Learning outcomes of the subject

Describe the distinct methodologies for sample preparation prior to MS analysis: protein enrichment, protein digestion and protein/peptide fractionation



Differentiate between shotgun and targeted proteomics, as well as describe different bottom-up proteomics approaches: data dependent acquisition (DDA) & data independent acquisition (DIA).



Perform the steps involved in a workflow to identify the proteins present in a complex mixture.



Analyze protemics data. Filter MS-based data following specific criteria and perfom bioinformatic analyses to extract the biological meaning.



Plan an experiment using appropriate methods taking into account the constraints of the available technology, sample number, and the underlying hypothesis.

Ordinary call: orientations and renunciation

Attendance is compulsory. Excused absences may be made up with the activity indicated by the person in charge of the session.



The intervention of the student in the classes will be valued, the questions and comments made in each session will be valued. A high participation and attendance to 100% of the sessions allows to pass the course.



An unexcused attendance of less than 80% of the sessions will result in the failure of the course.

In the case of absence with a justified cause (more than 30%), an exam/test of the subject adjusted to the specific situation will be carried out.

Extraordinary call: orientations and renunciation

The extraordinary call will involve the realization of an exam/test of the subject that will consist of the development of a topic of the subject to choose between two chosen at random.

Bibliography

Compulsory materials

e-Gela platform from the UPV/EHU https://egela.ehu.eus/login/index.php

Basic bibliography

Manual de proteómica, Volumen I. Sociedad Española de Proteómica, 2014

Manual de proteómica, Volumen II. Sociedad Española de Proteómica, 2019

Mass spectrometry data analysis in proteomics. R. Matthiesen. Humana Press, Springer, Heidelberg, 2013

Proteomics for biological discovery. T.D. Veenstra & J.R. Yates III. Wiley, Hoboken, New Jersey, 2006

In-depth bibliography

Aebersold R, Mann M. (2016) Mass-spectrometric exploration of proteome structure and function. Nature 537:347-355



Cox J, Mann M. (2011) Quantitative, high-resolution proteomics for data-driven systems biology. Annu. Rev. Biochem. 80:273-299



Ebhardt HA, Root A, Sander C, Aebersold R. (2015) Applications of targeted proteomics in systems biology and translational medicine. Proteomics 15:3193-3208



Geyer PE, Holdt LM, Teupser D, Mann M. (2017) Revisiting biomarker discovery by plasma proteomics. Mol. Syst. Biol.13:942



Lundberg E, Borner GHH. (2019) Spatial proteomics: a powerful discovery tool for cell biology. Nature Reviews. 25(5):285-302



Meissner F, Geddes-McAlister J, Mann M, Bantscheff M. (2022). The emerging role of mass spectrometry-based proteomics in drug discovery. Nature Reviews DrugDiscovery. 21, 637-654.



Olsen JV, Mann M. (2012) Status of large-scale analysis of post-translational modifications by mass spectrometry. Mol.Cell. Proteomics 12:3444-3452



Picotti P, Aebersold R. (2012) Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat. Methods 9:555-566



Sabidó E, Selevsek N, Aebersold R. (2012) Mass spectrometry-based proteomics for systems biology. Curr. Opin.Biotechnol. 23:591-597



Uzozie AC, Aebersold R. (2018) Advancing translational research and precision medicine with targeted proteomics. J.Proteomics 189:1-10



Walther TC, Mann M. (2010) Mass spectrometry-based proteomics in cell biology. J. Cell Biol. 190:491-500