# | Title | Journal | Year | Citations |
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1 | Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment | Journal of Proteome Research | 2011 | 4,935 |
2 | Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC−MS/MS) for Large-Scale Protein Analysis: The Yeast Proteome | Journal of Proteome Research | 2003 | 1,557 |
3 | Open Mass Spectrometry Search Algorithm | Journal of Proteome Research | 2004 | 1,350 |
4 | Proteomic Analysis of the Mode of Antibacterial Action of Silver Nanoparticles | Journal of Proteome Research | 2006 | 1,331 |
5 | DTASelect and Contrast: Tools for Assembling and Comparing Protein Identifications from Shotgun Proteomics | Journal of Proteome Research | 2002 | 1,327 |
6 | Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data | Journal of Proteome Research | 2019 | 1,228 |
7 | Chemometrics in Metabonomics | Journal of Proteome Research | 2007 | 1,124 |
8 | Statistical Analysis of Membrane Proteome Expression Changes inSaccharomycescerevisiae | Journal of Proteome Research | 2006 | 1,042 |
9 | GlycoWorkbench: A Tool for the Computer-Assisted Annotation of Mass Spectra of Glycans | Journal of Proteome Research | 2008 | 917 |
10 | Quantitative Metabolome Analysis Using Capillary Electrophoresis Mass Spectrometry | Journal of Proteome Research | 2003 | 912 |
11 | Counting the Zinc-Proteins Encoded in the Human Genome | Journal of Proteome Research | 2006 | 887 |
12 | Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index, and Gender by Implementing a Comprehensive Workflow for Univariate and OPLS Statistical Analyses | Journal of Proteome Research | 2015 | 886 |
13 | Mass Spectrometric Quantitation of Peptides and Proteins Using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA) | Journal of Proteome Research | 2004 | 773 |
14 | Universal and Confident Phosphorylation Site Localization Using phosphoRS | Journal of Proteome Research | 2011 | 732 |
15 | Systems Biology, Proteomics, and the Future of Health Care: Toward Predictive, Preventative, and Personalized Medicine | Journal of Proteome Research | 2004 | 680 |
16 | Open Source System for Analyzing, Validating, and Storing Protein Identification Data | Journal of Proteome Research | 2004 | 667 |
17 | More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MS | Journal of Proteome Research | 2011 | 595 |
18 | Standard Operating Procedures for Serum and Plasma Collection: Early Detection Research Network Consensus Statement Standard Operating Procedure Integration Working Group | Journal of Proteome Research | 2009 | 578 |
19 | Comparative Study of Three Proteomic Quantitative Methods, DIGE, cICAT, and iTRAQ, Using 2D Gel- or LC−MALDI TOF/TOF | Journal of Proteome Research | 2006 | 557 |
20 | Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases | Journal of Proteome Research | 2008 | 551 |
21 | Zinc through the Three Domains of Life | Journal of Proteome Research | 2006 | 544 |
22 | Rapid and Noninvasive Metabonomic Characterization of Inflammatory Bowel Disease | Journal of Proteome Research | 2007 | 539 |
23 | Phase Transfer Surfactant-Aided Trypsin Digestion for Membrane Proteome Analysis | Journal of Proteome Research | 2008 | 536 |
24 | MyriMatch: Highly Accurate Tandem Mass Spectral Peptide Identification by Multivariate Hypergeometric Analysis | Journal of Proteome Research | 2007 | 530 |
25 | Characterization and Comprehensive Proteome Profiling of Exosomes Secreted by Hepatocytes | Journal of Proteome Research | 2008 | 530 |
26 | Functional Anthology of Intrinsic Disorder. 1. Biological Processes and Functions of Proteins with Long Disordered Regions | Journal of Proteome Research | 2007 | 525 |
27 | Isobaric Labeling-Based Relative Quantification in Shotgun Proteomics | Journal of Proteome Research | 2014 | 520 |
28 | Combination of FASP and StageTip-Based Fractionation Allows In-Depth Analysis of the Hippocampal Membrane Proteome | Journal of Proteome Research | 2009 | 507 |
29 | Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography−Tandem Mass Spectrometry | Journal of Proteome Research | 2010 | 505 |
30 | Analytical Strategies in Metabonomics | Journal of Proteome Research | 2007 | 497 |
31 | iTRAQ Underestimation in Simple and Complex Mixtures: “The Good, the Bad and the Ugly” | Journal of Proteome Research | 2009 | 469 |
32 | Within-Day Reproducibility of an HPLC−MS-Based Method for Metabonomic Analysis: Application to Human Urine | Journal of Proteome Research | 2007 | 459 |
33 | A New Strategy for Identification of N-Glycosylated Proteins and Unambiguous Assignment of Their Glycosylation Sites Using HILIC Enrichment and Partial Deglycosylation | Journal of Proteome Research | 2004 | 452 |
34 | Properties of13C-Substituted Arginine in Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) | Journal of Proteome Research | 2003 | 439 |
35 | Cell-Specific Aptamer Probes for Membrane Protein Elucidation in Cancer Cells | Journal of Proteome Research | 2008 | 434 |
36 | Characterization of Molecular Recognition Features, MoRFs, and Their Binding Partners | Journal of Proteome Research | 2007 | 433 |
37 | Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases | Journal of Proteome Research | 2008 | 426 |
38 | High Resolution “Ultra Performance” Liquid Chromatography Coupled to oa-TOF Mass Spectrometry as a Tool for Differential Metabolic Pathway Profiling in Functional Genomic Studies | Journal of Proteome Research | 2005 | 423 |
39 | An Assessment of Software Solutions for the Analysis of Mass Spectrometry Based Quantitative Proteomics Data | Journal of Proteome Research | 2008 | 423 |
40 | Global Analysis of TDP-43 Interacting Proteins Reveals Strong Association with RNA Splicing and Translation Machinery | Journal of Proteome Research | 2010 | 422 |
41 | MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra | Journal of Proteome Research | 2014 | 416 |
42 | Metabolic Profiling of Human Colorectal Cancer Using High-Resolution Magic Angle Spinning Nuclear Magnetic Resonance (HR-MAS NMR) Spectroscopy and Gas Chromatography Mass Spectrometry (GC/MS) | Journal of Proteome Research | 2009 | 414 |
43 | Coomassie Staining as Loading Control in Western Blot Analysis | Journal of Proteome Research | 2011 | 410 |
44 | Accurate and Sensitive Peptide Identification with Mascot Percolator | Journal of Proteome Research | 2009 | 399 |
45 | Quantitative Profiling of Proteins in Complex Mixtures Using Liquid Chromatography and Mass Spectrometry | Journal of Proteome Research | 2002 | 398 |
46 | Value of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics | Journal of Proteome Research | 2010 | 398 |
47 | Human PlasmaN-Glycoproteome Analysis by Immunoaffinity Subtraction, Hydrazide Chemistry, and Mass Spectrometry | Journal of Proteome Research | 2005 | 394 |
48 | Deep-Learning-Based Drug–Target Interaction Prediction | Journal of Proteome Research | 2017 | 381 |
49 | The Proteomes of Human Parotid and Submandibular/Sublingual Gland Salivas Collected as the Ductal Secretions | Journal of Proteome Research | 2008 | 376 |
50 | Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics | Journal of Proteome Research | 2006 | 375 |