Absolute protein quantification allows differentiation of cell-specific metabolic routes and functions

Proteomics

Volumn 15, Issue 7, 2015, Pages 1316-1325

  Wiśniewski, Jacek R ^a   Koepsell, Hermann ^b   Gizak, Agnieszka ^c   Rakus, Dariusz ^c  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^b UNIVERSITY OF WÜRZBURG   (Germany)

^c UNIVERSITY OF WROC AW   (Poland)

Author keywords

Absolute protein quantitation; Animal proteomics; Mitochondrion; Red muscle fiber; Small intestine mucosa; Total protein approach

Indexed keywords

AMINO ACID; MITOCHONDRIAL PROTEIN; PROTEOME;

ABSORPTION; ANIMAL TISSUE; ARTICLE; BILE SECRETION; CANCER CELL LINE; CATABOLISM; CELL DIFFERENTIATION; CELL SPECIFICITY; ERYTHROCYTE; HUMAN; HUMAN CELL; INTESTINE MUCOSA; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLIC CAPACITY; METABOLISM; NONHUMAN; NUTRIENT; PRIORITY JOURNAL; PROTEIN ANALYSIS; QUANTITATIVE ANALYSIS; SLOW MUSCLE FIBER; ANIMAL; ANTIBODY SPECIFICITY; CHEMISTRY; HCT116 CELL LINE; K562 CELL LINE; MCF 7 CELL LINE; MOUSE; TANDEM MASS SPECTROMETRY;

ANIMALIA; MAMMALIA;

ANIMALS; HCT116 CELLS; HUMANS; K562 CELLS; MCF-7 CELLS; METABOLIC NETWORKS AND PATHWAYS; MICE; MITOCHONDRIAL PROTEINS; ORGAN SPECIFICITY; PROTEOME; TANDEM MASS SPECTROMETRY;

EID: 84926100026     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201400456     Document Type: Article

References (35)

1. Boyer, J. L., Bile formation and secretion. Compr. Physiol. 2013, 3, 1035-1078.
2. Gorboulev, V., Schurmann, A., Vallon, V., Kipp, H. et al., Na(+)-D-glucose cotransporter SGLT1 is pivotal for intestinal glucose absorption and glucose-dependent incretin secretion. Diabetes 2012, 61, 187-196.
3. Koepsell, H., The SLC22 family with transporters of organic cations, anions and zwitterions. Mol. Aspects Med. 2013, 34, 413-435.
4. Young, J. D., Yao, S. Y., Baldwin, J. M., Cass, C. E., Baldwin, S. A., The human concentrative and equilibrative nucleoside transporter families, SLC28 and SLC29. Mol. Aspects Med. 2013, 34, 529-547.
5. Bantscheff, M., Lemeer, S., Savitski, M. M., Kuster, B., Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present. Anal. Bioanal. Chem. 2012, 404, 939-965.
6. Beck, M., Schmidt, A., Malmstroem, J., Claassen, M. et al., The quantitative proteome of a human cell line. Mol. Syst. Biol. 2011, 7, 549.
7. Braisted, J. C., Kuntumalla, S., Vogel, C., Marcotte, E. M. et al., The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results. BMC Bioinformatics 2008, 9, 529.
8. Ishihama, Y., Oda, Y., Tabata, T., Sato, T. et al., Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Proteomics 2005, 4, 1265-1272.
9. Schwanhausser, B., Busse, D., Li, N., Dittmar, G. et al., Global quantification of mammalian gene expression control. Nature 2011, 473, 337-342.
10. Ahrne, E., Molzahn, L., Glatter, T., Schmidt, A., Critical assessment of proteome-wide label-free absolute abundance estimation strategies. Proteomics 2013, 13, 2567-2578.
11. Arike, L., Valgepea, K., Peil, L., Nahku, R. et al., Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli. J. Proteomics 2012, 75, 5437-5448.
12. Wisniewski, J. R., Ostasiewicz, P., Dus, K., Zielinska, D. F. et al., Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma. Mol. Syst. Biol. 2012, 8, 611.
13. Wisniewski, J. R., Hein, M. Y., Cox, J., Mann, M., A 'proteomic ruler' for protein copy number and concentration estimation without spike-in standards. Mol. Cell. Proteomics 2014, 13, 3497-3506.
14. Wisniewski, J. R., Rakus, D., Multi-enzyme digestion FASP and the 'Total Protein Approach'-based absolute quantification of the Escherichia coli proteome. J. Proteomics 2014, 109, 322-331.
15. Wisniewski, J. R., Mann, M., Consecutive proteolytic digestion in an enzyme reactor increases depth of proteomic and phosphoproteomic analysis. Anal. Chem. 2012, 84, 2631-2637.
16. Wisniewski, J. R., Dus, K., Mann, M., Proteomic workflow for analysis of archival formalin-fixed and paraffin-embedded clinical samples to a depth of 10 000 proteins. Proteomics Clin. Appl. 2013, 7, 225-233.
17. Cox, J., Mann, M., MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 2008, 26, 1367-1372.
18. Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A. et al., Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 2011, 10, 1794-1805.
19. Mootha, V. K., Bunkenborg, J., Olsen, J. V., Hjerrild, M. et al., Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell 2003, 115, 629-640.
20. Sen, U., Dasgupta, J., Choudhury, D., Datta, P. et al., Crystal structures of HbA2 and HbE and modeling of hemoglobin delta 4: interpretation of the thermal stability and the antisickling effect of HbA2 and identification of the ferrocyanide binding site in Hb. Biochemistry 2004, 43, 12477-12488.
21. Kratz, A., Ferraro, M., Sluss, P. M., Lewandrowski, K. B., Case records of the Massachusetts General Hospital. Weekly clinicopathological exercises. Laboratory reference values. N. Engl. J. Med. 2004, 351, 1548-1563.
22. Righetti, P. G., Boschetti, E., Combinatorial peptide libraries to overcome the classical affinity-enrichment methods in proteomics. Amino Acids 2013, 45, 219-229.
23. Santucci, L., Candiano, G., Petretto, A., Lavarello, C. et al., Combinatorial ligand libraries as a two-dimensional method for proteome analysis. J. Chromatogr. A 2013, 1297, 106-112.
24. Rich-Denson, C., Kimura, R. E., Evidence in vivo that most of the intraluminally absorbed glucose is absorbed intact into the portal vein and not metabolized to lactate. Biochem. J. 1988, 254, 931-934.
25. Wu, G., Urea synthesis in enterocytes of developing pigs. Biochem. J. 1995, 312(Pt 3), 717-723.
26. Mueckler, M., Thorens, B., The SLC2 (GLUT) family of membrane transporters. Mol. Aspects Med. 2013, 34, 121-138.
27. Klaassen, C. D., Aleksunes, L. M., Xenobiotic, bile acid, and cholesterol transporters: function and regulation. Pharmacol. Rev. 2010, 62, 1-96.
28. Koepsell, H., Lips, K., Volk, C., Polyspecific organic cation transporters: structure, function, physiological roles, and biopharmaceutical implications. Pharm. Res. 2007, 24, 1227-1251.
29. McConnell, R. E., Benesh, A. E., Mao, S., Tabb, D. L., Tyska, M. J., Proteomic analysis of the enterocyte brush border. Am. J. Physiol. Gastrointest. Liver Physiol. 2011, 300, G914-G926.
30. Belanger, M., Allaman, I., Magistretti, P. J., Brain energy metabolism: focus on astrocyte-neuron metabolic cooperation. Cell Metab. 2011, 14, 724-738.
31. Pellerin, L., Magistretti, P. J., Sweet sixteen for ANLS. J. Cereb. Blood Flow Metab. 2012, 32, 1152-1166.
32. Vander Heiden, M. G., Cantley, L. C., Thompson, C. B., Understanding the Warburg effect: the metabolic requirements of cell proliferation. Science 2009, 324, 1029-1033.
33. Duchen, M. R., Mitochondria in health and disease: perspectives on a new mitochondrial biology. Mol. Aspects Med. 2004, 25, 365-451.
34. Pagliarini, D. J., Calvo, S. E., Chang, B., Sheth, S. A. et al., A mitochondrial protein compendium elucidates complex I disease biology. Cell 2008, 134, 112-123.
35. Vizcaíno, J. A, Côté, R. G., Csordas, A., Dianes, J. A. et al., The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 2013, 41, D1063-D1069.