Abstract
The diversity of biological samples and dynamic range of analytes being analyzed can prove to be an analytical challenge and is particularly prevalent to proteomic studies. Maximizing the peak capacity of the workflow employed can extend the dynamic range and increase identification rates. The focus of this chapter is to present means of achieving this for various analytical techniques such as liquid chromatography, mass spectrometry, and ion mobility. A combination of these methods can be used as part of a data-independent acquisition strategy, thereby limiting issues such as chimericy when analyzing regions of extreme analyte density.
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References
Giddings JC (1984) Two-dimensional separations: concept and promise. Anal Chem 56:1258A–1260A, 1262A, 1264A
Swartz ME (2007) Separation science & technology, vol 8. Academic, pp 145–147
Van Deemter JJ, Zuiderweg FJ, Klinkenberg A (1956) Longitudinal diffusion and resistance to mass transfer as causes of nonideality in chromatography. Chem Eng Sci 5:271
Plumb R, Castro-Perez J, Granger J, Beattie I, Joncour K, Wright A (2004) Ultra-performance liquid chromatography coupled to quadrupole-orthogonal time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 18:2331–2337
Levy AL, Chung D (1953) Two-dimensional chromatography of amino acids on buffered papers. Anal Chem 25:396–399
Honneger CG (1961) Dünnschicht-Ionophorese und Dünnschicht-Ionophorese-Chromatographie. Helv Chim Acta 44:173
Rabilloud T (2002) Two-dimensional gel electrophopresis in proteomics: old, old fashioned, but it still climbs up the mountains. Proteomics 2:3–10
Neue UD, Mazzeo JR (2001) A theoretical study of the optimization of gradients at elevated temperature. J Sep Sci 24:921–929
Karger BL, Snyder LR, Horvarth C (1973) An introduction to separation science. Wiley, New York
Li X, Stoll DR, Carr PW (2009) Equation for peak capacity estimation in two-dimensional liquid chromatography. Anal Chem 81:845–850
Dowell JA, Frost DC, Zhang J, Li L (2008) Comparison of two-dimensional fractionation techniques for shotgun proteomics. Anal Chem 80:6715–6723
Washburn MP, Wolters D, Yates JR (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19:242–247
Wolters DA, Washburn MP, Yates JR (2001) An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem 73:5683–5690
Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP (2003) Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J Proteome Res 2:43–50
Vollmer M, Horth P, Nagele E (2004) Optimization of two-dimensional off-line LC/MS separations to improve resolution of complex proteomic samples. Anal Chem 76:5180–5185
Opiteck GJ, Jorgenson JW, Anderegg RJ (1997) Two-dimensional SEC/RPLC coupled to mass spectrometry for the analysis of peptides. Anal Chem 69:2283–2291
Alvarez-Manilla G, James I, Guo Y, Warren NL, Orlando R, Pierce M (2006) Tools for glycoproteomic analysis: size exclusion chromatography facilitates identification of tryptic glycopeptides with N-linked glycosylation sites. J Proteome Res 5:701–708
Preud’homme H, Far J, Gil-Casal S, Lobinski R (2012) Large-scale identification of selenium metabolites by online size-exclusion-reversed phase liquid chromatography with combined inductively coupled plasma (ICP-MS) and electrospray ionization linear trap-orbitrap mass spectrometry (ESI-MSn). Metallomics 4:422–432
Barqawi H, Ostas E, Liu B, Carpenter JF, Binder WH (2012) Multidimensional characterization of α, ɷ-telechelic poly(Є-caprolactone)s via online coupling of 2D chromatographic methods (LC/SEC) and ESI-TOF/MALDI-TOF-MS. Macromolecules 45:9779–9790
Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H (2008) A multidimensional chromatography technology for in-depth phosphoproteome analysis. Mol Cell Proteomics 7:1389–1396
Palma SD, Zoumaro-Djayoon A, Peng M, Post H, Preisinger C, Munoz J, Heck AJR (2013) Finding the same needles in the haystack? A comparison of phosphotyrosine peptides enriched by immuno-affinity precipitation and metal-based affinity chromatography. J Proteomics 91:331–337
Frantzi M, Zoidakis J, Papadopulos T, Zürbig P, Katafigiotis J, Stravodimos K, Lazaris A, Giannopoulou I, Ploumidis A, Mischak H, Mullen W, Vlahou A (2013) IMAC fractionation in combination with LC-MS reveals H2B and NIF-1 peptides as potential bladder cancer biomarkers. J Proteome Res 12:3969–3979
Liu S, Hughes C, Lajoie G (2012) Recent advances and special considerations for the analysis of phosphorylated peptides by LC-ESI-MS/MS. Curr Anal Chem 8:35–42
Stasyk T, Huber LA (2012) Mapping in vivo signal transduction defects by phosphoproteomics. Trends Mol Med 18:43–51
Boersema PJ, Divecha N, Heck AJR, Mohammed S (2007) Evaluation and optimization of ZIC-HILIC-RP as an alternative MudPIT strategy. J Proteome Res 6:937–946
Xie F, Smith RD, Shen Y (2012) Advanced proteomic liquid chromatography. J Chromatogr A 1261:78–90
Wang C, Yuan J, Wang Z, Huang L (2013) Separation of one-pot procedure released O-glycans as 1-phenyl-3-methyl-5-pyrazolone derivatives by hydrophilic interaction and reversed-phase liquid chromatography followed by identification using electrospray mass spectrometry and tandem mass spectrometry. J Chromatogr A 1274:107–117
Lau E, Lam MPY, Siu SO, Kong RPW, Chan WL, Zhou Z, Huang J, Lo C, Chu IK (2011) Combinatorial use of offline SCX and online RP-RP liquid chromatography for iTRAQ-based quantitative proteomics applications. Mol Biosyst 7:1399–1408
Gilar M, Olivova P, Daly AE, Gebler JC (2005) Orthogonality of separation in two-dimensional liquid chromatography. Anal Chem 77:6426–6434
Gilar M, Olivova P, Daly AE, Gebler JC (2005) Two-dimensional separation of peptides using RP-RP-HPLC system with different pH in first and second separation dimensions. J Sep Sci 28:1694–1703
Francois I, Cabooter D, Sandra K, Lynen F, Desmet G, Sandra P (2009) Tryptic digest analysis by comprehensive reversed phasextwo reversed phase liquid chromatography (RP-LCx2RP-LC) at different pH’s. J Sep Sci 32:1137–1144
Francois I, de Villiers A, Tienpont B, David F, Sandra P (2008) Comprehensive two-dimensional liquid chromatography applying two parallel columns in the second dimension. J Chromatogr A 1178:33–42
Siu SO, Lam MPY, Lau E, Kong RPW, Lee SMY, Chu IK (2011) Fully automated two-dimensional reversed-phase capillary liquid chromatography with online tandem mass spectrometry for shotgun proteomics. Proteomics 11:2308–2319
Zhou F, Cardoza JD, Ficarro SB, Adelment GO, Lazaro JB, Marto JA (2010) Online nanoflow RP-RP-MS reveals dynamics of multicomponent Ku complex in response to DNA damage. J Proteome Res 9:6242–6255
Scigelova M, Hornshaw M, Giannokulas A, Makarov A (2011) Fourier transform mass spectrometry. MCP 1–19. doi:10.1074/mcp.M111.009431
Morris HR, Paxton T, Dell A, Langhorn B, Berg M, Bordoli RS, Hoyes J, Bateman RH (1996) High sensitivity collisionally-activated decomposition tandem mass spectrometry on a novel quadrupole/orthogonal-acceleration time-of-flight mass spectrometer. Rapid Commun Mass Spectrom 10:889–896
Pringle SD, Giles K, Wildgoose JL, Williams JP, Slade SE, Thalassinos K, Bateman RH, Bowers MT, Scrivens JH (2007) An investigation of the mobility separation of some peptide and protein ions using a new hybrid quadrupole/travelling wave IMS/oa-ToF instrument. Int J Mass Spectrom 261:1–12
Mason EA, McDaniel EW (1973) The mobility and diffusion of ions in gases. Wiley, New York
Ruotolo BT, Giles K, Campuzano I, Sandercock AM, Bateman RH, Robinson CV (2005) Evidence for macromolecular protein rings in the absence of bulk water. Science 310:1658
Harvey SR, Macphee CE, Barran PE (2011) Ion mobility mass spectrometry for peptide analysis. Methods 54:454–461
Giles K, Pringle SD, Worhtington KR, Little D, Wildgoose JL, Bateman RH (2004) Applications of a travelling wave-based radio-frequency-only stacked ring ion guide. Rapid Commun Mass Spectrom 18:2401–2414
Dugourd P, Hudgins RR, Clemmer DE, Jarrold MF (1997) High-resolution ion mobility measurements. Rev Sci Instrum 68:1122–1129
Shvartsburg AA, Smith RD (2008) Fundamentals of travelling wave ion mobility spectrometry. Anal Chem 80:9689–9699
Houel S, Abernathy R, Renganathan K, Meyer-Arendt K, Ahn NG, Old WM (2010) Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies. J Proteome Res 9:4152–4160
Michalski A, Cox J, Mann M (2011) More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J Proteome Res 10:1785–1793
Rodriguez-Suarez E, Hughes C, Gethings L, Giles K, Wildgoose J, Stapels M, Fadgen KE, Geromanos SJ, Vissers JPC, Elortza F, Langridge JI (2012) An ion mobility assisted data independent LC-MS strategy for the analysis of complex biological samples. Curr Anal Chem 9:199–211
Geromanos SJ, Hughes C, Golick D, Ciavarini S, Gorenstein MV, Richardson K, Hoyes JB, Vissers JP, Langridge JI (2011) Simulating and validating proteomics data and search results. Proteomics 11:1189–1211
Thalassinos K, Vissers JP, Tenzer S, Levin Y, Thompson JW, Daniel D, Mann D, Delong MR, Moseley MA, America AH, Ottens AK, Cavey GS, Efstathiou G, Scrivens JH, Langridge JI, Germoanos SJ (2012) Design and application of a data-independent precursor and product ion repository. J Am Soc Mass Spectrom 23:1808–1820
Geromanos SJ, Vissers JPC, Silva JC, Dorschel CA, Li GZ, Gorenstein MV, Bateman RH, Langridge JI (2009) The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependent LC-MS/MS. Proteomics 9:1683–1695
Silva JC, Denny R, Dorschel CA, Gorenstein M, Kass IJ, Li GZ, McKenna T, Nold MJ, Richardson K, Young P, Geromanos S (2005) Quantitative proteomic analysis by accurate mass retention time pairs. Anal Chem 77:2187–2200
Li GZ, Vissers JPC, Silva JC, Golick D, Gorenstein MV, Geromanos SJ (2009) Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures. Proteomics 9:1696–1719
Kohl M, Megger DA, Trippler M, Meckel H, Ahrens M, Bracht T, Weber F, Hoffmann AC, Baba HA, Sitek B, Schlaak JF, Meyer HE, Stephan C, Eisenacher M (2014) A practical data processing workflow for multi-OMICS projects. Biochem Biophys Acta 1844:52–62
Chesney RW (1999) The idiopathic nephrotic syndrome. Curr Opin Pediatr 11:158–161
Vaezzadeh AR, Briscoe AC, Steen H, Lee RS (2010) One-step sample concentration, purification, and albumin depletion method for urinary proteomics. J Proteome Res 9:6082–6089
Want EJ, Wilson ID, Gika H, Theodoridis G, Plumb RS, Shockcor J, Holmes E, Nicholson JK (2010) Global metabolic profiling procedures for urine using UPLC-MS. Nat Protoc 5:1005–1018
Acknowledgements
The authors would like to thank our collaborators who have provided figures and granted permission to use their collateral. In particular we would like to acknowledge Dr. Stefan Tenzer, Dr. Eva Rodriguez-Suárez, Dr. Sandra Kraljević Pavelić, Dr. Martin Gilar, Dr. John Shockcor, Kenneth Fountain, and Eric Grumbach. Finally Dr. Johannes P.C. Vissers is thanked for constructive comments during review.
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Gethings, L.A., Connolly, J.B. (2014). Simplifying the Proteome: Analytical Strategies for Improving Peak Capacity. In: Woods, A., Darie, C. (eds) Advancements of Mass Spectrometry in Biomedical Research. Advances in Experimental Medicine and Biology, vol 806. Springer, Cham. https://doi.org/10.1007/978-3-319-06068-2_3
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