Reproducibility of combinatorial peptide ligand libraries for proteome capture evaluated by selected reaction monitoring

Journal of Proteomics

Volumn 89, Issue , 2013, Pages 215-226

  Di Girolamo, Francesco ^a,b,c   Righetti, Pier Giorgio ^b   Soste, Martin ^a   Feng, Yuehan ^a   Picotti, Paola ^a  

^a ETH ZURICH   (Switzerland)

^b POLITECNICO DI MILANO   (Italy)

^c BAMBINO GESÙ CHILDREN S HOSPITAL   (Italy)

Author keywords

Combinatorial peptide ligand libraries; Mass spectrometry; Reproducibility; Selected reaction monitoring

Indexed keywords

LIGAND; PEPTIDE; PROTEOME; PEPTIDE LIBRARY; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; COMBINATORIAL LIBRARY; COMBINATORIAL PEPTIDE LIGAND LIBRARY; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ISOLATION; REPRODUCIBILITY; SACCHAROMYCES CEREVISIAE; SELECTED REACTION MONITORING; SYSTEMS BIOLOGY; CHEMISTRY; METABOLISM; PEPTIDE LIBRARY; PROCEDURES; PROTEOMICS;

PEPTIDE LIBRARY; PROTEOME; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84880349225     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2013.05.037     Document Type: Article

References (37)

1. Keshishian H., Addona T., Burgess M., Kuhn E., Carr S.A. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol Cell Proteomics 2007, 6:2212-2229.
2. Berna M.J., Zhen Y., Watson D.E., Hale J.E., Ackermann B.L. Strategic use of immunoprecipitation and LC/MS/MS for trace-level protein quantification: myosin light chain 1, a biomarker of cardiac necrosis. Anal Chem 2007, 79:4199-4205.
3. Anderson N.L., Anderson N.G., Haines L.R., Hardie D.B., Olafson R.W., Pearson T.W. Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J Proteome Res 2004, 3:235-244.
4. Zhang H., Li X.J., Martin D.B., Aebersold R. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol 2003, 21:660-666.
5. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999, 17:994-999.
6. Boschetti E., Lomas L., Citterio A., Righetti P.G. Romancing the "hidden proteome", Anno Domini two zero zero seven. J Chromatogr A 2007, 1153:277-290.
7. Lam K.S., Salmon S.E., Hersh E.M., Hruby V.J., Kazmierski W.M., Knapp R.J. A new type of synthetic peptide library for identifying ligand-binding activity. Nature 1991, 354:82-84.
8. Buettner J.A., Dadd C.A., Baumbach G.A., Masecar B.L., Hammond D.J. Chemically derived peptide libraries: a new resin and methodology for lead identification. Int J Pept Protein Res 1996, 47:70-83.
9. Boschetti E., Righetti P.G. The ProteoMiner in the proteomic arena: a non-depleting tool for discovering low-abundance species. J Proteomics 2008, 71:255-264.
10. Righetti P.G., Boschetti E. The ProteoMiner and the FortyNiners: searching for gold nuggets in the proteomic arena. Mass Spectrom Rev 2008, 27:596-608.
11. Boschetti E., Righetti P.G. The art of observing rare protein species in proteomes with peptide ligand libraries. Proteomics 2009, 9:1492-1510.
12. Righetti P.G., Boschetti E., Kravchuk A.V., Fasoli E. The proteome buccaneers: how to unearth your treasure chest via combinatorial peptide ligand libraries. Expert Rev Proteomics 2010, 7:373-385.
13. Thulasiraman V., Lin S., Gheorghiu L., Lathrop J., Lomas L., Hammond D., et al. Reduction of the concentration difference of proteins in biological liquids using a library of combinatorial ligands. Electrophoresis 2005, 26:3561-3571.
14. Castagna A., Cecconi D., Sennels L., Rappsilber J., Guerrier L., Fortis F., et al. Exploring the hidden human urinary proteome via ligand library beads. J Proteome Res 2005, 4:1917-1930.
15. Santucci L., Candiano G., Bruschi M., D'Ambrosio C., Petretto A., Scaloni A., et al. Combinatorial peptide ligand libraries for the analysis of low-expression proteins: validation for normal urine and definition of a first protein MAP. Proteomics 2012, 12:509-515.
16. Sennels L., Salek M., Lomas L., Boschetti E., Righetti P.G., Rappsilber J. Proteomic analysis of human blood serum using peptide library beads. J Proteome Res 2007, 6:4055-4062.
17. Au J.S., Cho W.C., Yip T.T., Yip C., Zhu H., Leung W.W., et al. Deep proteome profiling of sera from never-smoked lung cancer patients. Biomed Pharmacother 2007, 61:570-577.
18. Guerrier L., Claverol S., Fortis F., Rinalducci S., Timperio A.M., Antonioli P., et al. Exploring the platelet proteome via combinatorial, hexapeptide ligand libraries. J Proteome Res 2007, 6:4290-4303.
19. Roux-Dalvai F., Gonzalez de Peredo A., Simo C., Guerrier L., Zanella A., et al. Extensive analysis of the cytoplasmic proteome of human erythrocytes using the peptide ligand library technology and advanced mass spectrometry. Mol Cell Proteomics 2008, 7:2254-2269.
20. Guerrier L., Claverol S., Finzi L., Paye F., Fortis F., Boschetti E., et al. Contribution of solid-phase hexapeptide ligand libraries to the repertoire of human bile proteins. J Chromatogr A 2007, 1176:192-205.
21. Mouton-Barbosa E., Roux-Dalvai F., Bouyssie D., Berger F., Schmidt E., Righetti P.G., et al. In-depth exploration of cerebrospinal fluid by combining peptide ligand library treatment and label-free protein quantification. Mol Cell Proteomics 2010, 9:1006-1021.
22. Rivers J., Hughes C., McKenna T., Woolerton Y., Vissers J.P., Langridge J.I., et al. Asymmetric proteome equalization of the skeletal muscle proteome using a combinatorial hexapeptide library. PLoS One 2011, 6:e28902.
23. Antonioli P., Fortis F., Guerrier L., Rinalducci S., Zolla L., Righetti P.G., et al. Capturing and amplifying impurities from purified recombinant monoclonal antibodies via peptide library beads: a proteomic study. Proteomics 2007, 7:1624-1633.
24. Fortis F., Guerrier L., Areces L.B., Antonioli P., Hayes T., Carrick K., et al. A new approach for the detection and identification of protein impurities using combinatorial solid phase ligand libraries. J Proteome Res 2006, 5:2577-2585.
25. Boschetti E., Righetti P.G. Breakfast at Tiffany's? Only with a low-abundance proteomic signature!. Electrophoresis 2012, 33:2228-2239.
26. Dwivedi R.C., Krokhin O.V., Cortens J.P., Wilkins J.A. Assessment of the reproducibility of random hexapeptide peptide library-based protein normalization. J Proteome Res 2010, 9:1144-1149.
27. Li L., Sun C.J., Freeby S., Yee D., Kieffer-Jaquinod S., Guerrier L., et al. Protein sample treatment with peptide ligand library: coverage and consistency. J Proteomics Bioinform 2009, 2:485-494.
28. Hartwig S., Czibere A., Kotzka J., Passlack W., Haas R., Eckel J., et al. Combinatorial hexapeptide ligand libraries (ProteoMiner): an innovative fractionation tool for differential quantitative clinical proteomics. Arch Physiol Biochem 2009, 115:155-160.
29. Overgaard A.J., Thingholm T.E., Larsen M.R., Tarnow L., Rossing P., McGuire J.N., et al. Quantitative iTRAQ-based proteomic identification of candidate biomarkers for diabetic nephropathy in plasma of type 1 diabetic patients. Clin Proteomics 2010, 6:105-114.
30. Fonslow B.R., Carvalho P.C., Academia K., Freeby S., Xu T., Nakorchevsky A., et al. Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT. J Proteome Res 2011, 10:3690-3700.
31. Meng R., Gormley M., Bhat V.B., Rosenberg A., Quong A.A. Low abundance protein enrichment for discovery of candidate plasma protein biomarkers for early detection of breast cancer. J Proteomics 2011, 75:366-374.
32. Elias J.E., Gygi S.P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 2007, 4:207-214.
33. Ghaemmaghami S., Huh W.K., Bower K., Howson R.W., Belle A., Dephoure N., et al. Global analysis of protein expression in yeast. Nature 2003, 425:737-741.
34. Rudomin E.L., Carr S.A., Jaffe J.D. Directed sample interrogation utilizing an accurate mass exclusion-based data-dependent acquisition strategy (AMEx). J Proteome Res 2009, 8:3154-3160.
35. Domon B., Aebersold R. Options and considerations when selecting a quantitative proteomics strategy. Nat Biotechnol 2010, 28:710-721.
36. Picotti P., Bodenmiller B., Mueller L.N., Domon B., Aebersold R. Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 2009, 138:795-806.
37. Fasoli E., Sanz L., Wagstaff S., Harrison R.A., Righetti P.G., Calvete J.J. Exploring the venom proteome of the African puff adder, Bitis arietans, using a combinatorial peptide ligand library approach at different pHs. J Proteomics 2010, 73:932-942.