C-STrap sample preparation method-in-situ cysteinyl peptide capture for bottom-up proteomics analysis in the strap format

PLoS ONE

Volumn 10, Issue 9, 2015, Pages

  Zougman, Alexandre ^a   Banks, Rosamonde E ^a  

^a ST JAMES S UNIVERSITY HOSPITAL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CYSTEINE; MAMMALIAN TARGET OF RAPAMYCIN; TRYPSIN; PEPTIDE; PROTEIN BINDING; TARGET OF RAPAMYCIN KINASE;

ARTICLE; C SUSPENSION TRAPPING METHOD; CONTROLLED STUDY; METHODOLOGY; PROCESS DEVELOPMENT; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN PROCESSING; PROTEOMICS; SYSTEM ANALYSIS; CHEMISTRY; HELA CELL LINE; HUMAN; IMMUNOPRECIPITATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLISM; PROCEDURES;

CHROMATOGRAPHY, LIQUID; HELA CELLS; HUMANS; IMMUNOPRECIPITATION; MASS SPECTROMETRY; PEPTIDES; PROTEIN BINDING; PROTEOMICS; TOR SERINE-THREONINE KINASES;

EID: 84947243629     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0138775     Document Type: Article

References (16)

1. Zubarev RA. The challenge of the proteome dynamic range and its implications for in-depth proteomics. Proteomics. 2013; 13(5):723-6. doi: 10.1002/pmic.201200451 PMID: 23307342.
2. Liu T, Qian WJ, Chen WN, Jacobs JM, Moore RJ, Anderson DJ, et al. Improved proteome coverage by using high efficiency cysteinyl peptide enrichment: the human mammary epithelial cell proteome. Proteomics. 2005; 5(5):1263-73. doi: 10.1002/pmic.200401055 PMID: 15742320; PubMed Central PMCID: PMC1769322.
3. Nakano K, Fukui T, Matsubara H. Sequence homology between potato and rabbit muscle phosphroylases. Isolation of cysteinyl peptides by covalent chromatography from the potato enzyme and their amino acid sequences. Journal of biochemistry. 1980; 87(3):919-27. PMID: 7390969.
4. Palani A, Lee JS, Huh J, Kim M, Lee YJ, Chang JH, et al. Selective enrichment of cysteine-containing peptides using SPDP-functionalized superparamagnetic Fe(3)O(4)@SiO(2) nanoparticles: application to comprehensive proteomic profiling. Journal of proteome research. 2008; 7(8):3591-6. doi: 10.1021/pr800067x PMID: 18563925.
5. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature biotechnology. 1999; 17(10):994-9. doi: 10.1038/13690 PMID: 10504701.
6. Hansen KC, Schmitt-Ulms G, Chalkley RJ, Hirsch J, Baldwin MA, Burlingame AL. Mass spectrometric analysis of protein mixtures at low levels using cleavable C-13-isotope-coded affinity tag and multidimensional chromatography. Mol Cell Proteomics. 2003; 2(5):299-314. doi: 10.1074/mcp.M#00021-MCP200 WOS:000184270600003. PMID: 12766231
7. Fujioka H, Tsunehiro M, Kawaguchi M, Kuramoto Y, Kurosaki H, Hieda Y, et al. Simple enrichment of thiol-containing biomolecules by using zinc(II)-cyclen-functionalized magnetic beads. Journal of separation science. 2014; 37(13):1601-9. doi: 10.1002/jssc.201400135 PMID: 24737618.
8. Zougman A, Selby PJ, Banks RE. Suspension trapping (STrap) sample preparation method for bottomup proteomics analysis. Proteomics. 2014; 14(9):1006-0. doi: 10.1002/pmic.201300553 PMID: 24678027.
9. Wisniewski JR. Proteomic sample preparation from formalin fixed and paraffin embedded tissue. J Vis Exp. 2013;(79). doi: 10.3791/50589 PMID: 24022122; PubMed Central PMCID: PMC3857359.
10. Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nature biotechnology. 2008; 26(12):1367-72. doi: 10.1038/nbt.1511 PMID: 19029910.
11. Rappsilber J, Mann M, Ishihama Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nature protocols. 2007; 2(8):1896-906. doi: 10.1038/nprot.2007.261 PMID: 17703201.
12. Bandhakavi S, Kim YM, Ro SH, Xie H, Onsongo G, Jun CB, et al. Quantitative nuclear proteomics identifies mTOR regulation of DNA damage response. Mol Cell Proteomics. 2010; 9(2):403-14. doi: 10.1074/mcp.M900326-MCP200 PMID: 19955088; PubMed Central PMCID: PMC2830849.
13. Hsu PP, Kang SA, Rameseder J, Zhang Y, Ottina KA, Lim D, et al. The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signaling. Science. 2011; 332(6035):1317-22. doi: 10.1126/science.1199498 PMID: 21659604; PubMed Central PMCID: PMC3177140.
14. Xie X, Gong Z, Mansuy-Aubert V, Zhou QL, Tatulian SA, Sehrt D, et al. C2 domain-containing phosphoprotein CDP138 regulates GLUT4 insertion into the plasma membrane. Cell metabolism. 2011; 14 (3):378-89. doi: 10.1016/j.cmet.2011.06.015 PMID: 21907143; PubMed Central PMCID: PMC3172579.
15. Harada K, Frankel AD. Identification of two novel arginine binding DNAs. The EMBO journal. 1995; 14 (23):5798-811. PMID: 8846773; PubMed Central PMCID: PMC394698.
16. Weith HL, Wiebers JL, Gilham PT. Synthesis of cellulose derivatives containing the dihydroxyboryl group and a study of their capacity to form specific complexes with sugars and nucleic acid components. Biochemistry. 1970; 9(22):4396-401. PMID: 5472711.