Proteomics Optional Master Course

Proteomics Optional Master Course

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  • January 26, 2016
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Handouts (use your login password to open files)



Literature as background to the lectures of the

Optional Master Course “Biomedical Proteomics” FEB. 2016


Monday FEB 1 literature


Mass-spectrometry-based draft of the human proteome.  

Wilhelm M, Schlegl J, Hahne H, Moghaddas Gholami A, Lieberenz M, Savitski MM, Ziegler E, Butzmann L, Gessulat S, Marx H, Mathieson T, Lemeer S, Schnatbaum K, Reimer U, Wenschuh H, Mollenhauer M, Slotta-Huspenina J, Boese JH, Bantscheff M, Gerstmair A, Faerber F, Kuster B. Nature. 2014 May 29;509(7502):582-7. doi: 10.1038/nature13319.


A draft map of the human proteome.

Kim MS, Pinto SM, Getnet D, ……….. Gowda H, Pandey A. Nature. 2014 May 29;509(7502):575-81. doi: 10.1038/nature13302. PMID: 24870542


Commentaries on the Nature “draft human proteome papers”

Drafts of the human proteome. 

Lawrence RT, Villén J. Nat Biotechnol. 2014 Aug;32(8):752-3. doi: 10.1038/nbt.2982. No abstract available. PMID: 25101745 [PubMed – in process]


The human proteome takes the spotlight. 

Doerr A. Nat Methods. 2014 Jul;11(7):709. No abstract available. PMID: 25110780 [PubMed – indexed for MEDLINE] 


Tuesday FEB 2 literature


The coming age of complete, accurate, and ubiquitous proteomes. 

Mann M, Kulak NA, Nagaraj N, Cox J. Mol Cell. 2013 Feb 21;49(4):583-90. doi: 10.1016/j.molcel.2013.01.029. PMID: 23438854 [PubMed – indexed for MEDLINE] Free Article


Mass spectrometry-based proteomics: from cancer biology to protein biomarkers, drug targets, and clinical applications.

Jimenez CR, Verheul HM.

Am Soc Clin Oncol Educ Book. 2014:e504-10. doi: 10.14694/EdBook_AM.2014.34.e504. Free Article


Reproducible quantitative proteotype data matrices for systems biology.

Röst HL, Malmström L, Aebersold R.

Mol Biol Cell. 2015 Nov 5;26(22):3926-31. doi: 10.1091/mbc.E15-07-0507.

PMID: 26543201


Wednessday FEB 3 literature


Proteomics: a pragmatic perspective. 

Mallick P, Kuster B. Nat Biotechnol. 2010 Jul;28(7):695-709. doi: 10.1038/nbt.1658. Epub 2010 Jul 9. Review. PMID: 20622844 [PubMed – indexed for MEDLINE]


Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry.

Gillette MA, Carr SA.

Nat Methods. 2013 Jan;10(1):28-34. doi: 10.1038/nmeth.2309.

PMID: 23269374



Thursday FEB 4 literature


Mass spectrometry-driven phosphoproteomics: patterning the systems biology mosaic.

Jünger MA, Aebersold R.

Wiley Interdiscip Rev Dev Biol. 2014 Jan-Feb;3(1):83-112. doi: 10.1002/wdev.121. Epub 2013 Jul 2.


Recent findings and technological advances in phosphoproteomics for cells and tissues.

von Stechow L, Francavilla C, Olsen JV.

Expert Rev Proteomics. 2015;12(5):469-87. doi: 10.1586/14789450.2015.1078730.

PMID: 26400465


Role of phosphoproteomics in the development of personalized cancer therapies.

Cutillas PR.

Proteomics Clin Appl. 2015 Apr;9(3-4):383-95. doi: 10.1002/prca.201400104. Epub 2015 Feb 27. Review.

PMID: 25488289


Friday FEB 5, Monday FEB 8, Tuesday FEB 9, Wednesday FEB 10


PRAKTICUM, use spare time to prepare presentation of primary research paper

See below list primary research papers to chose for literature presentation


Wednesday FEB 10 literature presentation


Thursday FEB 11 literature


From proteome lists to biological impact–tools and strategies for the analysis of large MS data sets.

Malik R, Dulla K, Nigg EA, Körner R.

Proteomics. 2010 Mar;10(6):1270-83. doi: 10.1002/pmic.200900365. Review.


Targeting molecular networks for drug research.

Pinto JP, Machado RS, Xavier JM, Futschik ME.

Front Genet. 2014 Jun 4;5:160. doi: 10.3389/fgene.2014.00160. eCollection 2014. Review.




LIST of primary proteomics papers for presentation on Wednessday FEB 10

Each student selects one paper from the below list; NB make sure not to pick the same paper


Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps.

Guo T, Kouvonen P, Koh CC, Gillet LC, Wolski WE, Röst HL, Rosenberger G, Collins BC, Blum LC, Gillessen S, Joerger M, Jochum W, Aebersold R.

Nat Med. 2015 Apr;21(4):407-13. doi: 10.1038/nm.3807. Epub 2015 Mar 2. PMID: 25730263


Proteogenomic characterization of human colon and rectal cancer.

Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC; NCI CPTAC.

Nature. 2014 Sep 18;513(7518):382-7. doi: 10.1038/nature13438. Epub 2014 Jul 20. PMID: 25043054


Global proteome analysis of the NCI-60 cell line panel.

Moghaddas Gholami A, Hahne H, Wu Z, Auer FJ, Meng C, Wilhelm M, Kuster B.

Cell Rep. 2013 Aug 15;4(3):609-20. doi: 10.1016/j.celrep.2013.07.018. Epub 2013 Aug 8. PMID:


Colorectal cancer candidate biomarkers identified by tissue secretome proteome profiling.

de Wit M, Kant H, Piersma SR, Pham TV, Mongera S, van Berkel MP, Boven E, Pontén F, Meijer GA, Jimenez CR, Fijneman RJ.

J Proteomics. 2014 Mar 17;99:26-39. doi: 10.1016/j.jprot.2014.01.001. Epub 2014 Jan 10. PMID:


The secretome of colon cancer stem cells contains drug-metabolizing enzymes.

Emmink BL, Verheem A, Van Houdt WJ, Steller EJ, Govaert KM, Pham TV, Piersma SR, Borel Rinkes IH, Jimenez CR, Kranenburg O.

J Proteomics. 2013 Oct 8;91:84-96. doi: 10.1016/j.jprot.2013.06.027. Epub 2013 Jul 5. PMID: 23835434


Surface proteomic analysis of osteosarcoma identifies EPHA2 as receptor for targeted drug delivery.

Posthumadeboer J, Piersma SR, Pham TV, van Egmond PW, Knol JC, Cleton-Jansen AM, van Geer MA, van Beusechem VW, Kaspers GJ, van Royen BJ, Jiménez CR, Helder MN.

Br J Cancer. 2013 Oct 15;109(8):2142-54. doi: 10.1038/bjc.2013.578. Epub 2013 Sep 24. PMID:


Exosomal ITGA3 interferes with non-cancerous prostate cell functions and is increased in urine exosomes of metastatic prostate cancer patients.

Bijnsdorp IV, Geldof AA, Lavaei M, Piersma SR, van Moorselaar RJ, Jimenez CR.

J Extracell Vesicles. 2013 Dec 23;2. doi: 10.3402/jev.v2i0.22097. eCollection 2013. PMID: 24371517


Proteomics of mouse BRCA1-deficient mammary tumors identifies DNA repair proteins with potential diagnostic and prognostic value in human breast cancer.

Warmoes M, Jaspers JE, Pham TV, Piersma SR, Oudgenoeg G, Massink MP, Waisfisz Q, Rottenberg S, Boven E, Jonkers J, Jimenez CR.

Mol Cell Proteomics. 2012 Jul;11(7):M111.013334. doi: 10.1074/mcp.M111.013334. Epub 2012 Feb 24. PMID: 22366898


Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer.

Rikova K, Guo A, Zeng Q, Possemato A, Yu J, Haack H, Nardone J, Lee K, Reeves C, Li Y, Hu Y, Tan Z, Stokes M, Sullivan L, Mitchell J, Wetzel R, Macneill J, Ren JM, Yuan J, Bakalarski CE, Villen J, Kornhauser JM, Smith B, Li D, Zhou X, Gygi SP, Gu TL, Polakiewicz RD, Rush J, Comb MJ.

Cell. 2007 Dec 14;131(6):1190-203. PMID: 18083107



Instruction Literature Presentation



  • Students select a paper from the list of provided papers.
  • All students read the paper that he/she selected
  • The student prepares a ~15 min presentation about the selected paper.
  • This is followed by a short discussion by all students (~5-10 min) of this paper.


Structure of the presentation:

Introduction on the background (what was done before? Why is this field of interest?) and the aims (why was this study done? What was the hypothesis?) of the paper followed by a discussion of the the main results, good and weak points, possible future studies, technology applied etc.


You will receive a grade for the literature study (25% of final grade):

Evaluation will be based upon:

Clarity slides, not too much text, clear figures, good structure?

Planning/duration, is the presentation balanced and within the 15 min?

Overall story, is it clear/well presented?

Content, is the message of the paper clear ?

-Discussion, did the student discuss the paper with an analytical/critical view?


How to prepare for the Literature study presentations?


Students are expected to study the papers in detail.

During and after reading each paper you should ask yourself (for example) the following questions:

  • Do I agree with the authors?
  • What was the hypothesis?
  • Do the results confirm or reject the original hypothesis?
  • Why did the authors do this work?
  • How did they do this work and why did they do it in this way?
  • Are the methods used the most obvious? Would I do it in the same way?
  • How were the experiments carried out and did they do it properly?
  • How did they interpret the results?
  • Did they make the right decisions and conclusions?
  • What are their suggestion for further study?
  • Which are the strong points and which are the weak points of this paper.
  • What is my own overall conclusion?
  • Do I have other recommendations for further study?
  • Do I like the topic, if so, why or why not?
  • Do I like to work in this field, if so, why or why not?
  • When the paper concerns fundamental research, how can I translate this work into a clinical application?

It is recommended to make a short summary of the above mentioned questions and answers and to use this summary in the literature session.



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