during the lectures. In addition, the student should go into the main topics using primary and secondary information sources, including information retrieval through on-line computer searches. Problem-solving classes will be used to clarify questions raised during such work.
• Team work: The teaching in smaller groups will be performed in groups. Such groups will be maintained for any other activity which could take place, for example, in problem-solving classes. Also, ability to interact with other people and to engage in team-working will be promoted.

Student workload (hours) for each specific section is given in the following table:

IMPORTANT: Exceptionally, if required by sanitary conditions, non-face-to-face teaching activities may be included. In that case, the students will be informed of the changes made.

The procedures, different aspects and the criteria used for the assessment of student performance is given in the following table. The weight of each assessment procedure in the final mark of the student (in both examination sessions: regular and extra) also given:

Exceptionally, if required by sanitary conditions, non-face-to-face evaluation methods may be included. In that case, the students will be informed of the changes made.

• Proteomics: Methods and Protocols (Methods in Molecular Biology), J. Reinders, A. Sickmann (Eds.) Humana Press, 2009
• Quantitative Proteomics by Mass Spectrometry (Methods in Molecular Biology), S. Sechi (Ed.) Humana Press, 2007
• The Evolution from Protein Chemistry to Proteomics: Basic Science to clinical Application, R.L. Lundblad, CRC Press, 2006
• M. Bantscheff et al. (2007) Quantitative mass spectrometry in proteomics: a critical review. Anal. Bioanal. Chem. 389:1017-1031.
• J. Bettmer et al. (2009) The emerging role of ICP-MS in proteomic analysis. J. Proteom. 72:989-1005.
• F. Calderon_celis et al. (2018) Standardization approaches in absolute quantitativeproteomics with mass spectrometry, Mass Spectrometry Reviews DOI: 10.1002/mas.21542
• Manual de Proteómica (2014), Sociedad Española de Proteómca (SeProt), Ed. F. Corrales y J. Calvete