ID Numbers for Cross Referencing : Volume 3 Proteomics This list will help you include cross references to other articles in GGPB. Find the article that you wish to cross refer to, note its corresponding unique ID number e.g (g203206) and then insert that unique ID number into your text. Please do not insert the article title, just its unique ID number. This makes your work easier (less typing) and it gives us a unique identifier to ensure that accurate and unambiguous cross-referencing is obtained. Thank you for using the unique ID numbers. Please remember you can cross reference to articles outside the section in which your article appears. 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