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1. Full Text MudPIT: Multidimensional protein identification technology
by Delahunty, Claire M and Yates III, John R
BioTechniques, ISSN 0736-6205, 11/2007, Volume 43, Issue 5, pp. 563 - 569
Large-scale biology emerged out of the efforts to sequence genomes of important organisms. Based on resources created by whole genome sequencing, large-scale... 
PEPTIDES | DATABASE | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | C-ELEGANS | MASS-SPECTROMETRY | PROTEOMICS | Protein Engineering - methods | Humans | Mass Spectrometry | Chromatography, Liquid | Proteins - analysis | HeLa Cells | Proteins - isolation & purification | Protein Engineering - trends
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2. Full Text An Automated Multidimensional Protein Identification Technology for Shotgun Proteomics
by Wolters, Dirk A and Washburn, Michael P and Yates, John R
Analytical Chemistry, ISSN 0003-2700, 12/2001, Volume 73, Issue 23, pp. 5683 - 5690
We describe an automated method for shotgun proteomics named multidimensional protein identification technology (MudPIT), which combines multidimensional... 
YEAST | CHEMISTRY, ANALYTICAL | SOLUBILIZATION | PEPTIDES | DATABASE | COMPLEXES | 2-DIMENSIONAL GEL-ELECTROPHORESIS | SEPARATION | TANDEM MASS-SPECTROMETRY | MEMBRANE-PROTEINS | SACCHAROMYCES-CEREVISIAE | Reproducibility of Results | Spectrometry, Mass, Electrospray Ionization | Chromatography, Liquid | Proteins - analysis | Proteome - chemistry | Saccharomyces cerevisiae - chemistry | Autoanalysis | Proteins | Usage | Liquid chromatography | Identification and classification | Mass spectrometry
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3. Full Text Proteomic analysis by multidimensional protein identification technology
by Florens, Laurence and Washburn, Michael P
Methods in molecular biology (Clifton, N.J.), ISSN 1064-3745, 2006, Volume 328, pp. 159 - 175
Multidimensional chromatography coupled to mass spectrometry is an emerging technique for the analysis of complex protein mixtures. One approach in this... 
Computational Biology - methods | Animals | Spectrometry, Mass, Electrospray Ionization | Time Factors | Databases, Protein | Humans | Mass Spectrometry | Chromatography - methods | Proteome | Chromatography, High Pressure Liquid | Proteins - chemistry | Proteomics - methods
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4. Full Text Arabidopsis cell wall proteome defined using multidimensional protein identification technology
by Bayer, Emmanuelle M and Bottrill, Andrew R and Walshaw, John and Vigouroux, Marielle and Naldrett, Mike J and Thomas, Carole L and Maule, Andrew J
PROTEOMICS, ISSN 1615-9853, 01/2006, Volume 6, Issue 1, pp. 301 - 311
With the completion of the sequencing of the Arabidopsis genome and the recent advances in proteomic technology, the identification of proteins from highly... 
Cell wall proteome | Arabidopsis | Multidimensional protein identification technology | cell wall proteome | GLYCOSYLPHOSPHATIDYLINOSITOL-ANCHORED PROTEINS | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | GENOMIC ANALYSIS | MASS-SPECTROMETRY | PREDICTION | FAMILY | THALIANA | ENZYMES | PLANTS | multidimensional protein identification technology | RICE | Proteome | Protein Processing, Post-Translational | Arabidopsis - chemistry | Cell Wall - chemistry | Arabidopsis Proteins - chemistry | Computational Biology
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5. Full Text Proteomic analysis of urine exosomes by multidimensional protein identification technology (MudPIT)
by Wang, Zhen and Hill, Salisha and Luther, James M and Hachey, David L and Schey, Kevin L
PROTEOMICS, ISSN 1615-9853, 01/2012, Volume 12, Issue 2, pp. 329 - 338
Exosomes are membrane vesicles that are secreted by cells upon fusion of multivesicular bodies with the plasma membrane. Exosomal proteomics has emerged as a... 
ESCRT pathway | Animal proteomics | Microvesicles | Exosomes | MECHANISM | VESICLES | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | EXTERNALIZATION | BIOMARKERS | IN-VITRO | TRANSFERRIN RECEPTOR | BIOGENESIS | Biomarkers - urine | Humans | Urine - chemistry | Biomarkers - analysis | Computational Biology | Male | Proteome - analysis | Microscopy, Electron | Proteome - chemistry | Young Adult | Tandem Mass Spectrometry | Databases, Protein | Adult | Female | Endosomal Sorting Complexes Required for Transport - chemistry | Exosomes - chemistry | Proteomics - methods | Biomarkers - chemistry | Exosomes - ultrastructure | Proteins | Urine | Databases | proteomics | Therapeutic applications | biomarkers | exosomes | Plasma membranes | Membrane vesicles | Digestion | microvesicles
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6. Full Text Proteomic Analysis of Human Parotid Gland Exosomes by Multidimensional Protein Identification Technology (MudPIT)
by Gonzalez-Begne, Mireya and Lu, Bingwen and Han, Xuemei and Hagen, Fred K and Hand, Arthur R and Melvin, James E and Yates, John R
Journal of Proteome Research, ISSN 1535-3893, 03/2009, Volume 8, Issue 3, pp. 1304 - 1314
Human ductal saliva contributes over a thousand unique proteins to whole oral fluids. The mechanism by which most of these proteins are secreted by salivary... 
Acinar cells | Parotid saliva | MudPIT | Exosomes | Protein markers | protein markers | GRANULE EXOCYTOSIS | HUMAN SALIVARY PROTEOME | DIPEPTIDYL-PEPTIDASE-IV | GEL ELECTROPHORESIS | URINARY BIOMARKERS | BIOCHEMICAL RESEARCH METHODS | SJOGRENS-SYNDROME | MASS-SPECTROMETRY | EPITHELIAL-CELL EXOSOMES | acinar cells | PLEURAL EFFUSIONS | parotid saliva | ACINAR-CELLS | Exosomes - metabolism | Saliva - metabolism | Humans | Saliva - secretion | Parotid Gland - secretion | Proteome - metabolism | Endosomes - metabolism | Parotid Gland - metabolism
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7. Full Text Large-scale analysis of the yeast proteome by multidimensional protein identification technology
by Wolters, Dirk and Yates, John R and Washburn, Michael P
Nature Biotechnology, ISSN 1087-0156, 03/2001, Volume 19, Issue 3, pp. 242 - 247
We describe a largely unbiased method for rapid and large-scale proteome analysis by multidimensional liquid chromatography, tandem mass spectrometry, and... 
LOW-FEMTOMOLE LEVEL | MEMBRANE H+-ATPASE | MESSENGER-RNA | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | ESCHERICHIA-COLI | GENE-PRODUCTS | 2-DIMENSIONAL GEL-ELECTROPHORESIS | SARCOPLASMIC-RETICULUM | IMMOBILIZED PH GRADIENTS | SACCHAROMYCES-CEREVISIAE | MASS-SPECTROMETRY | Protein Structure, Tertiary | Solubility | Models, Molecular | Proteome | Subcellular Fractions - metabolism | Saccharomyces cerevisiae - chemistry | Databases as Topic | Saccharomyces cerevisiae - metabolism | Fungal Proteins - analysis | Algorithms | Codon | Membrane Proteins - chemistry | Peptide Mapping | Mass Spectrometry | Chromatography, Liquid | Cell Membrane - metabolism | Membrane Proteins - metabolism | Saccharomyces cerevisiae - growth & development | Subcellular Fractions - chemistry
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8. Full Text Multidimensional protein identification technology
by Lohrig, Katharina and Wolters, Dirk
Methods in molecular biology (Clifton, N.J.), ISSN 1064-3745, 2009, Volume 564, pp. 143 - 153
Over the past years, large-scale analysis of proteomes gained increased interest to obtain a fast but nevertheless comprehensive overview about cellular... 
Proteins - metabolism | Proteins - chemistry | Proteomics - methods | Proteins - isolation & purification | Mass Spectrometry - methods | Humans
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9. Full Text Deep interactome profiling of membrane proteins by co-interacting protein identification technology
by Pankow, Sandra and Bamberger, Casimir and Calzolari, Diego and Bamberger, Andreas and Yates, John R
Nature Protocols, ISSN 1754-2189, 12/2016, Volume 11, Issue 12, pp. 2515 - 2528
Affinity purification coupled to mass spectrometry (APAP-MS) is the method of choice for analyzing protein-protein interactions, but common protocols... 
TRANSMEMBRANE CONDUCTANCE REGULATOR | TRANSLOCATION | NETWORK | GENE | BIOCHEMICAL RESEARCH METHODS | CYSTIC-FIBROSIS | PURIFICATION-MASS SPECTROMETRY | PROTEOMIC ANALYSIS | PLASMA-MEMBRANE | CFTR | DRUGGABLE GENOME | Cell Line, Tumor | Protein Interaction Mapping - methods | Membrane Proteins - metabolism | Humans | Mass Spectrometry | Properties | Observations | Interactomes | Protein-protein interactions | Membrane proteins
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10. Full Text A Set of Consensus Mammalian Mediator Subunits Identified by Multidimensional Protein Identification Technology
by Sato, Shigeo and Tomomori-Sato, Chieri and Parmely, Tari J and Florens, Laurence and Zybailov, Boris and Swanson, Selene K and Banks, Charles A.S and Jin, Jingji and Cai, Yong and Washburn, Michael P and Conaway, Ronald C and Conaway, Joan Weliky
Molecular Cell, ISSN 1097-2765, 2004, Volume 14, Issue 5, pp. 685 - 691
The Mediator is a multiprotein transcriptional coactivator that is expressed ubiquitously in eukaryotes from yeast to mammals and is required for induction of... 
RNA-POLYMERASE-II | YEAST | PATHWAYS | CELLS | TRANSCRIPTIONAL ACTIVATION | COACTIVATOR | DEPENDENT TRANSCRIPTION | NUCLEAR RECEPTORS | BIOCHEMISTRY & MOLECULAR BIOLOGY | HOMOLOGS | COFACTOR COMPLEX CRSP | CELL BIOLOGY | Cyclin-Dependent Kinases - metabolism | Nuclear Proteins - analysis | Transcription Factors - chemistry | Humans | Multiprotein Complexes | Protein Subunits - analysis | Trans-Activators - analysis | RNA Polymerase II - metabolism | Trans-Activators - chemistry | Trans-Activators - genetics | Carrier Proteins - chemistry | Mediator Complex | Proteomics - methods | Carrier Proteins - analysis | Cyclin-Dependent Kinases - genetics | Nuclear Proteins - genetics | Protein Subunits - genetics | Drosophila Proteins - chemistry | Saccharomyces cerevisiae Proteins - genetics | Transcription Factors - genetics | Drosophila Proteins - analysis | Nuclear Proteins - chemistry | Macromolecular Substances | Carrier Proteins - genetics | Adaptor Proteins, Signal Transducing | Carrier Proteins - metabolism | RNA Polymerase II - genetics | Protein Subunits - chemistry | Transcription Factors - analysis | Drosophila Proteins - genetics | HeLa Cells | Saccharomyces cerevisiae Proteins - analysis | Saccharomyces cerevisiae Proteins - chemistry
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11. Full Text Analysis of Quantitative Proteomic Data Generated via Multidimensional Protein Identification Technology
by Washburn, Michael P and Ulaszek, Ryan and Deciu, Cosmin and Schieltz, David M and Yates, John R
Analytical Chemistry, ISSN 0003-2700, 04/2002, Volume 74, Issue 7, pp. 1650 - 1657
We describe the analysis of quantitative proteomic samples via multidimensional protein identification technology (MudPIT). Ratio amounts of the soluble... 
CHEMISTRY, ANALYTICAL | PEPTIDES | EXPRESSION | MASS-SPECTROMETRY | Peptide Fragments - analysis | Spectrometry, Mass, Electrospray Ionization | Proteins - analysis | Statistics as Topic | Chromatography, High Pressure Liquid | Proteome - analysis | Nitrogen Isotopes | Proteome - metabolism | Saccharomyces cerevisiae - chemistry | Proteins | Peptides | Time-of-flight mass spectrometry | Analysis | Chromatography | Methods
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12. Full Text Multidimensional Protein Identification Technology (MudPIT) Analysis of Ubiquitinated Proteins in Plants
by Rudy Maor and Alex Jones and Thomas S. Nühse and David J. Studholme and Scott C. Peck and Ken Shirasu
Molecular & Cellular Proteomics, ISSN 1535-9476, 04/2007, Volume 6, Issue 4, pp. 601 - 610
Protein conjugation with ubiquitin, known as ubiquitination, is a key regulatory mechanism to control protein abundance, localization, and activity in... 
PROTEASOME PROTEOLYTIC PATHWAY | IN-VIVO | BIOCHEMICAL RESEARCH METHODS | UBIQUITYLATION | DEGRADATION | ARABIDOPSIS | BOX PROTEINS | BINDING | LARGE-SCALE ANALYSIS | DISEASE RESISTANCE | AUXIN RECEPTOR | Plant Proteins - isolation & purification | Protein Structure, Tertiary | Amino Acid Sequence | Recombinant Fusion Proteins - isolation & purification | Arabidopsis Proteins - genetics | Cells, Cultured | Ubiquitin - metabolism | Molecular Sequence Data | Binding Sites - genetics | Recombinant Fusion Proteins - metabolism | Arabidopsis - metabolism | Arabidopsis - genetics | Arabidopsis Proteins - isolation & purification | Arabidopsis Proteins - metabolism | Plant Proteins - genetics | Chromatography, Affinity | Base Sequence | Recombinant Fusion Proteins - genetics | Plant Proteins - metabolism | Proteomics - methods | DNA, Plant - genetics
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13. Full Text Automated Ultra-High-Pressure Multidimensional Protein Identification Technology (UHP-MudPIT) for Improved Peptide Identification of Proteomic Samples
by Motoyama, Akira and Venable, John D and Ruse, Cristian I and Yates, John R
Analytical Chemistry, ISSN 0003-2700, 07/2006, Volume 78, Issue 14, pp. 5109 - 5118
Multidimensional separation is one of the most successful approaches for proteomics studies that deal with complex samples. We have developed an automated... 
PERFORMANCE LIQUID-CHROMATOGRAPHY | CHEMISTRY, ANALYTICAL | PHASE | PEAK-CAPACITY | GRADIENT ELUTION | COLUMN | SEPARATION | TANDEM MASS-SPECTROMETRY | HUMAN PLASMA PROTEOME | YEAST PROTEOME | IONIZATION | Amino Acid Sequence | Peptides - chemistry | Proteomics - instrumentation | Molecular Sequence Data | Proteins - chemistry | Proteomics - methods | Pressure | Proteins | Liquid chromatography | Structure | Properties | Analysis | Proteomics
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14. Full Text Large Scale Protein Profiling by Combination of Protein Fractionation and Multidimensional Protein Identification Technology (MudPIT)
by Emily I. Chen and Johannes Hewel and Brunhilde Felding-Habermann and John R. Yates III
Molecular & Cellular Proteomics, ISSN 1535-9476, 01/2006, Volume 5, Issue 1, pp. 53 - 56
In the past decade, shotgun proteomic analysis has been utilized extensively to answer complex biological questions. New challenges arise in large scale... 
MASS-SPECTROMETRY | PEPTIDES | BIOCHEMICAL RESEARCH METHODS | Breast Neoplasms - secondary | Chromatography, Ion Exchange | Biomarkers, Tumor - analysis | Humans | Isoelectric Focusing | Proteomics - instrumentation | Electrophoresis, Gel, Two-Dimensional | Chromatography, High Pressure Liquid | Biomarkers, Tumor - isolation & purification | Sequence Analysis, Protein | Breast Neoplasms - chemistry | Neoplasm Proteins - isolation & purification | Female | Neoplasm Proteins - analysis | Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization | Proteomics - methods | Tumor Cells, Cultured
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