Separation methodology to improve proteome coverage depth

References

• Ansong C, Purvine SO, Adkins JN, et al. Proteogenomics: needs and roles to be filled by proteomics in genome annotation. Brief Funct Genomic Proteomic 2008;7:50-62
   PubMedGoogle Scholar
• Paik YK, Jeong SK, Omenn GS, et al. The chromosome-centric human proteome project for cataloging proteins encoded in the genome. Nat Biotechnol 2012;30(3):221-3
   PubMed Web of Science ®Google Scholar
• Schwanhäusser B, Busse D, Li N, et al. Global quantification of mammalian gene expression control. Nature 2011;473(7347):337-42
   PubMed Web of Science ®Google Scholar
• Anderson NL. Counting the proteins in plasma. Clin Chem 2010;56(11):1775-6
   PubMed Web of Science ®Google Scholar
• Hortin GL, Sviridov D. The dynamic range problem in the analysis of the plasma proteome. J Proteomics 2010;73(3):629-36
   PubMed Web of Science ®Google Scholar
• Whiteaker JR, Zhang H, Eng JK, et al. Head-to-head comparison of serum fractionation techniques. J Proteome Res 2007;6:828-36
   PubMed Web of Science ®Google Scholar
• Anderson NL, Anderson NG, Pearson TW, et al. A Human proteome detection and quantitation project. Mol Cell Proteomics 2009;8(5):883-6
   PubMed Web of Science ®Google Scholar
• Mann M, Kulak NA, Nagaraj N, Cox J. The coming of age of complete, accurate, and ubiquitous proteomes. Mol Cell 2013;49(4):583-90
   PubMed Web of Science ®Google Scholar
• Beck M, Schmidt A, Malmstroem J, et al. The quantitative proteome of a human cell line. Mol Syst Biol 2011;7:549
   PubMed Web of Science ®Google Scholar
• Nagaraj N, Wisniewski JR, Geiger T, et al. Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol 2011;7:548
   PubMed Web of Science ®Google Scholar
• Hebert AS, Richards AL, Bailey DJ, et al. The one hour yeast proteome. Mol Cell Proteomics 2013;13(1):339-47
   Google Scholar
• Kelstrup CD, Young C, Lavallee R, et al. Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole orbitrap mass spectrometer. J Proteome Res 2012;11:3487-97
   PubMed Web of Science ®Google Scholar
• Andrews GL, Simons BL, Young JB, et al. Performance characteristics of a new hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600). Anal Chem 2011;83(13):5442-6
   PubMed Web of Science ®Google Scholar
• Senko MW, Remes PM, Canterbury JD, et al. Novel parallelized quadrupole/linear ion trap/orbitrap tribrid mass spectrometer improving proteome coverage and peptide identification rates. Anal Chem 2013;85(24):11710-14
   PubMed Web of Science ®Google Scholar
• Michalski A, Cox J, Mann M. 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 2011;10:1785-93
   PubMed Web of Science ®Google Scholar
• Sandra K, Moshir M, D’hondt F, et al. Highly efficient peptide separations in proteomics. Part 1. Unidimensional high performance liquid chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2008;866:48-63
   PubMed Web of Science ®Google Scholar
• Liu H, Finch JW, Lavallee MJ, et al. Effects of column length, particle size, gradient length and flow rate on peak capacity of nano-scale liquid chromatography for peptide separations. J Chromatogr A 2007;1147:30-6
   PubMed Web of Science ®Google Scholar
• Köcher T, Pichler P, Swart R, Mechtler K. Analysis of protein mixtures from whole-cell extracts by single-run nanoLC-MS/MS using ultralong gradients. Nat Protoc 2012;7(5):882-90
   PubMed Web of Science ®Google Scholar
• Hsieh EJ, Bereman MS, Durand S, et al. Effects of column and gradient lengths on peak capacity and peptide identification in nanoflow LC-MS/MS of complex proteomic samples. J Am Soc Mass Spectrom 2013;24:148-53
   PubMed Web of Science ®Google Scholar
• Blackler AR, Speers AE, Wu CC. Chromatographic benefits of elevated temperature for the proteomic analysis of membrane proteins. Proteomics 2008;8(19):3956-64
   PubMed Web of Science ®Google Scholar
• Schmidt A, Karas M, Dülcks T. Effect of different solution flow rates on analyte ion signals in Nano-ESI MS, or: when does ESI turn into Nano-ESI? J Am Soc Mass Spectrom 2003;14:492-500
   PubMed Web of Science ®Google Scholar
• Zhou F, Lu Y, Ficarro SB, et al. Nanoflow low pressure high peak capacity single dimension lc-ms/ms platform for high-throughput, in-depth analysis of mammalian proteomes. Anal Chem 2012;84:5133-9
   PubMed Web of Science ®Google Scholar
• Zhou F, Lu Y, Ficarro SB, et al. Genome-scale proteome quantification by DEEP SEQ mass spectrometry. Nat Commun 2013;4:2171
   PubMed Web of Science ®Google Scholar
• Thakur S, Geiger T, Chatterjee B, et al. Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation. Mol Cell Proteomics 2011;10(8):M110.003699
   PubMed Web of Science ®Google Scholar
• Pirmoradian M, Budamginta H, Chingin K, et al. Rapid and deep human proteome analysis by single-dimension shotgun proteomics. Mol Cell Proteomics 2013;12(11):3330-8
   PubMed Web of Science ®Google Scholar
• Nagaraj N, Kulak NA, Cox J, et al. System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top orbitrap. Mol Cell Proteomics 2012;11(3):M111.013722
   PubMed Web of Science ®Google Scholar
• Zubarev RA. The challenge of the proteome dynamic range and its implications for in-depth proteomics. Proteomics 2013;13(5):723-6
   PubMed Web of Science ®Google Scholar
• Olsen JV, Mann M. Status of large-scale analysis of post-translational modifications by mass spectrometry. Mol Cell Proteomics 2013;12(12):3444-52
   PubMed Web of Science ®Google Scholar
• Ros A, Faupek M, Mees H, et al. Protein purification by Off-Gel electrophoresis. Proteomics 2002;2:151-6
   PubMed Web of Science ®Google Scholar
• Michel PE, Reymond F, Arnaud IL, et al. Protein fractionation in a multicompartment device using Off-Gel isoelectric focusing. Electrophoresis 2003;24:3-11
   PubMed Web of Science ®Google Scholar
• Wilm M, Shevchenko A, Houthaeve T. Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 1996;379(6564):466-9
   PubMed Web of Science ®Google Scholar
• Lundby A, Olsen JV. GeLCMS for in-depth protein characterization and advanced analysis of proteomes. Methods Mol Biol 2011;753:143-55
   PubMedGoogle Scholar
• Piersma SR, Warmoes MO, de Wit M, et al. Whole gel processing procedure for GeLC-MS/MS based proteomics. Proteome Sci 2013;11:17-24
   PubMed Web of Science ®Google Scholar
• Wu Z, Gholami AM, Küster B. Systematic identification of the HSP90 regulated proteome. Mol Cell Proteomics 2012;11(6):M111.016675
   PubMed Web of Science ®Google Scholar
• Sandra K, Moshir M, D’hondt F, et al. Highly efficient peptide separations in proteomics. Part 2. Bi- and multidimensional liquid-based separation techniques. J Chromatogr B Analyt Technol Biomed Life Sci 2009;877:1019-39
   PubMed Web of Science ®Google Scholar
• Washburn MP, Wolters D, Yates JR 3rd. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001;19(3):242-7
   PubMed Web of Science ®Google Scholar
• Ritorto MS, Cook K, Tyagi K, et al. Hydrophilic strong anion exchange (hSAX) chromatography for highly orthogonal peptide separation of complex proteomes. J Proteome Res 2013;12(6):2449-57
   PubMed Web of Science ®Google Scholar
• Deeb SJ, D’Souza RCJ, Cox J, et al. Super-SILAC allows classification of diffuse large b-cell lymphoma subtypes by their expression profiles. Mol Cell Proteomics 2012;11:77-89
   PubMed Web of Science ®Google Scholar
• Toll H, Oberacher H, Swart R, Huber J. Separation, detection, and identification of peptides by ion-pair reversed-phase high-performance liquid chromatography-electrospray ionization mass spectrometry at high and low pH. J Chromatogr A 2005;1079(1-2):274-86
   PubMed Web of Science ®Google Scholar
• Dwivedi RC, Spicer V, Harder M, et al. Practical implementation of 2D HPLC scheme with accurate peptide retention prediction in both dimensions for high-throughput bottom-up proteomics. Anal Chem 2008;80(18):7036-42
   PubMed Web of Science ®Google Scholar
• Hörth P, Miller CA, Preckel T, Wenz C. Efficient fractionation and improved protein identification by peptide OFFGEL electrophoresis. Mol Cell Proteomics 2006;5(10):1968-74
   PubMed Web of Science ®Google Scholar
• Hubner NC, Ren S, Mann M. Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis. Proteomics 2008;8:4862-72
   PubMed Web of Science ®Google Scholar
• Cargile BJ, Sevinsky JR, Essader AS, Stephenson JL Jr, Bundy JL. Immobilized pH gradient isolelectric focusing as a first-dimension separation in shotgun proteomics. J Biomol Tech 2005;16(3):181-9
   PubMedGoogle Scholar
• Branca RM, Orre LM, Johansson HJ, et al. HiRIEF LC/MS enables deep proteome coverage and unbiased proteogenomics. Nat Methods 2014;11(1):59-62
   PubMed Web of Science ®Google Scholar
• PeptideAtlas. Available from: www.peptideatlas.org
   Google Scholar
• Atanassov I, Urlaub H. Increased proteome coverage by combining PAGE and peptide isoelectric focusing: comparative study of gel-based separation approaches. Proteomics 2013;13(20):2947-55
   PubMed Web of Science ®Google Scholar
• Wiśniewski JR, Zougman A, Nagaraj N, Mann M. Universal sample preparation method for proteome analysis. Nat Methods 2009;6(5):359-63
   PubMed Web of Science ®Google Scholar
• Wiśniewski JR, Ostasiewicz P, Mann M. High recovery FASP applied to the proteomic analysis of microdissected formalin fixed paraffin embedded cancer tissues retrieves known colon cancer markers. J Proteome Res 2011;10:3040-9
   PubMed Web of Science ®Google Scholar
• Wiśniewski JR, Duś K, Mann M. Proteomic workflow for the analysis of archival formalin-fixed and paraffin-embedded clinical samples to a depth of 10000 proteins. Proteomics Clin Appl 2013;7(3-4):225-33
   PubMed Web of Science ®Google Scholar
• Gillet LC, Navarro P, Tate S, et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics 2012;11(6):O111.016717
   PubMed Web of Science ®Google Scholar
• Chapman JD, Goodlett DR, Masselon CD. Multiplexed and data-independent tandem mass spectrometry for global proteome profiling. Mass Spectrom Rev 2013. [Epub ahead of print]
   PubMed Web of Science ®Google Scholar