Open tubular lab-on-column/mass spectrometry for targeted proteomics of nanogram sample amounts

PLoS ONE

Volumn 9, Issue 9, 2014, Pages

  Hustoft, Hanne Kolsrud ^a   Vehus, Tore ^a   Brandtzaeg, Ole Kristian ^a   Krauss, Stefan ^b   Greibrokk, Tyge ^a   Wilson, Steven Ray ^a   Lundanes, Elsa ^a  

^a UNIVERSITY OF OSLO   (Norway)

^b OSLO UNIVERSITY HOSPITAL   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

BETA CATENIN; LYSINE; NANOPARTICLE; TRYPSIN; WNT PROTEIN; BIOLOGICAL MARKER;

ANALYTIC METHOD; ANIMAL TISSUE; ARTICLE; AUTOMATION; FEMALE; HUMAN; HUMAN CELL; IMMOBILIZED ENZYME REACTOR; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MOUSE; NONHUMAN; ONLINE SYSTEM; OPEN TUBULAR ENZYME REACTOR; OPEN TUBULAR LAB ON COLUMN; PARTICLE SIZE; POROUS LAYER OPEN TUBULAR LIQUID CHROMATOGRAPHY; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN TARGETING; PROTEOMICS; SIGNAL TRANSDUCTION; CELL CULTURE; CHEMISTRY; PROCEDURES; TANDEM MASS SPECTROMETRY;

BIOLOGICAL MARKERS; CELLS, CULTURED; CHROMATOGRAPHY, LIQUID; HUMANS; MASS SPECTROMETRY; PROTEOMICS; TANDEM MASS SPECTROMETRY; WNT PROTEINS;

EID: 84907153239     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0106881     Document Type: Article

References (61)

1. Koomen JM, Haura EB, Bepler G, Sutphen R, Remily-Wood ER, et al. (2008) Proteomic contributions to personalized cancer care. Mol Cell Proteomics 7: 1780-1794.
2. Leung F, Musrap N, Diamandis EP, Kulasingam V (2013) Advances in mass spectrometry-based technologies to direct personalized medicine in ovarian cancer. Trans Proteomics 1: 74-86.
3. Compton C (2014) Data quality and personalized medicine. OE 13: 13-15.
4. Cooperberg MR, Simko JP, Cowan JE, Reid JE, Djalilvand A, et al. (2013) Validation of a cell-cycle progression gene panel to improve risk stratification in a contemporary prostatectomy cohort. J Clin Oncol 31: 1428-1434.
5. Maak M, Simon I, Nitsche U, Roepman P, Snel M, et al. (2013) Independent Validation of a Prognostic Genomic Signature (ColoPrint) for Patients With Stage II Colon Cancer. Ann Surg 257: 1053-1058 1010.1097/SLA.1050b1013e31827c31180.
6. Sveen A, Agesen TH, Nesbakken A, Meling GI, Rognum TO, et al. (2012) ColoGuidePro: a prognostic 7-gene expression signature for stage III colorectal cancer patients. Clin Cancer Res 18: 6001-6010.
7. van 't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AAM, et al. (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415: 530-536.
8. Guo Y, Xiao P, Lei S, Deng F, Xiao GG, et al. (2008) How is mRNA expression predictive for protein expression? A correlation study on human circulating monocytes. Acta Biochim Biophys Sin (Shanghai) 40: 426-436.
9. Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhardt J, et al. (2011) Global quantification of mammalian gene expression control. Nature 473: 337-342.
10. Mayne J, Starr AE, Ning Z, Chen R, Chiang CK, et al. (2014) Fine tuning of proteomic technologies to improve biological findings: advancements in 2011-2013. Anal Chem 86: 176-195.
11. Aebersold R, Burlingame AL, Bradshaw RA (2013) Western blots versus selected reaction monitoring assays: time to turn the tables? Mol Cell Proteomics 12: 2381-2382.
12. Picotti P, Aebersold R (2012) Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods 9: 555-566.
13. Xie F, Liu T, Qian WJ, Petyuk VA, Smith RD (2011) Liquid chromatographymass spectrometry-based quantitative proteomics. J Biol Chem 286: 25443-25449.
14. Nilsson T, Mann M, Aebersold R, Yates JR, Bairoch A, et al. (2010) Mass spectrometry in high-throughput proteomics: ready for the big time. Nat Meth 7: 681-685.
15. Azkargorta M, Wojtas MN, Abrescia NG, Elortza F (2014) Lysine Methylation Mapping of Crenarchaeal DNA-Directed RNA Polymerases by Collision-Induced and Electron-Transfer Dissociation Mass Spectrometry. J Proteome Res.
16. Chen C, Liu X, Zheng W, Zhang L, Yao J, et al. (2014) Screening of missing proteins in the human liver proteome by improved MRM-approach-based targeted proteomics. J Proteome Res 13: 1969-1978.
17. D'Aguanno S, Barcaroli D, Rossi C, Zucchelli M, Ciavardelli D, et al. (2014) p63 isoforms regulate metabolism of cancer stem cells. J Proteome Res 13: 2120-2136.
18. da Fonseca Pires S, Fialho LC Jr, Silva SO, Melo MN, de Souza CC, et al. (2014) Identification of virulence factors in leishmania infantum strains by a proteomic approach. J Proteome Res 13: 1860-1872.
19. Lv DW, Ge P, Zhang M, Cheng ZW, Li XH, et al. (2014) Integrative Network Analysis of the Signaling Cascades in Seedling Leaves of Bread Wheat by Large-Scale Phosphoproteomic Profiling. J Proteome Res.
20. Musunuri S, Wetterhall M, Ingelsson M, Lannfelt L, Artemenko K, et al. (2014) Quantification of the brain proteome in Alzheimer's disease using multiplexed mass spectrometry. J Proteome Res 13: 2056-2068.
21. Nolte H, Konzer A, Ruhs A, Jungblut B, Braun T, et al. (2014) Global protein expression profiling of zebrafish organs based on in vivo incorporation of stable isotopes. J Proteome Res 13: 2162-2174.
22. Poschmann G, Seyfarth K, Besong Agbo D, Klafki HW, Rozman J, et al. (2014) High-Fat Diet Induced Isoform Changes of the Parkinson's Disease Protein DJ-1. J Proteome Res.
23. Zhao X, Bak S, Pedersen AJ, Jensen ON, Hojlund K (2014) Insulin Increases Phosphorylation of Mitochondrial Proteins in Human Skeletal Muscle in Vivo. J Proteome Res.
24. Zhao X, Sidoli S, Wang L, Wang W, Guo L, et al. (2014) Comparative proteomic analysis of histone post-translational modifications upon ischemia/reperfusion-induced retinal injury. J Proteome Res 13: 2175-2186.
25. Nunez O, Nakanishi K, Tanaka N (2008) Preparation of monolithic silica columns for high-performance liquid chromatography. J Chromatogr A 1191: 231-252.
26. Svec F (2004) Preparation and HPLC applications of rigid macroporous organic polymer monoliths. J Sep Sci 27: 747-766.
27. Schappler J, Rudaz S, Veuthey JL, Guillarme D (2013) Coupling UHPLC with MS: The Needs, Challenges, and Applications. Ultra-High Performance Liquid Chromatography and its Applications: John Wiley & Sons, Inc. pp. 95-131.
28. Fekete S, Fekete J (2013) The Potential of Shell Particles in Fast Liquid Chromatography. Ultra-High Performance Liquid Chromatography and its Applications: John Wiley & Sons, Inc. pp. 133-167.
29. Massolini G, Calleri E (2005) Immobilized trypsin systems coupled on-line to separation methods: recent developments and analytical applications. J Sep Sci 28: 7-21.
30. Yamaguchi H, Miyazaki M (2013) Enzyme-immobilized reactors for rapid and efficient sample preparation in MS-based proteomic studies. PROTEOMICS 13: 457-466.
31. Rogeberg M, Vehus T, Grutle L, Greibrokk T, Wilson SR, et al. (2013) Separation optimization of long porous-layer open-tubular columns for nano-LC-MS of limited proteomic samples. J Sep Sci 36: 2838-2847.
32. Luo Q, Gu Y, Wu SL, Rejtar T, Karger BL (2008) Two-dimensional strong cation exchange/porous layer open tubular/mass spectrometry for ultratrace proteomic analysis using a 10 microm id poly(styrene-divinylbenzene) porous layer open tubular column with an on-line triphasic trapping column. Electrophoresis 29: 1604-1611.
33. Luo Q, Yue G, Valaskovic GA, Gu Y, Wu SL, et al. (2007) On-line 1D and 2D porous layer open tubular/LC-ESI-MS using 10-microm-i.d. poly(styrenedivinylbenzene) columns for ultrasensitive proteomic analysis. Anal Chem 79: 6174-6181.
34. Rogeberg M, Wilson SR, Greibrokk T, Lundanes E (2010) Separation of intact proteins on porous layer open tubular (PLOT) columns. J Chromatogr A 1217: 2782-2786.
35. Thakur D, Rejtar T, Wang D, Bones J, Cha S, et al. (2011) Microproteomic analysis of 10,000 laser captured microdissected breast tumor cells using shortrange sodium dodecyl sulfate-polyacrylamide gel electrophoresis and porous layer open tubular liquid chromatography tandem mass spectrometry. J Chromatogr A 1218: 8168-8174.
36. Yue G, Luo Q, Zhang J, Wu SL, Karger BL (2007) Ultratrace LC/MS proteomic analysis using 10-microm-i.d. Porous layer open tubular poly(styrenedivinylbenzene) capillary columns. Anal Chem 79: 938-946.
37. Hustoft HK, Brandtzaeg OK, Rogeberg M, Misaghian D, Torsetnes SB, et al. (2013) Integrated enzyme reactor and high resolving chromatography in "subchip" dimensions for sensitive protein mass spectrometry. Sci Rep 3: 3511.
38. Lau T, Chan E, Callow M, Waaler J, Boggs J, et al. (2013) A Novel Tankyrase Small-Molecule Inhibitor Suppresses APC Mutation-Driven Colorectal Tumor Growth. Cancer Res 73: 3132-3144.
39. Abele S, Smejkal P, Yavorska O, Foret F, Macka M (2010) Evanescent waveinitiated photopolymerisation as a new way to create monolithic open-tubular capillary columns: use as enzymatic microreactor for on-line protein digestion. Analyst 135: 477-481.
40. Amankwa LN, Kuhr WG (1992) Trypsin-Modified Fused-Silica Capillary Microreactor for Peptide-Mapping by Capillary Zone Electrophoresis. Anal Chem 64: 1610-1613.
41. Hu JW, Shen YH, Qin WJ, Zhang YJ, Qian XH (2012) Preparation of Multilayer Open Capillary Immobilized Enzyme Reactor and Its Application in Digestion of Proteins. Chem J Chin U 33: 268-275.
42. Licklider L, Kuhr WG (1994) Optimization of Online Peptide-Mapping by Capillary Zone Electrophoresis. Anal Chem 66: 4400-4407.
43. Stigter EC, de Jong GJ, van Bennekom WP (2007) Development of an opentubular trypsin reactor for on-line digestion of proteins. Anal Bioanal Chem 389: 1967-1977.
44. Safdar M, Spross J, Janis J (2014) Microscale immobilized enzyme reactors in proteomics: latest developments. J Chromatogr A 1324: 1-10.
45. Huang T, Mi JQ, Zhang XX (2006) Capillary electrochromatography of amino acids with a protein-bonded porous-layer open-tubular column. J Sep Sci 29: 277-281.
46. Promega (2014) Trypsin/Lys-C Mix.
47. Kocher T, Pichler P, Pra MD, Rieux L, Swart R, et al. (2014) Development and performance evaluation of an ultra-low flow nano liquid chromatographytandem mass spectrometry set-up. PROTEOMICS: n/a-n/a.
48. Kim JH, Inerowicz D, Hedrick V, Regnier F (2013) Integrated sample preparation methodology for proteomics: analysis of native proteins. Anal Chem 85: 8039-8045.
49. Sproß J, Brauch S, Mandel F, Wagner M, Buckenmaier S, et al. (2013) Multidimensional nano-HPLC coupled with tandem mass spectrometry for analyzing biotinylated proteins. Anal Bioanal Chem 405: 2163-2173.
50. MacDonald BT, Tamai K, He X (2009) Wnt/beta-catenin signaling: components, mechanisms, and diseases. Dev Cell 17: 9-26.
51. Wang M, Weiss M, Simonovic M, Haertinger G, Schrimpf SP, et al. (2012) PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life. Molecular & Cellular Proteomics 11: 492-500.
52. Miyaki M, Konishi M, Kikuchi-Yanoshita R, Enomoto M, Igari T, et al. (1994) Characteristics of somatic mutation of the adenomatous polyposis coli gene in colorectal tumors. Cancer Res 54: 3011-3020.
53. Neufeld KL, Zhang F, Cullen BR, White RL (2000) APC-mediated downregulation of beta-catenin activity involves nuclear sequestration and nuclear export. EMBO Rep 1: 519-523.
54. Henderson BR, Fagotto F (2002) The ins and outs of APC and beta-catenin nuclear transport. EMBO Rep 3: 834-839.
55. Li VS, Ng SS, Boersema PJ, Low TY, Karthaus WR, et al. (2012) Wnt signaling through inhibition of beta-catenin degradation in an intact Axin1 complex. Cell 149: 1245-1256.
56. Serafino A, Moroni N, Zonfrillo M, Andreola F, Mercuri L, et al. (2014) WNTpathway components as predictive markers useful for diagnosis, prevention and therapy in inflammatory bowel disease and sporadic colorectal cancer. Oncotarget 5: 978-992.
57. Nasir A, Lopez A, Boulware D, Malafa M, Coppola D (2011) Correlation between COX-2 and APC Expression in Left Versus Right-sided Human Colon Cancer. Anticancer Res 31: 2191-2195.
58. Gallien S, Duriez E, Crone C, Kellmann M, Moehring T, et al. (2012) Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer. Mol Cell Proteomics 11: 1709-1723.
59. Wang T, Ma J, Wu S, Yuan H, Zhang L, et al. (2011) Integrated platform of capillary isoelectric focusing, trypsin immobilized enzyme microreactor and nanoreversed-phase liquid chromatography with mass spectrometry for online protein profiling. Electrophoresis 32: 2848-2856.
60. Jiang H, Yuan H, Liang Y, Xia S, Zhao Q, et al. (2012) A hydrophilic immobilized trypsin reactor with N-vinyl-2-pyrrolidinone modified polymer microparticles as matrix for highly efficient protein digestion with low peptide residue. J Chromatogr A 1246: 111-116.
61. Sun L, Zhu G, Li Y, Yang P, Dovichi NJ (2012) Coupling methanol denaturation, immobilized trypsin digestion, and accurate mass and time tagging for liquid-chromatography-based shotgun proteomics of low nanogram amounts of RAW 264.7 cell lysate. Anal Chem 84: 8715-8721.