Protein Analysis by Shotgun/Bottom-up Proteomics

Cites (825)

Items 401–600 of 825

1. Serum biomarkers of hepatitis B virus infected liver inflammation: A proteomic study
   Qing‐Yu He, George K.K. Lau, Yuan Zhou, Siu–Tsan Yuen, Marie C.M. Lin, Hsiang‐Fu Kung, Jen‐Fu Chiu · 2003 · PROTEOMICS
2. A Proteomics Search Algorithm Specifically Designed for High-Resolution Tandem Mass Spectra
   Craig D. Wenger, Joshua J. Coon · 2013 · Journal of Proteome Research
3. Peptide separation with immobilized pI strips is an attractive alternative to in‐gel protein digestion for proteome analysis
   Nina C. Hubner, Shubin Ren, Matthias Mann · 2008 · PROTEOMICS
4. Proteolytic 18O Labeling for Comparative Proteomics: Evaluation of Endoprotease Glu-C as the Catalytic Agent
   Kristy J. Reynolds, Xudong Yao, Catherine Fenselau · 2002 · Journal of Proteome Research
5. A comparison of immobilized pH gradient isoelectric focusing and strong‐cation‐exchange chromatography as a first dimension in shotgun proteomics
   Amal S. Essader, Benjamin J. Cargile, Jonathan L. Bundy, James L. Stephenson · 2005 · PROTEOMICS
6. Quadrupole time‐of‐flight versus triple‐quadrupole mass spectrometry for the determination of phosphopeptides by precursor ion scanning
   Hanno Steen, Bernhard Küster, Matthias Mann · 2001 · Journal of Mass Spectrometry
7. Regulation of Calcium/Calmodulin-dependent Kinase IV by O-GlcNAc Modification
   Wagner B. Dias, Win D. Cheung, Zihao Wang, Gerald Warren Hart · 2009 · Journal of Biological Chemistry
8. Evaluation of Gas-Phase Rearrangement and Competing Fragmentation Reactions on Protein Phosphorylation Site Assignment Using Collision Induced Dissociation-MS/MS and MS3
   Amanda M. Palumbo, Gavin E. Reid · 2008 · Analytical Chemistry
9. Comprehensive native glycan profiling with isomer separation and quantitation for the discovery of cancer biomarkers
   Serenus S. Hua, Hyun Joo An, Süreyya Özcan, Grace S. Ro, Stephanie Soares, Ralph Devere White, Carlito B. Lebrilla · 2011 · The Analyst
10. Target-Decoy Approach and False Discovery Rate: When Things May Go Wrong
    Nitin Gupta, Nuno Bandeira, Uri Keich, Pavel A. Pevzner · 2011 · Journal of the American Society for Mass Spectrometry
11. Influence of Basic Residue Content on Fragment Ion Peak Intensities in Low-Energy Collision-Induced Dissociation Spectra of Peptides
    David L. Tabb, Yingying Huang, Vicki Hopper Wysocki, John R. Yates · 2004 · Analytical Chemistry
12. Hyperplexing: a method for higher-order multiplexed quantitative proteomics provides a map of the dynamic response to rapamycin in yeast
    Dephoure, Noah, Gygi, Steven P. · 2012 · Science Signaling
13. Microwave-assisted Protein Preparation and Enzymatic Digestion in Proteomics
    Wei Sun, Shijuan Gao, Linjie Wang, Yong Chen, Shuzhen Wu, Xiaorong Wang, Dexian Zheng, Youhe Gao · 2005 · Molecular & Cellular Proteomics
14. Optimization and Evaluation of a Sheathless Capillary Electrophoresis–Electrospray Ionization Mass Spectrometry Platform for Peptide Analysis: Comparison to Liquid Chromatography–Electrospray Ionization Mass Spectrometry
    Klaus Faserl, Bettina Sarg, Leopold Kremser, Herbert H. Lindner · 2011 · Analytical Chemistry
15. High Precision Quantitative Proteomics Using iTRAQ on an LTQ Orbitrap: A New Mass Spectrometric Method Combining the Benefits of All
    Thomas Köcher, Peter Pichler, Michael Schutzbier, Christoph Stingl, Axel Kaul, Nils Teucher, Gerd P Hasenfuss, Josef Martin Penninger, Karl Mechtler · 2009 · Journal of Proteome Research
16. Identification of S100A8 and S100A9 as Serological Markers for Colorectal Cancer
    Hye Jung Kim, Hyun Ju Kang, Seung‐Taek Lee, Seung-Taek Lee, Myeong‐Hee Yu, Hoguen Kim, Cheolju Lee · 2009 · Journal of Proteome Research
17. 15N Metabolic Labeling of Mammalian Tissue with Slow Protein Turnover
    Daniel B. McClatchy, Meng‐Qiu Dong, Christine C. Wu, John D. Venable, John R. Yates · 2007 · Journal of Proteome Research
18. Proteome analysis of yeast response to various nutrient limitations
    Annemieke Kolkman, Pascale A. S. Daran-Lapujade, Asier Fullaondo, Maurien M. A. Olsthoorn, Jack T. Pronk, Monique Slijper, Albert J. R. Heck · 2006 · Molecular Systems Biology
19. iTRAQ Reagent-Based Quantitative Proteomic Analysis on a Linear Ion Trap Mass Spectrometer
    Timothy J. Griffin, Hongwei Xie, Sricharan Bandhakavi, Jonathan Popko, Archana Mohan, John V. Carlis, LeeAnn Higgins · 2007 · Journal of Proteome Research
20. The phosphoproteome of toll‐like receptor‐activated macrophages
    Gabriele Weintz, Jesper V. Olsen, Katja Frühauf, Magdalena Niedzielska, Ido Amit, Jonathan Jantsch, Jörg Mages, Cornelie Frech, Lars Dölken, Matthias Mann et al. · 2010 · Molecular Systems Biology
21. Site-Specific GlcNAcylation of Human Erythrocyte Proteins
    Zihao Wang, Kyoungsook Park, Frank I. Comer, Linda C. Hsieh‐Wilson, Christopher D. Saudek, Gerald Warren Hart · 2008 · Diabetes
22. Proteomic patterns predict acute graft-versus-host disease after allogeneic hematopoietic stem cell transplantation
    Eva M. Weissinger, Eric Schiffer, Bernd Hertenstein, James L.M. Ferrara, Ernst Holler, Michael Stadler, Hans‐Jochem Kolb, Axel Rolf Zander, Petra Zürbig, Markus Kellmann et al. · 2007 · Blood
23. Semisupervised Model-Based Validation of Peptide Identifications in Mass Spectrometry-Based Proteomics
    Hyungwon Choi, Alexey I. Nesvizhskii · 2007 · Journal of Proteome Research
24. Pheromone-Dependent Destruction of the Tec1 Transcription Factor Is Required for MAP Kinase Signaling Specificity in Yeast
    Marie Z. Bao, Monica A. Schwartz, Greg T. Cantin, John R. Yates, Hiten D. Madhani · 2004 · Cell
25. 18O-Labeling of N-Glycosylation Sites To Improve the Identification of Gel-Separated Glycoproteins Using Peptide Mass Mapping and Database Searching
    Bernhard Küster, Matthias Mann · 1999 · Analytical Chemistry
26. A Proteomics Grade Electron Transfer Dissociation-Enabled Hybrid Linear Ion Trap-Orbitrap Mass Spectrometer
    Graeme C. McAlister, W. Travis Berggren, Jens Griep‐Raming, Stevan R. Horning, Alexander Makarov, Doug Phanstiel, George C. Stafford, Danielle L. Swaney, John E. P. Syka, Vlad Zabrouskov et al. · 2008 · Journal of Proteome Research
27. Fatty Acid Binding Protein as a Serum Marker for the Early Diagnosis of Stroke
    Catherine G. Zimmermann‐Ivol, Pierre R. Burkhard, Josette Le Floch-Rohr, Laure Allard, Denis F. Hochstrasser, Jean‐Charles Sanchez · 2003 · Molecular & Cellular Proteomics
28. The dynamic state of protein turnover: It's about time
    Izumi V. Hinkson, Joshua Eric Elias · 2011 · Trends in Cell Biology
29. Improving the Comprehensiveness and Sensitivity of Sheathless Capillary Electrophoresis–Tandem Mass Spectrometry for Proteomic Analysis
    Wang, Yueju, Fonslow, Bryan R., Wong, Catherine C. L., Nakorchevsky, Aleksey, Yates, John R. · 2012 · Analytical Chemistry
30. Method Development of Efficient Protein Extraction in Bone Tissue for Proteome Analysis
    Jiang, Xiaogang, Ye, Mingliang, Jiang, Xinning, Liu, Guangpeng, Feng, Shun, Cui, Lei, Zou, Hanfa · 2007 · Journal of Proteome Research
31. Solvent Assisted Inlet Ionization: An Ultrasensitive New Liquid Introduction Ionization Method for Mass Spectrometry
    Vincent S. Pagnotti, Nicholas D. Chubatyi, Charles N. McEwen · 2011 · Analytical Chemistry
32. Zwitterionic Hydrophilic Interaction Liquid Chromatography (ZIC-HILIC and ZIC-cHILIC) Provide High Resolution Separation and Increase Sensitivity in Proteome Analysis
    Serena Di Palma, Paul J. Boersema, Albert J. R. Heck, Shabaz Mohammed · 2011 · Analytical Chemistry
33. PEPPeR, a Platform for Experimental Proteomic Pattern Recognition
    Jacob D. Jaffe, D.R. Mani, Kyriacos C. Leptos, George McDonald Church, Michael A. Gillette, Steven A. Carr · 2006 · Molecular & Cellular Proteomics
34. The Disulfide Proteome and Other Reactive Cysteine Proteomes: Analysis and Functional Significance
    Maria Lindahl, Alejandro Mata-Cabana, T. Kieselbach · 2011 · Antioxidants and Redox Signaling
35. Serum Proteomics and Biomarker Discovery Across the Spectrum of Nonalcoholic Fatty Liver Disease
    Lauren Nicole Bell, Janice L. Theodorakis, Raj Vuppalanchi, Romil Saxena, Kerry G. Bemis, Mu Wang, Naga Chalasani · 2009 · Hepatology
36. SISCAPA Peptide Enrichment on Magnetic Beads Using an In-line Bead Trap Device
    N. Leigh Anderson, Angela Jackson, DEREK S. H. SMITH, Darryl B. Hardie, Christoph H. Borchers, Terry W. Pearson · 2009 · Molecular & Cellular Proteomics
37. Multiple Reaction Monitoring Cubed for Protein Quantification at the Low Nanogram/Milliliter Level in Nondepleted Human Serum
    Tanguy Fortin, Arnaud Salvador, Jean‐Philippe Charrier, Christof Lenz, Florence Bettsworth, Xavier Lacoux, Geneviève Choquet‐Kastylevsky, Jérôme Lemoine · 2009 · Analytical Chemistry
38. Laserspray Ionization, a New Atmospheric Pressure MALDI Method for Producing Highly Charged Gas-phase Ions of Peptides and Proteins Directly from Solid Solutions
    Sarah Trimpin, Ellen D. Inutan, Thushani N. Herath, Charles N. McEwen · 2009 · Molecular & Cellular Proteomics
39. Ultra-High-Pressure RPLC Hyphenated to an LTQ-Orbitrap Velos Reveals a Linear Relation between Peak Capacity and Number of Identified Peptides
    Thomas Köcher, Remco Swart, Karl Mechtler · 2011 · Analytical Chemistry
40. Predicting Electrospray Response from Chromatographic Retention Time
    Nadja B. Cech, Jennifer R. Krone, Christie G. Enke · 2000 · Analytical Chemistry
41. Software Lock Mass by Two-Dimensional Minimization of Peptide Mass Errors
    Jürgen Cox, Annette Michalski, Matthias Mann · 2011 · Journal of the American Society for Mass Spectrometry
42. The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells
    J. Muñoz, T. Low, Y. Kok, A. Chin, C. Frese, Vanessa Ding, A. Choo, A. Heck · 2011 · Molecular Systems Biology
43. Automated Ultra-High-Pressure Multidimensional Protein Identification Technology (UHP-MudPIT) for Improved Peptide Identification of Proteomic Samples
    Akira Motoyama, John D. Venable, Cristian I. Ruse, John R. Yates · 2006 · Analytical Chemistry
44. Measurement of human plasma proteome dynamics with 2H2O and liquid chromatography tandem mass spectrometry
    John C. Price, William E. Holmes, Kelvin W. Li, Nicholas A. Floreani, Richard A. Neese, Scott Turner, Marc K. Hellerstein · 2011 · Analytical Biochemistry
45. Straightforward ladder sequencing of peptides using a Lys-N metalloendopeptidase
    Nadia Taouatas, Mădălina M. Drugan, Albert J. R. Heck, Shabaz Mohammed · 2008 · Nature Methods
46. The post-genomic era of interactive proteomics: Facts and perspectives
    Daniel Auerbach, Safia Thaminy, Michael O. Hottiger, Igor Štagljar · 2002 · PROTEOMICS
47. On-Line LC−MS Approach Combining Collision-Induced Dissociation (CID), Electron-Transfer Dissociation (ETD), and CID of an Isolated Charge-Reduced Species for the Trace-Level Characterization of Proteins with Post-Translational Modifications
    Shiaw‐Lin Wu, Andreas F. R. Hühmer, Zhiqi Hao, Barry L. Karger · 2007 · Journal of Proteome Research
48. Identification of Novel Phosphorylation Sites on Xenopus laevis Aurora A and Analysis of Phosphopeptide Enrichment by Immobilized Metal-affinity Chromatography
    Claire E. Haydon, Patrick A. Eyers, Lauren D. Aveline-Wolf, Katheryn A. Resing, James L. Maller, Natalie G. Ahn · 2003 · Molecular & Cellular Proteomics
49. Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry
    Ari M. Frank, Stephen W. Tanner, Vineet Bafna, Pavel A. Pevzner · 2005 · Journal of Proteome Research
50. Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome
    Brosch, Markus, Saunders, Gary I., Frankish, Adam, Collins, Mark O., Yu, Lu, Wright, James, Verstraten, Ruth, Adams, David J., Harrow, Jennifer, Choudhary, Jyoti S. et al. · 2011 · Genome Research
51. A proteomic approach for the discovery of protease substrates
    Andrew J. Bredemeyer, Renate M. Lewis, James P. Malone, Alan Davis, Julia Gross, R. Reid Townsend, Timothy James Ley · 2004 · Proceedings of the National Academy of Sciences
52. Intact-protein-based High-resolution Three-dimensional Quantitative Analysis System for Proteome Profiling of Biological Fluids
    Hong Wang, Shawn G. Clouthier, Vladimir Galchev, David E. Misek, Ulrich A. Duffner, Chang-Ki Min, Rong Zhao, John Tra, Gilbert S. Omenn, James L.M. Ferrara et al. · 2005 · Molecular & Cellular Proteomics
53. DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring
    David L. Tabb, Zeqiang Ma, Daniel B. Martin, Amy‐Joan L. Ham, Matthew Chambers · 2008 · Journal of Proteome Research
54. One-Dimensional Capillary Liquid Chromatographic Separation Coupled with Tandem Mass Spectrometry Unveils the Escherichia coli Proteome on a Microarray Scale
    Mio Iwasaki, Shohei Miwa, Tohru Ikegami, Masaru Tomita, Nobuo Tanaka, Yasushi Ishihama · 2010 · Analytical Chemistry
55. An LC-IMS-MS Platform Providing Increased Dynamic Range for High-Throughput Proteomic Studies
    Erin Shammel Baker, Eric A. Livesay, Danny Orton, Ronald Jay Moore, William Danielson, David C. Prior, Yehia Ibrahim, Brian L. Lamarche, Anoop M. Mayampurath, Athena Schepmoes et al. · 2009 · Journal of Proteome Research
56. The use of a zwitterionic detergent in two-dimensional gel electrophoresis of trout liver microsomes
    Gary H. Perdew, Henry W. Schaup, Daniel P. Selivonchick · 1983 · Analytical Biochemistry
57. Normalization and Statistical Analysis of Quantitative Proteomics Data Generated by Metabolic Labeling
    Lily Ting, Mark J. Cowley, Seah Lay Hoon, Michael Guilhaus, Mark J. Raftery, Ricardo Cavicchioli · 2009 · Molecular & Cellular Proteomics
58. Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry as an Alternative Proteomics Platform to Ultraperformance Liquid Chromatography-Electrospray Ionization-Tandem Mass Spectrometry for Samples of Intermediate Complexity
    Li, Yihan, Champion, Matthew M., Sun, Liangliang, Champion, Patricia A. DiGiuseppe, Wojcik, Roza, Dovichi, Norman J. · 2012 · Analytical Chemistry
59. A protease for 'middle-down' proteomics
    Cong Wu, John C. Tran, Leonid Zamdborg, Kenneth R. Durbin, Mingxi Li, Dorothy R. Ahlf, Bryan P. Early, Paul M. Thomas, Jonathan V. Sweedler, Neil L. Kelleher · 2012 · Nature Methods
60. Simultaneous and Extensive Site-specific N- and O-Glycosylation Analysis in Protein Mixtures
    Charles C. Nwosu, Richard R. Seipert, John S. Strum, Serenus S. Hua, Hyun Joo An, Angela M. Zivkovic, Bruce J. German, Carlito B. Lebrilla · 2011 · Journal of Proteome Research
61. IDEAL-Q, an Automated Tool for Label-free Quantitation Analysis Using an Efficient Peptide Alignment Approach and Spectral Data Validation
    Chih‐Chiang Tsou, Chia‐Feng Tsai, Ying-Hao Tsui, Putty‐Reddy Sudhir, Yi-Ting Wang, Yu‐Ju Chen, Jeou-Yuan Chen, Ting‐Yi Sung, Wen−Lian Hsu · 2009 · Molecular & Cellular Proteomics
62. Protein Phosphorylation and Expression Profiling by Yin-Yang Multidimensional Liquid Chromatography (Yin-Yang MDLC) Mass Spectrometry
    Jie Dai, Wenhai Jin, Quanhu Sheng, Chia‐Hui Shieh, Jiarui Wu, Rong Zeng · 2006 · Journal of Proteome Research
63. Comparative proteomics based on stable isotope labeling and affinity selection
    Fred E. Regnier, Larry Riggs, Roujian Zhang, Li Xiong, Peiran Liu, Asish B. Chakraborty, Erin H. Seeley, Cathy S. Sioma, Robert A. Thompson · 2002 · Journal of Mass Spectrometry
64. Extended Range Proteomic Analysis (ERPA): A New and Sensitive LC−MS Platform for High Sequence Coverage of Complex Proteins with Extensive Post-translational ModificationsComprehensive Analysis of Beta-Casein and Epidermal Growth Factor Receptor (EGFR)
    Shiaw‐Lin Wu, Jeongkwon Kim, William S. Hancock, Barry L. Karger · 2005 · Journal of Proteome Research
65. Abacus: A computational tool for extracting and pre‐processing spectral count data for label‐free quantitative proteomic analysis
    Damian Fermin, Venkatesha Basrur, Anastasia K. Yocum, Alexey I. Nesvizhskii · 2011 · PROTEOMICS
66. Absolute Quantification of Multisite Phosphorylation by Selective Reaction Monitoring Mass Spectrometry
    Viveka Mayya, Karim Rezual, Linfeng Wu, Michael B. Fong, David K. M. Han · 2006 · Molecular & Cellular Proteomics
67. Functional Roles of Ubiquitin-Like Domain (ULD) and Ubiquitin-Binding Domain (UBD) Containing Proteins
    Caroline Grabbe, Ivan Đikić · 2009 · Chemical Reviews
68. Statistical Validation of Peptide Identifications in Large-Scale Proteomics Using the Target-Decoy Database Search Strategy and Flexible Mixture Modeling
    Hyungwon Choi, Debashis Ghosh, Alexey I. Nesvizhskii · 2007 · Journal of Proteome Research
69. Quantitative Shotgun Proteomics of Enriched Heterocysts from Nostoc sp. PCC 7120 Using 8-Plex Isobaric Peptide Tags
    Saw Yen Ow, Tanai Cardona, Arnaud Taton, Ann Magnuson, Peter C. Lindblad, Karin Stensjö, Phillip Craig Wright · 2008 · Journal of Proteome Research
70. Highly Efficient Phosphopeptide Enrichment by Calcium Phosphate Precipitation Combined with Subsequent IMAC Enrichment
    Xumin Zhang, Juanying Ye, Ole Nørregaard Jensen, Peter Roepstorff · 2007 · Molecular & Cellular Proteomics
71. Annotation of a Serum N-Glycan Library for Rapid Identification of Structures
    Danielle L. Aldredge, Hyun Joo An, Ning Tang, Keith Waddell, Carlito B. Lebrilla · 2012 · Journal of Proteome Research
72. A Systematic Investigation into the Nature of Tryptic HCD Spectra
    Annette Michalski, Nadin Neuhauser, Jürgen Cox, Matthias Mann · 2012 · Journal of Proteome Research
73. Breaking the histone code with quantitative mass spectrometry
    Laura-Mae P. Britton, Michelle Gonzales-Cope, Barry M. Zee, Benjamin Aaron Garcia · 2011 · Expert Review of Proteomics
74. Fast and Efficient Proteolysis by Microwave-Assisted Protein Digestion Using Trypsin-Immobilized Magnetic Silica Microspheres
    Shuang Lin, Guoping Yao, Dawei Qi, Yan Li, Chunhui Deng, Pengyuan Yang, Xiangmin Zhang · 2008 · Analytical Chemistry
75. Improvement in Peptide Detection for Proteomics Analyses Using NanoLC−MS and High-Field Asymmetry Waveform Ion Mobility Mass Spectrometry
    Karine Venne, Éric Bonneil, Kevin Eng, Pierre Thibault · 2005 · Analytical Chemistry
76. Recent advances in charting protein–protein interaction: mass spectrometry-based approaches
    Anne‐Claude Gavin, Kenji Maeda, Sebastian Kühner · 2010 · Current Opinion in Biotechnology
77. Effect of Peptide-to-TiO2 Beads Ratio on Phosphopeptide Enrichment Selectivity
    Qingrun Li, Zhibin Ning, Jia-shu Tang, Song Nie, Rong Zeng · 2009 · Journal of Proteome Research
78. A Systematic Characterization of Mitochondrial Proteome from Human T Leukemia Cells
    Karim Rezaul, Linfeng Wu, Viveka Mayya, Sun‐Il Hwang, David C. Han · 2004 · Molecular & Cellular Proteomics
79. A century of mass spectrometry: from atoms to proteomes
    John R. Yates · 2011 · Nature Methods
80. TagRecon: High-Throughput Mutation Identification through Sequence Tagging
    Surendra Dasari, Matthew Chambers, Robbert J.C. Slebos, Lisa J. Zimmerman, Amy‐Joan L. Ham, David L. Tabb · 2010 · Journal of Proteome Research
81. Development of a mass fingerprinting tool for automated interpretation of oligosaccharide fragmentation data
    Hiren Jitendra Joshi, Mathew J. Harrison, Benjamin Luke Schulz, Catherine A. Cooper, Nicolle H. Packer, Niclas G. Karlsson · 2004 · PROTEOMICS
82. Titanium dioxide as a chemo-affinity solid phase in offline phosphopeptide chromatography prior to HPLC-MS/MS analysis
    Michael Mazanek, Goran Mituloviæ, Franz Herzog, Christoph Stingl, James R. A. Hutchins, Jan‐Michael Peters, Karl Mechtler · 2006 · Nature Protocols
83. Proteomics: New technologies and clinical applications
    Martin Latterich, Mark Abramovitz, Brian R Leyland-Jones · 2008 · European Journal of Cancer
84. Altered Glycosylation of Proteins in Cancer: What Is the Potential for New Anti-Tumour Strategies
    Susan Ann Brooks, Tracey M. Carter, Louise Royle, David John Harvey, S. Fry, C. Kinch, R. A. Dwek, Pauline Mary Rudd · 2008 · Anti-Cancer Agents in Medicinal Chemistry
85. Off-Line Coupling of High-Resolution Capillary Electrophoresis to MALDI-TOF and TOF/TOF MS
    Tomáš Rejtar, Ping Hu, Péter Juhász, Jennifer M. Campbell, Marvin L. Vestal, Jan Preisler, Barry L. Karger · 2002 · Journal of Proteome Research
86. Capillary Electrophoresis−Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Using a Vacuum Deposition Interface
    Jan Preisler, Ping Hu, Tomáš Rejtar, Barry L. Karger · 2000 · Analytical Chemistry
87. Separation and Identification of Isomeric Glycopeptides by High Field Asymmetric Waveform Ion Mobility Spectrometry
    Andrew J. Creese, Helen J. Cooper · 2012 · Analytical Chemistry
88. Identification of carbonylated proteins from enriched rat skeletal muscle mitochondria using affinity chromatography‐stable isotope labeling and tandem mass spectrometry
    Danni L. Meany, Hongwei Xie, LaDora V. Thompson, Edgar A. Arriaga, Timothy J. Griffin · 2007 · PROTEOMICS
89. Shotgun proteomics: integrating technologies to answer biological questions.
    William Hayes McDonald, John R Yates · 2003 · PubMed
90. Redox regulation of protein misfolding, mitochondrial dysfunction, synaptic damage, and cell death in neurodegenerative diseases
    Tomohiro Nakamura, Dong‐Hyung Cho, Stuart A. Lipton · 2012 · Experimental Neurology
91. Two‐stage Off‐Gel™ isoelectric focusing: Protein followed by peptide fractionation and application to proteome analysis of human plasma
    Manfred Heller, Philippe Michel, Patrick Morier, David Crettaz, Christian Wenz, Jean‐Daniel Tissot, Frédéric Reymond, Joël S. Rossier · 2005 · Electrophoresis
92. Oligosaccharide Profiles of the Prostate Specific Antigen in Free and Complexed Forms from the Prostate Cancer Patient Serum and in Seminal Plasma: a Glycopeptide Approach
    Michiko Tajiri, Chikara Οhyama, Yoshinao Wada · 2007 · Glycobiology
93. Global and targeted quantitative proteomics for biomarker discovery
    Timothy D. Veenstra · 2006 · Journal of Chromatography B
94. Development of phosphopeptide enrichment techniques for phosphoproteome analysis
    Guanghui Han, Mingliang Ye, Hanfa Zou · 2008 · The Analyst
95. A Proteome Strategy for Fractionating Proteins and Peptides Using Continuous Free-Flow Electrophoresis Coupled Off-Line to Reversed-Phase High-Performance Liquid Chromatography
    Robert L. Moritz, Hong Ji, Frédéric Schütz, Lisa Connolly, Eugene A. Kapp, Terence Paul Speed, Richard J. Simpson · 2004 · Analytical Chemistry
96. Global absolute quantification of a proteome: Challenges in the deployment of a QconCAT strategy
    Philip Brownridge, Stephen W. Holman, Simon J. Gaskell, Chris M. Grant, Victoria M. Harman, Simon J. Hubbard, Karin Lanthaler, Craig Lawless, ronan.ocualain not provided, Paul F. G. Sims et al. · 2011 · PROTEOMICS
97. Rapid empirical discovery of optimal peptides for targeted proteomics
    Stergachis, Andrew B, MacLean, Brendan, Lee, Kristen, Stamatoyannopoulos, John A, MacCoss, Michael J · 2011 · Nature Methods
98. Plasma proteome of severe acute respiratory syndrome analyzed by two-dimensional gel electrophoresis and mass spectrometry
    Jenn‐Han Chen, Yu‐Wang Chang, Chen‐Wen Yao, Tzong‐Shi Chiueh, Su‐Chin Huang, Ko-yi Chien, An Chen, Feng‐Yee Chang, Chi‐Huey Wong, Yu‐Ju Chen · 2004 · Proceedings of the National Academy of Sciences
99. S-nitrosylation: A radical way to protect the heart
    Elizabeth Murphy, Mark Jeffrey Kohr, Junhui Sun, Tiffany Tuyen Minh Nguyen, Charles Steenbergen · 2011 · Journal of Molecular and Cellular Cardiology
100. Quantitative Profile of Five Murine Core Proteomes Using Label-free Functional Proteomics
     Pedro R. Cutillas, Bart Vanhaesebroeck · 2007 · Molecular & Cellular Proteomics
101. Enhanced Sensitivity in Proteomics Experiments Using FAIMS Coupled with a Hybrid Linear Ion Trap/Orbitrap Mass Spectrometer
     Julian A. Saba, Éric Bonneil, Christelle Pomiès, Kevin Eng, Pierre Thibault · 2009 · Journal of Proteome Research
102. Comparison of Full Versus Partial Metabolic Labeling for Quantitative Proteomics Analysis in Arabidopsis thaliana
     Edward L. Huttlin, Adrian D. Hegeman, Amy C. Harms, Michael R. Sussman · 2007 · Molecular & Cellular Proteomics
103. Absolute Quantification of Proteins in Solutions and in Polyacrylamide Gels by Mass Spectrometry
     Jan Havliš, Andrej Shevchenko · 2004 · Analytical Chemistry
104. Mechanistic Insights into the Multistage Gas-Phase Fragmentation Behavior of Phosphoserine- and Phosphothreonine-Containing Peptides
     Amanda M. Palumbo, Jetze J. Tepe, Gavin E. Reid · 2008 · Journal of Proteome Research
105. Laser Capture Microdissection and Protein Microarray Analysis of Human Non-small Cell Lung Cancer
     Amy J. VanMeter, Adrianna S. Rodriguez, Elise D. Bowman, Jin Jen, Curtis C. Harris, Jianghong Deng, Valerie S. Calvert, Alessandra Silvestri, Claudia Fredolini, Vikas Chandhoke et al. · 2008 · Molecular & Cellular Proteomics
106. Characterization of Global Yeast Quantitative Proteome Data Generated from the Wild-Type and Glucose Repression Saccharomyces cerevisiae Strains: The Comparison of Two Quantitative Methods
     Renata Usaite, James Akira Wohlschlegel, John D. Venable, Sung K. Park, Jens Nielsen, Lisbeth Olsson A, John R. Yates · 2008 · Journal of Proteome Research
107. Digestion and depletion of abundant proteins improves proteomic coverage
     Bryan R. Fonslow, Benjamin D. Stein, Kristofor J. Webb, Tao Xu, Jeong Ho Choi, Sung Kyu Park, John R. Yates · 2012 · Nature Methods
108. Profiling Protein Markers Associated with Lymph Node Metastasis in Prostate Cancer by DIGE-based Proteomics Analysis
     Jun Pang, Weipeng Liu, Xiaopeng Liu, Li Ling, Youqiang Fang, Qi-Peng Sun, Shaojun Liu, Ming-Tao Li, Zu-Lan Su, Xin Gao · 2009 · Journal of Proteome Research
109. Implications of 15N‐metabolic labeling for automated peptide identification in Arabidopsis thaliana
     Clark J. Nelson, Edward L. Huttlin, Adrian D. Hegeman, Amy C. Harms, Michael R. Sussman · 2007 · PROTEOMICS
110. Sensitive multiplexed analysis of kinase activities and activity-based kinase identification
     Kazuishi Kubota, Rana Anjum, Yonghao Yu, Ryan C. Kunz, Jannik N. Andersen, Manfred Kraus, Heike Keilhack, Kumiko Nagashima, Stefan Krauss, Cloud Peter Paweletz et al. · 2009 · Nature Biotechnology
111. Proteomic Analysis of Ubiquitinated Proteins from Human MCF-7 Breast Cancer Cells by Immunoaffinity Purification and Mass Spectrometry
     Julian Vasilescu, Jeffrey C. Smith, Martin Ethier, Daniel Figeys · 2005 · Journal of Proteome Research
112. Effective removal of albumin from serum
     David Colantonio, Christy Dunkinson, Diane E. Bovenkamp, Jennifer E. Van Eyk · 2005 · PROTEOMICS
113. Improvements in Proteomic Metrics of Low Abundance Proteins through Proteome Equalization Using ProteoMiner Prior to MudPIT
     Bryan R. Fonslow, Paulo C. Carvalho, Katrina Academia, Steve Freeby, Tao Xu, Aleksey Nakorchevsky, Aran Paulus, John R. Yates · 2011 · Journal of Proteome Research
114. Methods for analyzing peptides and proteins on a chromatographic timescale by electron-transfer dissociation mass spectrometry
     Namrata D. Udeshi, Philip Daniel Compton, Jeffrey Shabanowitz, Donald F. Hunt, Kristie Lindsay Rose · 2008 · Nature Protocols
115. Phosphoproteome Analysis Reveals Regulatory Sites in Major Pathways of Cardiac Mitochondria
     Ning Deng, Jun Zhang, Chenggong Zong, Yueju Wang, Haojie Lu, Pengyuan Yang, Wenhai Wang, Glen W. Young, Yibin Wang, Paavo Kôrge et al. · 2010 · Molecular & Cellular Proteomics
116. Ultra-Low Flow Electrospray Ionization-Mass Spectrometry for Improved Ionization Efficiency in Phosphoproteomics
     Anthonius A. M. Heemskerk, Jean‐Marc Busnel, Bart Schoenmaker, Rico J. E. Derks, Oleg I. Klychnikov, Paul J. Hensbergen, André M. Deelder, Oleg A. Mayboroda · 2012 · Analytical Chemistry
117. Acceleration of Microwave-Assisted Enzymatic Digestion Reactions by Magnetite Beads
     Wei‐Yu Chen, Yu‐Chie Chen · 2007 · Analytical Chemistry
118. Sequence similarity‐driven proteomics in organisms with unknown genomes by LC‐MS/MS and automated de novo sequencing
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119. Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development
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132. Novel Application of Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) in Shotgun Proteomics: Comprehensive Profiling of Rat Kidney Proteome
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174. Assessing the Dynamic Range and Peak Capacity of Nanoflow LC−FAIMS−MS on an Ion Trap Mass Spectrometer for Proteomics
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175. Development of Mass Spectrometry-Based Shotgun Method for Proteome Analysis of 500 to 5000 Cancer Cells
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181. Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations
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200. Electrostatic-Spray Ionization Mass Spectrometry
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