MASS SPECTROMETRY IN PROTEOMICS
I INTRODUCTION TO PART I INSTRUMENTATION AND DEVELOPMENTS INTRODUCTION / IONIZATION TECHNIQUES FOR MACROMOLECULES / 252CF PLASMA DESORPTION IONIZATION / FAST ATOM/ION BOMBARDMENT / TYPE OF FRAGMENT IONS AND NOMENCLATURE / EXAMPLES ON ANALYTICAL SOLUTIONS BASED ON FAB–MS / DETECTION OF ABNORMALITIES IN HEMOGLOBIN / GLYCOPROTEIN STRUCTURE DETERMINATION / EARLY SCANNING FUNCTIONS ON SECTOR MACHINES / ELECTROSPRAY IONIZATION / MATRIX-ASSISTED LASER DESORPTION IONIZATION / MALDI AT HIGH PRESSURE / DESORPTION IONIZATION ON SILICON (DIOS) / DELAYED EXTRACTION / ION DETECTION / MICROCHANNEL PLATES (MCPS) / CRYOGENIC DETECTORS / SUPERCONDUCTING TUNNEL JUNCTION / THERMAL DETECTORS / TYPES OF ANALYZERS / QUADRUPOLE MASS FILTER / THREE-DIMENSIONAL QUADRUPOLE ION TRAP / LINEAR ION TRAP / TIME OF FLIGHT / FOURIER TRANSFORM ION CYCLOTRON RESONANCE / HYBRID ANALYZERS / QUADRUPOLE TIME OF FLIGHT / ION MOBILITY–TOF / LINEAR ION TRAP–FT–ICR / ION TRAP–TOF / TANDEM MASS SPECTROMETRY / POSTSOURCE DECAY / MS–MS MEASUREMENTS / COLLISIONAL ACTIVATION / 110 CURRENT MS INSTRUMENTATION IN PROTEOME ANALYSES / 1101 MALDI–TOF / 1102 MALDI–TOF–TOF / 1103 FT–ICR–MS / 1104 ION MOBILITY–MS / 111 CURRENT MS-BASED PROTEOMICS / 1111 DELIVERING PEPTIDES TO ION SOURCE / 1112 PEPTIDE SEQUENCING AND DATABASE SEARCHING / 1113 PEPTIDE MASS FINGERPRINTING / 1114 SEARCHING WITH MS–MS DATA / 1115 DATABASES FOR MS DATA SEARCH / 112 RECENT ACHIEVEMENTS AND FUTURE CHALLENGES / 1121 CURRENT APPLICATIONS / 1122 SIGNAL TRANSDUCTION PATHWAYS / 113 CONCLUDING REMARKS / REFERENCES / PROTEOMICS IN CANCER RESEARCH TWO-DIMENSIONAL GEL ELECTROPHORESIS / SURFACE-ENHANCED LASER DESORPTION IONIZATION / PROTEIN MICROARRAYS / GETTING MORE THAN JUST SIMPLE CHANGE IN PROTEIN EXPRESSION / LASER CAPTURE MICRODISSECTION / PANCREATIC DUCTAL ADENOCARCINOMA / ANALYSES BASED ON CHIP TECHNOLOGY / SELDI ANALYSIS OF PANCREATIC DUCTAL ADENOCARCINOMA / PROTEIN PRO?LING FOLLOWING TREATMENT WITH DNA METHYLATION/HISTONE DEACETYLATION INHIBITORS / PROTEOMIC PRO?LING OF PDAC FOLLOWING TREATMENT WITH TRICHOSTATIN A / PROTEOMIC PRO?LING OF PDAC FOLLOWING TREATMENT WITH 5?-AZA-2?-DEOXYCYTIDINE / PROTEOMIC ANALYSIS OF HUMAN BREAST CARCINOMA / TWO-DE ANALYSIS IN BREAST CANCER / PROTEOMIC PRO?LING OF BREAST CANCER CELL MEMBRANES / PROTEOMIC ANALYSIS ON SELECTED TISSUE SAMPLES / PROTEOMIC PRO?LING OF CHEMORESISTANT CANCER CELLS / PROTEIN ALTERATIONS IN PANCREAS CARCINOMA CELLS EXPOSED TO ANTICANCER DRUG / PROTEOMIC PRO?LING OF CERVIX SQUAMOUS CELL CARCINOMA TREATED WITH CISPLATIN / SIGNAL PATHWAY PRO?LING OF PROSTATE CANCER / EMERGING ROLE OF FUNCTIONAL AND ACTIVITY-BASED PROTEOMICS IN DISEASE UNDERSTANDING / ACTIVITY-BASED PROTEIN PRO?LING / PROBING PROTEIN FUNCTIONS USING CHROMOPHORE-ASSISTED LASER INACTIVATION / ROLE OF PROTEIN–TYROSINE KINASES / 210 CONCLUDING REMARKS AND FUTURE PROSPECTS / CURRENT STRATEGIES FOR PROTEIN QUANTIFICATION STRATEGIES BASED ON LABELING A SPECI?C AMINO ACID RESIDUE / ISOTOPE-CODED AF?NITY TAGS / TWO-DIMENSIONAL GEL ELECTROPHORESIS/MALDI–TOF–MS / LABELING LYSINE RESIDUES / LABELING TRYPTOPHAN RESIDUES / METHIONINE-CONTAINING PEPTIDES / GLOBAL INTERNAL STANDARD TECHNOLOGY / ACYLATION / ESTERI?CATION / INCORPORATION OF HEAVY ISOTOPES / DIFFERENTIAL IN-GEL ELECTROPHORESIS / QUANTI?CATION OF MODI?ED PROTEINS / DETECTION AND QUANTI?CATION OF PHOSPHORYLATED PROTEINS / DETECTION AND QUANTI?CATION OF GLYCOSYLATED PROTEINS / UBIQUITINATION / COMMENTS AND CONSIDERATIONS / METHOD OF SEPARATION / DETECTION / OTHER APPROACHES / IMAGING MASS SPECTROMETRY / MICROARRAYS IN PROTEIN QUANTI?CATION / PROTEIN RECOGNITION MOLECULES / SURFACE CHEMISTRY / SOME APPLICATIONS / EMERGING ROLE OF MICRO?UIDIC DEVICES / SAMPLE PREPARATION AND SAMPLE DELIVERY / CONCLUDING REMARKS /