ID Numbers for Cross Referencing : Volume 3 Proteomics
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Core Methodologies
Expression Proteomics
Interaction Proteomics
Functional Proteomics
Proteome Diversity
Proteome Families
Structural Proteomics
Systems Biology
Section 1 Core Methodologies
ID Title
g301121 Core methodologies
g301203 FT-ICR
g301204 Tandem mass spectrometry database searching
g301209 Interpreting tandem mass spectra of peptides
g301212 Sample preparation for proteomics
g301220 Laser-based microdissection approaches and applications
g301301 Hybrid MS
g301302 Time-of-flight mass spectrometry
g301306 Protein fingerprinting
g301311 Nano-MALDI and Nano-ESI MS
g301314 Quadrupole ion traps and a new era of evolution
g301317 Multidimensional liquid chromatography tandem mass spectrometry for biological discovery
g301319 Quadrupole mass analyzers: Theoretical and practical considerations
g301405 Tutorial on tandem mass spectrometry database searching
g301410 Sample preparation for MALDI and electrospray
g301413 Improvement of sequence coverage in peptide mass fingerprinting
g301415 Handling membrane proteins
g301416 Techniques for ion dissociation (fragmentation) and scanning in MS/MS
g301418 Making nanocolumns and tips
Section 2 Expression Proteomics
ID Title
g302108 Separation-dependent approaches for protein expression profiling
g302110 Separation-independent approaches for protein expression profiling
g302201 ICAT and other labeling strategies for semiquantitative LC-based expression profiling
g302203 Protein arrays
g302207 Two-dimensional gel electrophoresis
g302305 Image analysis
g302312 2D DIGE
g302313 Detecting protein posttranslational modifications using small molecule probes and multiwavelength imaging devices
g302315 Real-time measurements of protein dynamics
g302402 Arraying proteins and antibodies
g302404 2-D Difference Gel Electrophoresis---an accurate quantitative method for protein analysis
g302406 Two-dimensional gel electrophoresis (2-DE)
g302409 MS-based methods for identification of 2-DE-resolved proteins
g302414 Basic techniques for the use of reverse phase protein microarrays for signal pathway profiling
Section 3 Interaction Proteomics
ID Title
g303111 Structural biology of protein complexes
g303113 Protein interactions in cellular signaling
g303204 The yeast interactome
g303206 Biochemistry of protein complexes
g303210 The C. elegans interactome project
g303216 Inferring gene function and biochemical networks from protein interactions
g303303 Human signaling pathways analyzed by protein interaction mapping
g303305 Protein interaction databases
g303307 Membrane-anchored protein complexes
g303308 Investigating protein--protein interactions in multisubunit proteins: the case of eukaryotic RNA polymerases
g303309 Computational methods for the prediction of protein interaction partners
g303314 Functional classification of proteins based on protein interaction data
g303315 Energy transfer-based approaches to study G protein-coupled receptor dimerization and activation
g303417 Basic techniques: Bioluminescence resonance energy transfer
Section 4 Functional Proteomics
ID Title
g304110 Probing cellular function with bioluminescence imaging
g304203 Small molecule fluorescent probes for protein labeling and their application to cell-based imaging (including FlAsH etc.)
g304206 Using photoactivatable GFPs to study protein dynamics and function
g304215 FRET-based reporters for intracellular enzyme activity
g304301 Photobleaching (FRAP/FLIP) and dynamic imaging
g304302 Quantum dots for multiparameter measurements
g304305 Probing protein function in cells using CALI
g304311 Elucidating protein dynamics and function using fluorescence correlation spectroscopy (FCS)
g304314 High content screening
g304316 Imaging protein function using fluorescence lifetime imaging microscopy (FLIM)
g304407 siRNA approaches in cell biology
g304412 Immunofluorescent labeling and fluorescent dyes
g304413 Quantitative image analysis and the Open Microscopy Environment
Section 5 Proteome Diversity
ID Title
g305104 Posttranslational modification of proteins
g305106 Glycosylation
g305205 Structure/function of O-glycans
g305207 Structure/function of N-glycans
g305209 GPI anchors
g305210 Protein phosphorylation analysis by mass spectrometry
g305301 Glycosylation in bacteria: that, what, how, why, now what?
g305303 O-glycan processing
g305308 O-Mannosylation
g305313 O-linked N-acetylglucosamine (O-GlcNAc)
g305318 Posttranslational cleavage of cell-surface receptors
g305319 S-nitrosylation and thiolation
g305411 Protein phosphorylation analysis---a primer
g305414 Mass spectrometry
g305415 Glycoproteomics
g305416 Glycosylphosphatidylinositol anchors---a structural perspective
g305417 Analysis of N- and O-linked glycans of glycoproteins
Section 6 Proteome Families  
ID Title
g306109 Classification of proteins into families
g306204 Metalloproteins
g306214 Structure comparison and protein structure classifications
g306216 Peptidases, families, and clans
g306217 Transporter protein families
g306301 The PRINTS protein fingerprint database: functional and evolutionary applications
g306302 The PIR SuperFamily (PIRSF) classification system
g306303 Pfam: The protein families database
g306305 Equivalog protein families in the TIGRFAMs database
g306307 COGs: an evolutionary classification of genes and proteins from sequenced genomes
g306310 InterPro
g306313 The CATH domain structure database
g306318 Functionally and structurally relevant residues in PROSITE motif descriptors
g306406 Classification of proteins by sequence signatures
g306408 Classification of proteins by clustering techniques
g306411 Getting the most out of protein family classification resources
Section 7 Structural Proteomics
ID Title
g307102 History and future of X-ray structure determination
g307110 What use is a protein structure?
g307204 Target selection for structural genomics
g307213 Structural genomics---expanding protein structural universe
g307214 Fundamentals of protein structure and function
g307301 Large complexes by X-ray methods
g307305 New approaches to bridging the timescale gap in the computer simulation of biomolecular processes
g307311 Large complexes and molecular machines by electron microscopy
g307312 Modeling membrane protein structures
g307317 The importance of protein structural dynamics and the contribution of NMR spectroscopy
g307403 X-ray crystallography
g307415 NMR
g307416 Electron microscopy as a tool for 3D structure determination in molecular structural biology
Section 8 Systems Biology
ID Title
g308104 Integrative approaches to biology in the twenty-first century
g308202 Functional inference from probabilistic protein interaction networks
g308203 Constraint-based modeling of metabolomic systems
g308205 Reverse engineering gene regulatory networks
g308206 Metabolic dynamics in cells viewed as multi-layered, distributed, mass-energy-information networks
g308208 A complex systems approach to understand how cells control their shape and make cell fate decisions
g308209 Functional networks in mammalian cells
g308211 Systems biology of the heart
g308212 Analyzing and reconstructing gene regulatory networks
g308213 Integrative modeling of the pancreatic β-cell
g308314 EGFR network
g308407 Data collection and analysis in systems biology