Protein Analysis by Shotgun/Bottom-up Proteomics

Cites (825)

Items 601–800 of 825

1. Electrostatic-Spray Ionization Mass Spectrometry
   Liang Qiao, Romain Sartor, Natalia Gasilova, Yu Lu, Elena Tobolkina, Baohong Liu, Hubert H. Girault · 2012 · Analytical Chemistry
2. Activated-Ion Electron Transfer Dissociation Improves the Ability of Electron Transfer Dissociation to Identify Peptides in a Complex Mixture
   Aaron R. Ledvina, Nicole A. Beauchene, Graeme C. McAlister, John E. P. Syka, Jae C. Schwartz, Jens Griep‐Raming, Michael S. Westphall, Joshua J. Coon · 2010 · Analytical Chemistry
3. Systematic Characterization of Nuclear Proteome during Apoptosis
   Sun‐Il Hwang, Deborah H. Lundgren, Viveka Mayya, Karim Rezaul, Ann E. Cowan, Jimmy K. Eng, David K. M. Han · 2006 · Molecular & Cellular Proteomics
4. Guidelines for reporting the use of mass spectrometry informatics in proteomics
   Pierre‐Alain Binz, Robert J. Barkovich, Ronald C. Beavis, David M. Creasy, David M. Horn, Randall K. Julian, Sean L. Seymour, Chris F. Taylor, Yves Vandenbrouck · 2008 · Nature Biotechnology
5. Computational principles of determining and improving mass precision and accuracy for proteome measurements in an Orbitrap
   Jürgen Cox, Matthias Mann · 2009 · Journal of the American Society for Mass Spectrometry
6. A Chaperone Trap Contributes to the Onset of Cystic Fibrosis
   Judith A. Coppinger, Darren M. Hutt, Abbas Razvi, Atanas V. Koulov, Sandra Pankow, John R. Yates, William E. Balch · 2012 · PLoS ONE
7. A High-throughput Approach for Subcellular Proteome
   Xiao-Sheng Jiang, Hu Zhou, Lei Zhang, Quanhu Sheng, Sujun Li, Long Li, Pei Hao, Yixue Li, Qi‐Chang Xia, Jiarui Wu et al. · 2004 · Molecular & Cellular Proteomics
8. Mass Transport in a Micro Flow-Through Vial of a Junction-at-the-Tip Capillary Electrophoresis-Mass Spectrometry Interface
   Xuefei Zhong, E. Jane Maxwell, David D. Y. Chen · 2011 · Analytical Chemistry
9. Atmospheric pressure ionization time-of-flight mass spectrometry coupled with fast liquid chromatography for quantitation and accurate mass measurement of five pharmaceutical drugs in human plasma
   Hongwei Zhang, Katja Heinig, Jack D. Henion · 2000 · Journal of Mass Spectrometry
10. Parallel Identification of New Genes in Saccharomyces cerevisiae
    Guy Oshiro, Lisa M. Wodicka, Michael P. Washburn, John R. Yates, David J. Lockhart, Elizabeth A. Winzeler · 2002 · Genome Research
11. Reactive-Electrospray-Assisted Laser Desorption/Ionization for Characterization of Peptides and Proteins
    Ivory X. Peng, Rachel R. Ogorzalek Loo, Jentaie Shiea, Joseph A. Loo · 2008 · Analytical Chemistry
12. Enhancing Peptide Identification Confidence by Combining Search Methods
    Gelio Alves, Wells W. Wu, Guanghui Wang, Rong‐Fong Shen, Yi‐Kuo Yu · 2008 · Journal of Proteome Research
13. Protein expression profiles in pediatric multiple sclerosis: potential biomarkers
    Kanokporn Noy Rithidech, Louise Honikel, Maria C. Milazzo, D Madigan, Regina M. Troxell, Lauren Krupp · 2009 · Multiple Sclerosis Journal
14. Mechanism of Cancer Cell Adaptation to Metabolic Stress
    Rui R Liu, Zhenjun Li, Shujun Bai, Haiyuan Zhang, Minghai Tang, Yunlong Lei, Lijuan Chen, Shufang Liang, Yinglan Zhao, Yuquan Wei et al. · 2008 · Molecular & Cellular Proteomics
15. Analysis of the Acidic Proteome with Negative Electron-Transfer Dissociation Mass Spectrometry
    Graeme C. McAlister, Jason D. Russell, Neil G. Rumachik, Alexander S. Hebert, John E. P. Syka, Lewis Y. Geer, Michael S. Westphall, David J. Pagliarini, Joshua J. Coon · 2012 · Analytical Chemistry
16. Triple SILAC to Determine Stimulus Specific Interactions in the Wnt Pathway
    Maximiliane Hilger, Matthias Mann · 2011 · Journal of Proteome Research
17. Preparation and characterization of methacrylate-based monolith for capillary hydrophilic interaction chromatography
    Ming-Luan Chen, Li‐Man Li, Bi‐Feng Yuan, Qiao Ma, Yu‐Qi Feng · 2012 · Journal of Chromatography A
18. Homology‐based functional proteomics by mass spectrometry: Application to the Xenopus microtubule‐associated proteome
    Adam J. Liska, Andrei V. Popov, Shamil R. Sunyaev, Peg Coughlin, Bianca Hermine Habermann, Anna Shevchenko, Peer Bork B, Eric Karsenti, Andrej Shevchenko · 2004 · PROTEOMICS
19. A label free quantitative proteomic analysis of the Saccharomyces cerevisiae nucleus
    Amber L. Mosley, Laurence A. Florens, Zhihui Wen, Michael P. Washburn · 2008 · Journal of Proteomics
20. Proteomic analysis of mitochondria from Caenorhabditis elegans
    Jing Li, Tanxi Cai, Peng Wu, Ziyou Cui, Xiu‐Lan Chen, Junjie Hou, Zhensheng Xie, Peng Xue, Linan Shi, Pingsheng Liu et al. · 2009 · PROTEOMICS
21. Tandem Mass Spectrometry with Ultrahigh Mass Accuracy Clarifies Peptide Identification by Database Retrieval
    Michael T. Boyne, Benjamin Aaron Garcia, Mingxi Li, Leonid Zamdborg, Craig D. Wenger, Shannee Babai, Neil L. Kelleher · 2008 · Journal of Proteome Research
22. Inlet Ionization: A New Highly Sensitive Approach for Liquid Chromatography/Mass Spectrometry of Small and Large Molecules
    Vincent S. Pagnotti, Ellen D. Inutan, Darrell D. Marshall, Charles N. McEwen, Sarah Trimpin · 2011 · Analytical Chemistry
23. Human proteome analysis by using reversed phase monolithic silica capillary columns with enhanced sensitivity
    Mio Iwasaki, Naoyuki Sugiyama, Nobuo Tanaka, Yasushi Ishihama · 2011 · Journal of Chromatography A
24. Wider Pore Superficially Porous Particles for Peptide Separations by HPLC
    Stephanie A. Schuster, Brian M. Wagner, Barry E. Boyes, J. J. Kirkland · 2010 · Journal of Chromatographic Science
25. Two-Dimensional Target Decoy Strategy for Shotgun Proteomics
    Marshall W. Bern, Yong Joo Kil · 2011 · Journal of Proteome Research
26. Network‐assisted protein identification and data interpretation in shotgun proteomics
    Jing Li, Lisa J. Zimmerman, Byung‐Hoon Park, David L. Tabb, Daniel C. Liebler, Bing Zhang · 2009 · Molecular Systems Biology
27. Enhanced Characterization of Complex Proteomic Samples Using LC−MALDI MS/MS: Exclusion of Redundant Peptides from MS/MS Analysis in Replicate Runs
    Hsuan-shen Chen, Tomáš Rejtar, Victor P. Andreev, Eugene V. Moskovets, Barry L. Karger · 2005 · Analytical Chemistry
28. Post-acquisition ETD spectral processing for increased peptide identifications
    David M. Good, Craig D. Wenger, Graeme C. McAlister, Dina L. Bai, Donald F. Hunt, Joshua J. Coon · 2009 · Journal of the American Society for Mass Spectrometry
29. Reducing agent-mediated precipitation of high-abundance plasma proteins
    Scott E. Warder, Lora A. Tucker, Tamara J. Strelitzer, Evelyn Mary McKeegan, Joseph L. Meuth, Paul Mark Jung, Anita Saraf, Bhawani Singh, Jie Lai‐Zhang, Gerard D. Gagné et al. · 2009 · Analytical Biochemistry
30. Computational and Statistical Analysis of Protein Mass Spectrometry Data
    William Stafford Noble, Michael J. MacCoss · 2012 · PLoS Computational Biology
31. Nanoflow Low Pressure High Peak Capacity Single Dimension LC-MS/MS Platform for High-Throughput, In-Depth Analysis of Mammalian Proteomes
    Feng Zhou, Yu Lu, Scott B. Ficarro, James T. Webber, Jarrod A. Marto · 2012 · Analytical Chemistry
32. Protein L-isoaspartyl methyltransferase regulates p53 activity
    Jaecheol Lee, Sung-Ung Kang, Yeji Jeon, Jong Woo Park, Jueng-Soo You, Shin-Won Ha, Narkhyun Bae, Gert Lübec, So Hee Kwon, Ju‐Seog Lee et al. · 2012 · Nature Communications
33. Liquid Chromatography MALDI MS/MS for Membrane Proteome Analysis
    Nan Zhang, Nan Li, Liang Li · 2004 · Journal of Proteome Research
34. Online Nanoflow Reversed Phase-Strong Anion Exchange-Reversed Phase Liquid Chromatography–Tandem Mass Spectrometry Platform for Efficient and In-Depth Proteome Sequence Analysis of Complex Organisms
    Feng Zhou, Timothy W. Sikorski, Scott B. Ficarro, James T. Webber, Jarrod A. Marto · 2011 · Analytical Chemistry
35. SprayQc: A Real-Time LC–MS/MS Quality Monitoring System To Maximize Uptime Using Off the Shelf Components
    Richard A. Scheltema, Matthias Mann · 2012 · Journal of Proteome Research
36. A Framework for Intelligent Data Acquisition and Real-Time Database Searching for Shotgun Proteomics
    Johannes Graumann, Richard A. Scheltema, Yong Zhang, J. Cox, Matthias Mann · 2011 · Molecular & Cellular Proteomics
37. Developing the next generation of cardiac markers: Disease-induced modifications of troponin I
    McDonough, Jason L., Van Eyk, Jennifer E. · 2004 · Progress in Cardiovascular Diseases
38. Hydroxyapatite affinity chromatography for the highly selective enrichment of mono‐ and multi‐phosphorylated peptides in phosphoproteome analysis
    Gianfranco Mamone, Gianluca Picariello, Pasquale Ferranti, Francesco Addeo · 2009 · PROTEOMICS
39. Probability Model for Assessing Proteins Assembled from Peptide Sequences Inferred from Tandem Mass Spectrometry Data
    Jian Feng, Daniel Q. Naiman, Bret Cooper · 2007 · Analytical Chemistry
40. Comparison of Extensive Protein Fractionation and Repetitive LC-MS/MS Analyses on Depth of Analysis for Complex Proteomes
    Huan Wang, Tony Chang-Wong, Hsin‐Yao Tang, David W. Speicher · 2009 · Journal of Proteome Research
41. Hybridization of Pulsed-Q Dissociation and Collision-Activated Dissociation in Linear Ion Trap Mass Spectrometer for iTRAQ Quantitation
    Tiannan Guo, Chee Sian Gan, Huoming Zhang, Yi Zhu, Oi Lian Kon, Siu Kwan Sze · 2008 · Journal of Proteome Research
42. Improving Protein Identification Sensitivity by Combining MS and MS/MS Information for Shotgun Proteomics Using LTQ-Orbitrap High Mass Accuracy Data
    Bingwen Lu, Akira Motoyama, Cristian I. Ruse, John D. Venable, John R. Yates · 2008 · Analytical Chemistry
43. Hydrophilic Strong Anion Exchange (hSAX) Chromatography for Highly Orthogonal Peptide Separation of Complex Proteomes
    Maria Stella Ritorto, Ken Cook, Kshitiz Tyagi, Patrick G. A. Pedrioli, Matthias Trost · 2013 · Journal of Proteome Research
44. Separation of peptide isomers and conformers by ultra performance liquid chromatography
    Dominic Winter, Rüdiger Pipkorn, Wolf Dieter Lehmann · 2009 · Journal of Separation Science
45. A Method for Automatically Interpreting Mass Spectra of 18O-Labeled Isotopic Clusters
    Christopher J. Mason, Terry M. Therneau, Jeanette E. Eckel‐Passow, Kenneth L. Johnson, Ann L. Oberg, Janet E. Olson, K. Sreekumaran Nair, David C. Muddiman, H. Robert Bergen · 2006 · Molecular & Cellular Proteomics
46. Electrospray‐assisted laser desorption/ionization and tandem mass spectrometry of peptides and proteins
    Ivory X. Peng, Jentaie Shiea, Rachel R. Ogorzalek Loo, Joseph A. Loo · 2007 · Rapid Communications in Mass Spectrometry
47. Motif-Specific Sampling of Phosphoproteomes
    Cristian I. Ruse, Daniel B. McClatchy, Bingwen Lu, Daniel Cociorva, Akira Motoyama, Sung Kyu Park, John R. Yates · 2008 · Journal of Proteome Research
48. Separation of a Set of Peptide Sequence Isomers Using Differential Ion Mobility Spectrometry
    Alexandre A. Shvartsburg, Andrew J. Creese, Richard D. Smith, Helen J. Cooper · 2011 · Analytical Chemistry
49. Application of Nano-LC-Based Glycomics Towards Biomarker Discovery
    Serenus S. Hua, Carlito B. Lebrilla, Hyun Joo An · 2011 · Bioanalysis
50. Phosphoproteome analysis of mouse liver using immobilized metal affinity purification and linear ion trap mass spectrometry
    Wenhai Jin, Jie Dai, Hu Zhou, Qi‐Chang Xia, Hanfa Zou, Rong Zeng · 2004 · Rapid Communications in Mass Spectrometry
51. Improvement of Phosphoproteome Analyses Using FAIMS and Decision Tree Fragmentation. Application to the Insulin Signaling Pathway in Drosophila melanogaster S2 Cells
    Gaëlle Bridon, Éric Bonneil, Tara L. Muratore‐Schroeder, Olivier Caron-Lizotte, Pierre Thibault · 2011 · Journal of Proteome Research
52. Off-Line Two-Dimensional Liquid Chromatography with Maximized Sample Loading to Reversed-Phase Liquid Chromatography-Electrospray Ionization Tandem Mass Spectrometry for Shotgun Proteome Analysis
    Nan Wang, Chuanhui Xie, J. Bryce Young, Liang Li · 2009 · Analytical Chemistry
53. Nanospray FAIMS Fractionation Provides Significant Increases in Proteome Coverage of Unfractionated Complex Protein Digests
    Kristian E. Swearingen, Michael R. Hoopmann, Richard S. Johnson, Ramsey A. Saleem, John D. Aitchison, Robert L. Moritz · 2011 · Molecular & Cellular Proteomics
54. Characterization of the Human Submandibular/Sublingual Saliva Glycoproteome Using Lectin Affinity Chromatography Coupled to Multidimensional Protein Identification Technology
    Mireya González–Begne, Bingwen Lu, Lujian Liao, Tao Xu, Gurrinder Singh Bedi, James E. Melvin, John R. Yates · 2011 · Journal of Proteome Research
55. A Novel Alignment Method and Multiple Filters for Exclusion of Unqualified Peptides To Enhance Label-Free Quantification Using Peptide Intensity in LC–MS/MS
    Xianyin Lai, Lianshui Wang, Haixu Tang, Frank A. Witzmann · 2011 · Journal of Proteome Research
56. Sensitivity and mass accuracy for proteins analyzed directly from polyacrylamide gels: Implications for proteome mapping
    Rachel R. Ogorzalek Loo, Charles Mitchell, Tracy I. Stevenson, Stephen A. Martin, Wade M. Hines, Péter Juhász, Dale H. Patterson, John M. Peltier, Joseph A. Loo, Philip Andrews · 1997 · Electrophoresis
57. SQID: An Intensity-Incorporated Protein Identification Algorithm for Tandem Mass Spectrometry
    Wenzhou Li, Ji Li, Jonathan Goya, Guanhong Tan, Vicki Hopper Wysocki · 2011 · Journal of Proteome Research
58. Statistical Analysis of Peptide Electron Transfer Dissociation Fragmentation Mass Spectrometry
    Robert J. Chalkley, Katalin F. Medzihradszky, Aenoch J. Lynn, Peter R. Baker, Alma L. Burlingame · 2009 · Analytical Chemistry
59. Gel‐based proteomics of Gram‐positive bacteria: A powerful tool to address physiological questions
    Michael Hecker, Haike Antelmann, Knut Büttner, Jörg Bernhardt · 2008 · PROTEOMICS
60. Rapid and Deep Profiling of Human Induced Pluripotent Stem Cell Proteome by One-shot NanoLC–MS/MS Analysis with Meter-scale Monolithic Silica Columns
    Ryota Yamana, Mio Iwasaki, Masaki Wakabayashi, Masato Nakagawa, Shinya Yamanaka, Yasushi Ishihama · 2012 · Journal of Proteome Research
61. Hydrophilic interaction chromatography coupled to electrospray mass spectrometry for the separation of peptides and protein digests
    Yuanzhong Yang, Reinhard I. Boysen, Milton T. W. Hearn · 2009 · Journal of Chromatography A
62. Increasing the mass accuracy of high‐resolution LC‐MS data using background ions – a case study on the LTQ‐Orbitrap
    Richard A. Scheltema, Muhammad Anas Kamleh, David Wildridge, Charles Ebikeme, David George Watson, Michael Peter Barrett, Ritsert C. Jansen, Rainer Breitling A · 2008 · PROTEOMICS
63. Proteome Scale Turnover Analysis in Live Animals Using Stable Isotope Metabolic Labeling
    Yaoyang Zhang, Stefan Reckow, Christian Webhofer, Michael Boehme, Philipp Gormanns, Wolfgang M. Egge-Jacobsen, Christoph W. Turck · 2011 · Analytical Chemistry
64. ProteinQuant Suite: a bundle of automated software tools for label‐free quantitative proteomics
    Benjamin F. Mann, Milan Maděra, Quanhu Sheng, Haixu Tang, Yehia S. Mechref, Miloš V. Novotný · 2008 · Rapid Communications in Mass Spectrometry
65. Magnetic bead-based hydrophilic interaction liquid chromatography for glycopeptide enrichments
    Chia-Hao Yeh, Shu‐Hui Chen, Ding-Tzai Li, Hong‐Ping Lin, Hung-Jen Huang, Chi‐I Chang, Wen-Ling Shih, Chi‐Liang Chern, Fong‐Ku Shi, Jue‐Liang Hsu · 2011 · Journal of Chromatography A
66. Instant spectral assignment for advanced decision tree-driven mass spectrometry
    Derek J. Bailey, Christopher M. Rose, Graeme C. McAlister, Justin Brumbaugh, Pengzhi Yu, Craig D. Wenger, Michael S. Westphall, James Alexander Thomson, Joshua J. Coon · 2012 · Proceedings of the National Academy of Sciences
67. Quantitative Proteomics Analysis of the Nuclear Fraction of Human CD4+ Cells in the Early Phases of IL-4-induced Th2 Differentiation
    Robert Moulder, Tapio Lönnberg, Laura L. Elo, Jan‐Jonas Filén, Eeva-Marja Rainio, Garry L. Corthals, Matej Orešič, Tuula A. Nyman, Tero A. Aittokallio, Riitta Lahesmaa · 2010 · Molecular & Cellular Proteomics
68. Identification of N-terminally arginylated proteins and peptides by mass spectrometry
    Tao Xu, Catherine C. L. Wong, Anna S. Kashina, John R. Yates · 2009 · Nature Protocols
69. A Novel Multidimensional Protein Identification Technology Approach Combining Protein Size Exclusion Prefractionation, Peptide Zwitterion−Ion Hydrophilic Interaction Chromatography, and Nano-Ultraperformance RP Chromatography/nESI-MS2 for the in-Depth Analysis of the Serum Proteome and Phosphoproteome: Application to Clinical Sera Derived from Humans with Benign Prostate Hyperplasia
    Spiros D. Garbis, Theodoros I. Roumeliotis, Stavros Ι. Tyritzis, Kostas M Zorpas, Kitty Pavlakis, Constantinos A. Constantinides · 2010 · Analytical Chemistry
70. Improved Precision of iTRAQ and TMT Quantification by an Axial Extraction Field in an Orbitrap HCD Cell
    Peter Pichler, Thomas Köcher, Johann Holzmann, Thomas Möhring, Gustav Ammerer, Karl Mechtler · 2011 · Analytical Chemistry
71. MASPIC: Intensity-Based Tandem Mass Spectrometry Scoring Scheme That Improves Peptide Identification at High Confidence
    Chandrasegaran Narasimhan, David L. Tabb, Nathan C. VerBerkmoes, Melissa R. Thompson, Robert L. Hettich, Edward C. Uberbacher · 2005 · Analytical Chemistry
72. A proteogenomic approach to map the proteome of an unsequenced pathogen – Leishmania donovani
    Harsh Pawar, Nandini A. Sahasrabuddhe, Santosh Renuse, Shivakumar Keerthikumar, Jyoti Nanda Sharma, Ghantasala S. Sameer Kumar, Abhilash K Venugopal, Nirujogi Raja Sekhar, Dhanashree S. Kelkar, Harshal Nemade et al. · 2012 · PROTEOMICS
73. Systematic Comparison of a Two-dimensional Ion Trap and a Three-dimensional Ion Trap Mass Spectrometer in Proteomics
    Viveka Mayya, Karim Rezaul, Yu‐Sheng Cong, David K. M. Han · 2004 · Molecular & Cellular Proteomics
74. Improve the Coverage for the Analysis of Phosphoproteome of HeLa Cells by a Tandem Digestion Approach
    Yangyang Bian, Mingliang Ye, Chunxia Song, Kai Cheng, Chunli Wang, Xiaoluan Wei, Jun Zhu, Rui Chen, Fangjun Wang, Hanfa Zou · 2012 · Journal of Proteome Research
75. Quantitative Proteomics and Protein Network Analysis of Hippocampal Synapses of CaMKIIα Mutant Mice
    Ka Wan Li, Stephan Miller, Oleg I. Klychnikov, Maarten Loos, Jianru Stahl-Zeng, Sabine Spijker, Mark R. Mayford, August Benjamin Smit · 2007 · Journal of Proteome Research
76. Gas-Phase Rearrangements Do Not Affect Site Localization Reliability in Phosphoproteomics Data Sets
    Mike Aguiar, Wilhelm Haas, Sean A. Beausoleil, Augustus John Rush, Steven P. Gygi · 2010 · Journal of Proteome Research
77. Simultaneous Analysis of Proteome, Phospho- and Glycoproteome of Rat Kidney Tissue with Electrostatic Repulsion Hydrophilic Interaction Chromatography
    Piliang Hao, Tiannan Guo, Siu Kwan Sze · 2011 · PLoS ONE
78. Optimization of Electron Transfer Dissociation via Informed Selection of Reagents and Operating Parameters
    Philip Daniel Compton, Joseph V. Strukl, Dina L. Bai, Jeffrey Shabanowitz, Donald F. Hunt · 2011 · Analytical Chemistry
79. Sweet silver: A formaldehyde‐free silver staining using aldoses as developing agents, with enhanced compatibility with mass spectrometry
    Mireille Chevallet, Sylvie Luche, Hélène Diemer, Jean‐Marc Strub, Alain VAN DORSSELAER, Thierry Rabilloud · 2008 · PROTEOMICS
80. Improving Depth in Phosphoproteomics by Using a Strong Cation Exchange-Weak Anion Exchange-Reversed Phase Multidimensional Separation Approach
    Marco L. Hennrich, Vincent Groenewold, Geert J.P.L. Kops, Albert J. R. Heck, Shabaz Mohammed · 2011 · Analytical Chemistry
81. What’s Driving False Discovery Rates?
    David L. Tabb · 2007 · Journal of Proteome Research
82. Application of 2‐D free‐flow electrophoresis/RP‐HPLC for proteomic analysis of human plasma depleted of multi high‐abundance proteins
    Robert L. Moritz, Andrew B. Clippingdale, Eugene A. Kapp, James S. Eddes, Hong Ji, S.B. Gilbert, Lisa Connolly, Richard J. Simpson · 2005 · PROTEOMICS
83. Potential biomarkers for diagnosis of sarcoidosis using proteomics in serum
    Judith A. P. Bons, Marjolein Drent, Freek G. Bouwman, Edwin C.M. Mariman, Marja P. van Dieijen‐Visser, Will K. W. H. Wodzig · 2007 · Respiratory Medicine
84. Enhanced Sensitivity for Selected Reaction Monitoring Mass Spectrometry-based Targeted Proteomics Using a Dual Stage Electrodynamic Ion Funnel Interface
    Mahmud Hossain, David T. Kaleta, Errol W. Robinson, Tao Liu, Rui Zhao, Jason S. Page, Ryan Kelly, Ronald Jay Moore, Keqi Tang, David Camp et al. · 2010 · Molecular & Cellular Proteomics
85. Quantitative Multiple Reaction Monitoring of Peptide Abundance Introduced via a Capillary Zone Electrophoresis–Electrospray Interface
    Yihan Li, Roza Wojcik, Norman J. Dovic̀hi, Matthew M. Champion · 2012 · Analytical Chemistry
86. Subzero Temperature Chromatography for Reduced Back-Exchange and Improved Dynamic Range in Amide Hydrogen/Deuterium Exchange Mass Spectrometry
    John D. Venable, Linda Okach, Sanjay Agarwalla, Ansgar Brock · 2012 · Analytical Chemistry
87. Accelerated High-Resolution Differential Ion Mobility Separations Using Hydrogen
    Alexandre A. Shvartsburg, Richard Smith · 2011 · Analytical Chemistry
88. Shotgun Protein Sequencing by Tandem Mass Spectra Assembly
    Nuno Bandeira, Haixu Tang, Vineet Bafna, Pavel A. Pevzner · 2004 · Analytical Chemistry
89. Identification of caspase‐3 degradome by two‐dimensional gel electrophoresis and matrix‐assisted laser desorption/ionization‐time of flight analysis
    Ah Young Lee, Byoung Chul Park, Mi Kyeong Jang, Sayeon Cho, Do Hee Lee, Sang Chul Lee, Pyung Keun Myung, Sung Goo Park · 2004 · PROTEOMICS
90. Alkylating Tryptic Peptides to Enhance Electrospray Ionization Mass Spectrometry Analysis
    Suzanne E. Kulevich, Brian L. Frey, Gloria Kreitinger, Lloyd M. Smith · 2010 · Analytical Chemistry
91. Sub-proteomic fractionation, iTRAQ, and OFFGEL-LC–MS/MS approaches to cardiac proteomics
    Chad M. Warren, David L. Geenen, Donald L. Helseth, Hua Xu, Ross John Solaro · 2010 · Journal of Proteomics
92. Moving cancer diagnostics from bench to bedside
    Xuewu Zhang, Lin Li, Dong Wei, Yeeleng Yap, Feng Chen · 2007 · Trends in biotechnology
93. Quantitative Comparison of Proteomic Data Quality between a 2D and 3D Quadrupole Ion Trap
    Adele R. Blackler, Aaron A. Klammer, Michael J. MacCoss, Christine C. Wu · 2006 · Analytical Chemistry
94. Precursor-Ion Mass Re-Estimation Improves Peptide Identification on Hybrid Instruments
    Roland Luethy, Darren Kessner, Jonathan Elliott Katz, Brendan MacLean, Robert Grothe, Kian Kani, Vitor Marcel Faça, Sharon J. Pitteri, Samir Hanash, David B. Agus et al. · 2008 · Journal of Proteome Research
95. Empirical Bayes Analysis of Quantitative Proteomics Experiments
    Adam A. Margolin, Shao‐En Ong, Monica Schenone, Robert J. Gould, Stuart L. Schreiber, Steven A. Carr, Todd R. Golub · 2009 · PLoS ONE
96. In-house construction of a UHPLC system enabling the identification of over 4000 protein groups in a single analysis
    Alba Cristobal, Marco L. Hennrich, Piero Giansanti, Soenita S. Goerdayal, Albert J. R. Heck, Shabaz Mohammed · 2012 · The Analyst
97. DBDigger: Reorganized Proteomic Database Identification That Improves Flexibility and Speed
    David L. Tabb, Chandrasegaran Narasimhan, Michael Brad Strader, Robert L. Hettich · 2005 · Analytical Chemistry
98. Verification of Biomarkers for Diabetic Retinopathy by Multiple Reaction Monitoring
    Kyunggon Kim, Sang Jin Kim, Hyeong Gon Yu, Jiyoung Yu, Kyong Soo Park, In‐Jin Jang, Youngsoo Kim · 2009 · Journal of Proteome Research
99. On-line Digestion System for Protein Characterization and Proteome Analysis
    Daniel López‐Ferrer, Konstantinos Pétritis, Natacha M. Lourette, Brian H. Clowers, Kim K. Hixson, Tyler H. Heibeck, David C. Prior, Ljiljana Paša‐Tolić, David Camp, Mikhail E. Belov et al. · 2008 · Analytical Chemistry
100. Ion Mobility Separation of Isomeric Phosphopeptides from a Protein with Variant Modification of Adjacent Residues
     Alexandre A. Shvartsburg, David L. Singer, Richard D. Smith, Ralf Hoffmann · 2011 · Analytical Chemistry
101. Single-Step Inline Hydroxyapatite Enrichment Facilitates Identification and Quantitation of Phosphopeptides from Mass-Limited Proteomes with MudPIT
     Bryan R. Fonslow, Sherry Niessen, Meha Singh, Catherine C. L. Wong, Tao Xu, Paulo C. Carvalho, Jeong Ho Choi, Sung Kyu Park, John R. Yates · 2012 · Journal of Proteome Research
102. Improved Identification of SUMO Attachment Sites Using C-Terminal SUMO Mutants and Tailored Protease Digestion Strategies
     James Akira Wohlschlegel, Erica S. Johnson, Steven I. Reed, John R. Yates · 2006 · Journal of Proteome Research
103. Comparison of columns packed with porous sub‐2 μm particles and superficially porous sub‐3 μm particles for peptide analysis at ambient and high temperature
     Joséphine Ruta, Davy Guillarme, Serge L. Rudaz, Jean‐Luc Veuthey · 2010 · Journal of Separation Science
104. Peek a peak: a glance at statistics for quantitative label-free proteomics
     Katharina Podwojski, Martin Eisenacher, Michael Kohl, Michael Turewicz, Helmut E. Meyer, Jörg Rahnenführer, Christian Stephan · 2010 · Expert Review of Proteomics
105. Liquid chromatography electron capture dissociation tandem mass spectrometry (LC-ECD-MS/MS) versus liquid chromatography collision-induced dissociation tandem mass spectrometry (LC-CID-MS/MS) for the identification of proteins
     Andrew J. Creese, Helen J. Cooper · 2007 · Journal of the American Society for Mass Spectrometry
106. Ultra Acidic Strong Cation Exchange Enabling the Efficient Enrichment of Basic Phosphopeptides
     Marco L. Hennrich, Henk van den Toorn, Vincent Groenewold, Albert J. R. Heck, Shabaz Mohammed · 2012 · Analytical Chemistry
107. A Complex Standard for Protein Identification, Designed by Evolution
     Marc Vaudel, Julia Maria Burkhart, Daniela Breiter, René Peiman Zahedi, Albert Sickmann, Lennart Martens · 2012 · Journal of Proteome Research
108. GeLCMS for In-Depth Protein Characterization and Advanced Analysis of Proteomes
     Alicia Lundby, Jesper Velgaard Olsen · 2011 · Methods in molecular biology
109. Glycoprofiling of the Human Salivary Proteome
     Melissa A. Sondej, Patricia A. Denny, Yongming Xie, Prasanna Ramachandran, Yan Si, Jona Takashima, Wenyuan Shi, David T. Wong, Joseph A. Loo, Paul C. Denny · 2008 · Clinical Proteomics
110. Fast Multiple Electron Capture Dissociation in a Linear Radio Frequency Quadrupole Ion Trap
     Hiroyuki Satake, Hideki Hasegawa, Atsumu Hirabayashi, Yuichiro Hashimoto, Takashi Baba, Katsuyoshi Masuda · 2007 · Analytical Chemistry
111. The Effects of Shared Peptides on Protein Quantitation in Label-Free Proteomics by LC/MS/MS
     Shuangshuang Jin, Donald S. Daly, David L. Springer, John H. Miller · 2007 · Journal of Proteome Research
112. Interpreting Sequences from Mastodon and T. rex
     John M. Asara, John S. Garavelli, David Anthony Slatter, Mary Higby Schweitzer, Lisa M. Freimark, Matthew J. Phillips, Lewis C. Cantley · 2007 · Science
113. Online Nanoflow RP−RP-MS Reveals Dynamics of Multicomponent Ku Complex in Response to DNA Damage
     Feng Zhou, Job D. Cardoza, Scott B. Ficarro, Guillaume Adelmant, Jean‐Bernard Lazaro, Jarrod A. Marto · 2010 · Journal of Proteome Research
114. Elimination of Systematic Mass Measurement Errors in Liquid Chromatography−Mass Spectrometry Based Proteomics Using Regression Models and a Priori Partial Knowledge of the Sample Content
     Vladislav Petyuk, Navdeep Jaitly, Ronald Jay Moore, Jie Ding, Thomas Metz, Keqi Tang, Matthew E Monroe, Aleksey V. Tolmachev, Joshua Adkins, Mikhail E. Belov et al. · 2007 · Analytical Chemistry
115. Quantitative proteomics using uniform 15N‐labeling, MASCOT, and the trans‐proteomic pipeline
     Magnus Palmblad, Laurence V. Bindschedler, Rainer Cramer · 2007 · PROTEOMICS
116. Analysis of Tandem Mass Spectra by FTMS for Improved Large-Scale Proteomics with Superior Protein Quantification
     Graeme C. McAlister, Doug Phanstiel, Craig D. Wenger, M. Violet Lee, Joshua J. Coon · 2009 · Analytical Chemistry
117. A Strategy for the Rapid Identification of Phosphorylation Sites in the Phosphoproteome
     Justin A. MacDonald, Aaron J. Mackey, William R. Pearson, Timothy Haystead · 2002 · Molecular & Cellular Proteomics
118. Screening for therapeutic targets of vorinostat by SILAC‐based proteomic analysis in human breast cancer cells
     Qun Yong Zhou, Raghothama Chaerkady, Patrick G. Shaw, Thomas W. Kensler, Akhilesh Pandey, Nancy E. Davidson · 2010 · PROTEOMICS
119. Boronic acid–lectin affinity chromatography. 1. Simultaneous glycoprotein binding with selective or combined elution
     Alex Monzo, Guenther Karl Bonn, András Guttman · 2007 · Analytical and Bioanalytical Chemistry
120. Can the false‐discovery rate be misleading?
     Rodrigo Camara Barboza, Daniel Cociorva, Tao Xu, Valmir Carneiro Barbosa, Jonás Perales, Richard Hemmi Valente, Felipe M. G. França, John R. Yates, Paulo C. Carvalho · 2011 · PROTEOMICS
121. Enhanced Separation and Characterization of Deamidated Peptides with RP-ERLIC-Based Multidimensional Chromatography Coupled with Tandem Mass Spectrometry
     Piliang Hao, Jingru Qian, Bamaprasad Dutta, Esther Sok Hwee Cheow, Kae Hwan Sim, Wei Meng, Sunil Shankar Adav, Andrew J. Alpert, Siu Kwan Sze · 2012 · Journal of Proteome Research
122. High peak capacity separations of peptides in reversed-phase gradient elution liquid chromatography on columns packed with porous shell particles
     Nicola Marchetti, Georges A. Guiochon · 2007 · Journal of Chromatography A
123. A workflow to increase the detection rate of proteins from unsequenced organisms in high‐throughput proteomics experiments
     Jonas Grossmann, Bernd Fischer, Katja Baerenfaller, Judith Owiti, Joachim M. Buhmann, Wilhelm Gruissem, Sacha Baginsky · 2007 · PROTEOMICS
124. Improved enrichment strategies for phosphorylated peptides on titanium dioxide using methyl esterification and pH gradient elution
     Eric S. Simon, Matthew Adam Young, Antonia Chan, Zhao Bao, Philip Andrews · 2008 · Analytical Biochemistry
125. Automatic Determination of O-Glycan Structure from Fragmentation Spectra
     David Theo Goldberg, Marshall W. Bern, Bensheng Li, Carlito B. Lebrilla · 2006 · Journal of Proteome Research
126. Phosphatase-Directed Phosphorylation-Site Determination: A Synthesis of Methods for the Detection and Identification of Phosphopeptides
     Matthew P. Torres, Roopa Thapar, William F. Marzluff, Christoph H. Borchers · 2005 · Journal of Proteome Research
127. Rapid Sample Processing for LC-MS-Based Quantitative Proteomics Using High Intensity Focused Ultrasound
     Daniel López‐Ferrer, Tyler H. Heibeck, Konstantinos Pétritis, Kim K. Hixson, Weijun Qian, Matthew E Monroe, Anoop M. Mayampurath, Ronald Jay Moore, Mikhail E. Belov, David Camp et al. · 2008 · Journal of Proteome Research
128. Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides
     Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steven P. Briggs, Vineet Bafna · 2012 · Journal of Computational Biology
129. Improving Proteomics Mass Accuracy by Dynamic Offline Lock Mass
     Ying Zhang, Zhihui Wen, Michael P. Washburn, Laurence A. Florens · 2011 · Analytical Chemistry
130. The Absolute Quantification Strategy
     Scott A. Gerber, Arminja Nadine Kettenbach, Augustus John Rush, Steven P. Gygi · 2007 · Methods in molecular biology
131. A label-free nano-liquid chromatography–mass spectrometry approach for quantitative serum peptidomics in Crohn's disease patients
     Paolo Nanni, Fredrik Levander, Giulia Roda, Alessandra Caponi, Peter James, Aldo Roda · 2009 · Journal of Chromatography B
132. Improving hydrogen/deuterium exchange mass spectrometry by reduction of the back‐exchange effect
     Marc Kipping, Angelika Schierhorn · 2003 · Journal of Mass Spectrometry
133. Comparison of different signal thresholds on data dependent sampling in orbitrap and LTQ mass spectrometry for the identification of peptides and proteins in complex mixtures
     Catherine C. L. Wong, Daniel Cociorva, John D. Venable, Tao Xu, John R. Yates · 2009 · Journal of the American Society for Mass Spectrometry
134. Toward objective evaluation of proteomic algorithms
     John R. Yates, Sung Kyu Robin Park, Claire M. Delahunty, Tao Xu, Jeffrey N. Savas, Daniel Cociorva, Paulo C. Carvalho · 2012 · Nature Methods
135. Higher-energy Collision-activated Dissociation Without a Dedicated Collision Cell
     Graeme C. McAlister, Douglas H. Phanstiel, Justin Brumbaugh, Michael S. Westphall, Joshua J. Coon · 2011 · Molecular & Cellular Proteomics
136. Native Capillary Isoelectric Focusing for the Separation of Protein Complex Isoforms and Subcomplexes
     Bryan R. Fonslow, Seong Anthony Woo Kang, Daniel R. Gestaut, Beth Graczyk, Trisha Nell Davis, David M. Sabatini, John R. Yates · 2010 · Analytical Chemistry
137. Quantitative Analysis of Brain Nuclear Phosphoproteins Identifies Developmentally Regulated Phosphorylation Events
     Lujian Liao, Daniel B. McClatchy, Sung Kyu Park, Tao Xu, Bingwen Lu, John R. Yates · 2008 · Journal of Proteome Research
138. Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles)
     Christopher R. Kinsinger, James Apffel, Mark S. Baker, Xiaopeng Bian, Christoph H. Borchers, Ralph A. Bradshaw, Mi‐Youn Brusniak, Daniel W. Chan, Eric W. Deutsch, Bruno Domon et al. · 2011 · Journal of Proteome Research
139. A High-Resolution Two Dimensional Gel- and Pro-Q DPS-Based Proteomics Workflow for Phosphoprotein Identification and Quantitative Profiling
     Ganesh Kumar Agrawal, Jay J. Thelen · 2009 · Methods in molecular biology
140. A Shotgun Proteomic Method for the Identification of Membrane-Embedded Proteins and Peptides
     Adele R. Blackler, Anna E Speers, Mark S. Ladinsky, Christine C. Wu · 2008 · Journal of Proteome Research
141. Implementing Photodissociation in an Orbitrap Mass Spectrometer
     Lisa A. Vasicek, Aaron R. Ledvina, Jared Shaw, Jens Griep‐Raming, Michael S. Westphall, Joshua J. Coon, Jennifer S. Brodbelt · 2011 · Journal of the American Society for Mass Spectrometry
142. Label-Free LC-MS Method for the Identification of Biomarkers
     Richard E. Higgs, Michael D. Knierman, Valentina Gelfanova, Jon P. Butler, John E. Hale · 2008 · Methods in molecular biology
143. Dynamics of Subcellular Proteomes During Brain Development
     Daniel B. McClatchy, Lujian Liao, Ji Hyoung Lee, Sung Kyu Park, John R. Yates · 2012 · Journal of Proteome Research
144. Heat shock protein 60 modified with O‐linked N‐acetylglucosamine is involved in pancreatic β‐cell death under hyperglycemic conditions
     Hoe Suk Kim, Eun Mi Kim, Jiae Lee, Won Ho Yang, Tae Yoon Park, Young Min Kim, Jin Won Cho · 2006 · FEBS Letters
145. Fractional Protein Synthesis Rates Measured by an Intraperitoneal Injection of a Flooding Dose of L-[ring-2H5]Phenylalanine in Pigs
     Kristjan Bregendahl, Lijuan Liu, John P. Cant, Henry S. Bayley, Brian W. McBride, Larry P. Milligan, Jong Tseng Yen, Ming Z. Fan · 2004 · Journal of Nutrition
146. Tunnel Frit: A Nonmetallic In-Capillary Frit for Nanoflow Ultra High-Performance Liquid Chromatography–Mass SpectrometryApplications
     Chao‐Jung Chen, Wei-Yun Chen, Mei‐Chun Tseng, Yet‐Ran Chen · 2011 · Analytical Chemistry
147. Characterisation and evaluation of metal-loaded iminodiacetic acid–silica of different porosity for the selective enrichment of phosphopeptides
     Lukas Trojer, Günther Stecher, Isabel Feuerstein, Said Hassan Lubbad, Guenther Karl Bonn · 2005 · Journal of Chromatography A
148. Isotope Dilution Mass Spectrometry and the National Reference System
     George N Bowers Jr, John D. Fassett, Edward G. White · 1993 · Analytical Chemistry
149. Different Impact of Staining Procedures Using Visible Stains and Fluorescent Dyes for Large-Scale Investigation of Proteomes by MALDI-TOF Mass Spectrometry
     François Chevalier, Delphine Centeno, Valérie Rofidal, Marc Tauzin, Olivier Martin, Nicolas Sommerer, Michel Rossignol · 2006 · Journal of Proteome Research
150. Improved Peptide Identification for Proteomic Analysis Based on Comprehensive Characterization of Electron Transfer Dissociation Spectra
     Rui-Xiang Sun, Meng‐Qiu Dong, Chun‐Qing Song, Hao Chi, Bing Yang, Li‐Yun Xiu, Tao Li, Zhiyi Jing, Chao Liu, Leheng Wang et al. · 2010 · Journal of Proteome Research
151. Increasing phosphoproteomic coverage through sequential digestion by complementary proteases
     Jason M. Gilmore, Arminja Nadine Kettenbach, Scott A. Gerber · 2011 · Analytical and Bioanalytical Chemistry
152. Statistical Analysis of Electron Transfer Dissociation Pairwise Fragmentation Patterns
     Wenzhou Li, Chi Song, Derek J. Bailey, George C. Tseng, Joshua J. Coon, Vicki Hopper Wysocki · 2011 · Analytical Chemistry
153. Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) versus Strong Cation Exchange (SCX) for Fractionation of iTRAQ-Labeled Peptides
     Piliang Hao, Jingru Qian, Yan Ren, Siu Kwan Sze · 2011 · Journal of Proteome Research
154. Perfluorooctanoic Acid for Shotgun Proteomics
     Chandra Sekhar Rao Kadiyala, Sara E. Tomechko, Masaru Miyagi · 2010 · PLoS ONE
155. Pyrolysis-gas chromatography/mass spectrometry of a coal extract and its fractions separated by planar chromatography: correlation of structural features with molecular mass
     Carlos A. Islas, I. Suelves, J. F. Carter, Alan A. Herod, Rafael Kandiyoti · 2000 · Rapid Communications in Mass Spectrometry
156. H-Score, a Mass Accuracy Driven Rescoring Approach for Improved Peptide Identification in Modification Rich Samples
     Mikhail M. Savitski, Toby Mathieson, Isabelle Becher, Marcus Bantscheff · 2010 · Journal of Proteome Research
157. Integration of Residue-Specific Acid Cleavage into Proteomic Workflows
     Stephen Swatkoski, Peter L. Gutiérrez, Joy M. Ginter, Alexey N. Petrov, Jonathan D. Dinman, Nathan J Edwards, Catherine Fenselau · 2007 · Journal of Proteome Research
158. A New Approach to High Sensitivity Liquid Chromatography-Mass Spectrometry of Peptides using Nanoflow Solvent Assisted Inlet Ionization
     Beixi Wang, Ellen D. Inutan, Sarah Trimpin · 2012 · Journal of the American Society for Mass Spectrometry
159. The Good and Bad Effects of Cysteine S-nitrosylation and Tyrosine Nitration upon Insulin Exocytosis: A Balancing Act
     Dean A. Wiseman, Debbie C. Thurmond · 2012 · Current Diabetes Reviews
160. Beyond hairballs: The use of quantitative mass spectrometry data to understand protein–protein interactions
     Gingras, Anne-Claude, Raught, Brian · 2012 · FEBS Letters
161. Addressing Trypsin Bias in Large Scale (Phospho)proteome Analysis by Size Exclusion Chromatography and Secondary Digestion of Large Post-Trypsin Peptides
     Bao Quoc Tran, Céline Hernandez, Patrice Waridel, Alexandra Potts, Jachen Barblan, Frédérique Lisacek, Manfredo Quadroni · 2010 · Journal of Proteome Research
162. The Problem with Peptide Presumption and Low Mascot Scoring
     Bret Cooper · 2011 · Journal of Proteome Research
163. Data-Dependent Electron Capture Dissociation FT−ICR Mass Spectrometry for Proteomic Analyses
     Helen J. Cooper, Shiva Akbarzadeh, John K. Heath, Martin Zeller · 2005 · Journal of Proteome Research
164. Protein Dynamics in Iron-Starved Mycobacterium tuberculosis Revealed by Turnover and Abundance Measurement Using Hybrid-Linear Ion Trap-Fourier Transform Mass Spectrometry
     Prahlad Rao, G. Marcela Rodríguez, Issar Smith, Qingbo Li · 2008 · Analytical Chemistry
165. Quantitative Proteomic Profiling Studies of Pancreatic Cancer Stem Cells
     Lan Dai, Chen Li, Kerby Shedden, Cheong Jun Lee, Chenwei Li, HuyVuong Quoc, Diane M. Simeone, David M. Lubman · 2010 · Journal of Proteome Research
166. High-throughput proteomics using matrix-assisted laser desorption/ ionization mass spectrometry
     Rainer Cramer, Johan Gobom, Eckhard Nordhoff · 2005 · Expert Review of Proteomics
167. A New Probabilistic Database Search Algorithm for ETD Spectra
     Rovshan G. Sadygov, David M. Good, Danielle L. Swaney, Joshua J. Coon · 2009 · Journal of Proteome Research
168. Ionic liquid 1-butyl-3-methyl imidazolium tetrafluoroborate for shotgun membrane proteomics
     Liangliang Sun, Dingyin Tao, Bin Han, Junfeng Ma, Guijie Zhu, Zhen Liang, Yichu Shan, Lihua Zhang, Yukui Zhang · 2010 · Analytical and Bioanalytical Chemistry
169. Mass Measurement Accuracy in Analyses of Highly Complex Mixtures Based Upon Multidimensional Recalibration
     Aleksey V. Tolmachev, Matthew E Monroe, Navdeep Jaitly, Vladislav Petyuk, Joshua Adkins, Richard D. Smith · 2006 · Analytical Chemistry
170. Depletion of highly abundant proteins in blood plasma by ammonium sulfate precipitation for 2D-PAGE analysis
     Andrea Mahn, Maritza Ismail · 2011 · Journal of Chromatography B
171. Combinatorial Use of Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) and Strong Cation Exchange (SCX) Chromatography for In-Depth Phosphoproteome Analysis
     Mostafa Zarei, Adrian Sprenger, Christine Gretzmeier, Jörn Dengjel · 2012 · Journal of Proteome Research
172. A Proteogenomic Survey of the Medicago truncatula Genome
     Jeremy D. Volkening, Derek J. Bailey, Christopher M. Rose, Paul A. Grimsrud, Maegen Howes‐Podoll, Muthusubramanian Venkateshwaran, Michael S. Westphall, Jean‐Michel Ané, Joshua J. Coon, Michael R. Sussman · 2012 · Molecular & Cellular Proteomics
173. Direct Maximization of Protein Identifications from Tandem Mass Spectra
     Marina Spivak, Jason Weston, Daniela M. Tomazela, Michael J. MacCoss, William Stafford Noble · 2011 · Molecular & Cellular Proteomics
174. Comparison of the Electron Capture Dissociation Fragmentation Behavior of Doubly and Triply Protonated Peptides from Trypsin, Glu-C, and Chymotrypsin Digestion
     Anastasia Kalli, Kristina Håkansson · 2008 · Journal of Proteome Research
175. Rapid Online Nonenzymatic Protein Digestion Combining Microwave Heating Acid Hydrolysis and Electrochemical Oxidation
     Franco Basile, Nicolas J. Hauser · 2010 · Analytical Chemistry
176. Sequence Tagging Reveals Unexpected Modifications in Toxicoproteomics
     Surendra Dasari, Matthew Chambers, Simona G. Codreanu, Daniel C. Liebler, Ben C. Collins, Stephen R. Pennington, William M. Gallagher, David L. Tabb · 2011 · Chemical Research in Toxicology
177. Sensitive Liquid Chromatography-Electrospray Mass Spectrometry Allows for the Analysis of the O-Glycosylation of Immunoprecipitated Proteins from Cells or Tissues: Application to MUC1 Glycosylation in Cancer
     Malin Bäckström, Kristina A. Thomsson, Hasse Karlsson, Gunnar C. Hansson · 2008 · Journal of Proteome Research
178. Microwave-Assisted Protein Solubilization for Mass Spectrometry-Based Shotgun Proteome Analysis
     Xiaoxia Ye, Liang Li · 2012 · Analytical Chemistry
179. Candidate biomarkers of chronic inflammatory demyelinating polyneuropathy (CIDP): Proteome analysis of cerebrospinal fluid
     Hayrettin Tumani, Martin Pfeifle, Vera Lehmensiek, Daniela Rau, Helga Mogel, Albert Christian Ludolph, Johannes Brettschneider · 2009 · Journal of Neuroimmunology
180. Increased Protein Identification Capabilities through Novel Tandem MS Calibration Strategies
     Si Wu, Nathan K. Kaiser, Da Meng, Gordon Anderson, Kai Zhang, James E. Bruce · 2005 · Journal of Proteome Research
181. Online Nanoscale ERLIC-MS Outperforms RPLC–MS for Shotgun Proteomics in Complex Mixtures
     Ebbing P. de Jong, Timothy J. Griffin · 2012 · Journal of Proteome Research
182. Depletion of Acidic Phosphopeptides by SAX To Improve the Coverage for the Detection of Basophilic Kinase Substrates
     Mingming Dong, Mingliang Ye, Kai Cheng, Chunxia Song, Yanbo Pan, Chunli Wang, Yangyang Bian, Hanfa Zou · 2012 · Journal of Proteome Research
183. p I ‐based phosphopeptide enrichment combined with nanoESI‐MS
     Chien‐Wen Hung, Hans-Dieter Kübler, Wolf Dieter Lehmann · 2007 · Electrophoresis
184. Rapid and efficient glycoprotein identification through microwave‐assisted enzymatic digestion
     Zaneer M. Segu, Loubna A. Hammad, Yehia S. Mechref · 2010 · Rapid Communications in Mass Spectrometry
185. Measurement of Protein S‐Nitrosylation during Cell Signaling
     Joan B. Mannick, Christopher M. Schonhoff · 2008 · Methods in enzymology on CD-ROM/Methods in enzymology
186. Isolation of Phosphopeptides by pI-Difference-Based Electrophoresis
     Yingda Xu, Robert W. Sprung, Sung Won Kwon, Sung Chan Kim, Yingming Zhao · 2007 · Journal of Proteome Research
187. Multidimensional protein fractionation using ProteomeLab PF 2D™ for profiling amyotrophic lateral sclerosis immunity: A preliminary report
     Joshua D. Schlautman, Wojciech Rożek, Robert Stetler, Rodney Lee Mosley, Howard Eliot Gendelman, Pawel S. Ciborowski · 2008 · Proteome Science
188. Increased concentration of tracee affects estimates of muscle protein synthesis
     Giuseppe Caso, G. C. Ford, K. Sreekumaran Nair, James A. Vosswinkel, Peter J. Garlick, Margaret A. McNurlan · 2001 · American Journal of Physiology-Endocrinology and Metabolism
189. Multidimensional Protein Identification Technology-Selected Reaction Monitoring Improving Detection and Quantification for Protein Biomarker Studies
     Christoph Krisp, Matthew J. McKay, Dirk Andreas Wolters, Mark P. Molloy · 2012 · Analytical Chemistry
190. Improved Sequence Tag Generation Method for Peptide Identification in Tandem Mass Spectrometry
     Xia Cao, Alexey I. Nesvizhskii · 2008 · Journal of Proteome Research
191. Proteomics of Pyrococcus furiosus , a Hyperthermophilic Archaeon Refractory to Traditional Methods
     Alice M. Lee, Joel R. Sevinsky, Jonathan L. Bundy, Amy Michele Grunden, James L. Stephenson · 2009 · Journal of Proteome Research
192. Measurement of Human Surfactant Protein-B Turnover in Vivo from Tracheal Aspirates Using Targeted Proteomics
     Daniela M. Tomazela, Bruce W. Patterson, Elizabeth Reed Hanson, Kimberly L. Spence, Tiffany B. Kanion, David H. Salinger, Paolo Vicini, Hugh Barret, Hillary B. Heins, Francis Sessions Cole et al. · 2010 · Analytical Chemistry
193. Simple modification of a protein database for mass spectral identification of N‐linked glycopeptides
     James Atwood, Satya Sanket Sahoo, Gerardo Álvarez-Manilla, Daniel Brent Weatherly, Kumar Kolli, Ron Orlando, William S. York · 2005 · Rapid Communications in Mass Spectrometry
194. Orthogonal Separation Techniques for the Characterization of the Yeast Nuclear Proteome
     Sharon Gauci, Liesbeth M. Veenhoff, Albert J. R. Heck, Jeroen Krijgsveld · 2009 · Journal of Proteome Research
195. Cell cycle phosphorylation of mitotic exit network (MEN) proteins
     Michele Haltiner Jones, Jamie M. Keck, Catherine C. L. Wong, Tao Xu, John R. Yates, Mark Winey · 2011 · Cell Cycle
196. Charge Prediction Machine: Tool for Inferring Precursor Charge States of Electron Transfer Dissociation Tandem Mass Spectra
     Paulo C. Carvalho, Daniel Cociorva, Catherine C. L. Wong, Maria da Gloria da C. Carvalho, Valmir Carneiro Barbosa, John R. Yates · 2009 · Analytical Chemistry
197. 24-Hour Lock Mass Protection
     Kimberly A. Lee, Chris Farnsworth, Wen Yu, Leo E. Bonilla · 2010 · Journal of Proteome Research
198. Evaluation of Front-End Higher Energy Collision-Induced Dissociation on a Benchtop Dual-Pressure Linear Ion Trap Mass Spectrometer for Shotgun Proteomics
     Michael S. Bereman, Jesse D. Canterbury, Jarrett D. Egertson, Julie A. Horner, Philip M. Remes, Jae C. Schwartz, Vlad Zabrouskov, Michael J. MacCoss · 2011 · Analytical Chemistry
199. Protein synthesis rates of human PBMC and PMN can be determined simultaneously in vivo by using small blood samples
     Stéphane Walrand, Christelle Guillet, Pierre Gachon, Paulette Rousset, Christophe Giraudet, Marie‐Paule Vasson, Yves Boirie‌ · 2004 · American Journal of Physiology-Cell Physiology
200. Dual Desorption Electrospray Ionization−Laser Desorption Ionization Mass Spectrometry on a Common Nanoporous Alumina Platform for Enhanced Shotgun Proteomic Analysis
     Ranu Nayak, Jian Liu, Ashis Kumar Sen, Daniel R. Knapp · 2008 · Analytical Chemistry