proteomics Protocols

Category: Proteomic Protocols: 2-D Gel Electrophoresis

A detailed protocol for 2-D Polyacrylamide Gel Electrophoresis using Prostate Tissue. Molecular Profiling Initiative. - [Read 2-D Polyacrylamide Gel Electrophoresis (Prostate Tissue)]

Category: Primary Cell Isolation and Culture Protocols: Laser Capture Microdissection Protocols

Protocol for 2-D polyacrylamide gel electrophoresis. Includes: 50 ml IEF Lysis Buffer; 10X Electrophoresis Running Buffer (10 L); 30% Acrylamide Stock (1 liter); Separating Acrylamide Gel; 50 ml Equilibration Buffer I; 50 ml Equilibration Buffer II; Transfer Buffer; Sample Preparation; Tissue Processing; Reswelling; Prepare Gradient Acrylamide Gel (9-18%); Transfer and Sequencing of Proteins. - [Read 2-D Polyacrylamide Gel Electrophoresis Protocol]

Category: Protein Protocols: Protein Phosphorylation Protocols

A Strategy for the Rapid Identification of Phosphorylation Sites in the Phosphoproteome. MacDonald et al., Molecular & Cellular Proteomics. 2002. - [Read A Strategy for the Rapid Identification of]

Category: Antibody Microarray Protocols

Antibody Microarrays Are a Powerful Tool for Proteomics. Genomics and Proteomics - [Read Antibody Microarrays Are a Powerful Tool for Proteomics]

Category: Plant Biology Protocols: Plant Proteins, Peptides and Antigens

BN-PAGE has become the method of choice for the investigation of the respiratory protein complexes of the electron transfer chains of a range of organisms. It allows the separation in two dimensions of extremely hydrophobic protein sets for analysis and also provides information on their native interactions. In this review we discuss the capabilities of BN-PAGE in proteomics and the wider investigation of protein:protein interactions with a focus on its use and potential in plant science. - [Read Blue-Native PAGE in Plants: A Tool in Analysis of Protein-Protein Interactions]

Category: Protein Protocols: Co-immunoprecipitation

Co-Immunoprecipitation Theory and Tips. Pierce. Evaluating a Co-IP Captured Interaction - [Read Co-Immunoprecipitation Theory and Tips]

Category: Proteomic Protocols

Coomasie and SYPRO Destaining Method Protocol. MSCLS Center for Mass Spectrometry and Proteomics - [Read Coomasie and SYPRO Destaining Method]

Category: Protein Staining Protocols

Protocol for coomassie blue staining. - [Read Coomassie Blue Staining Protocol]

Category: Primary Cell Isolation and Culture Protocols: Laser Capture Microdissection Protocols

Protocol for Immunoblot. Includes: Staining and Laser Capture Microdissection; Protein Separation by Polyacrylamide Gel Electrophoresis; Electrophoretic Transfer To a Membrane (Nylon, PVDF or Nitrocellulose); Primary and Secondary Antibody Incubations; Visualization. - [Read Immunoblot Protocol]

Category: Proteomic Protocols

In Gel Digestion Protocols for Silver Stained and Coomassie Stained Gels. (EMBL protocol). - [Read In Gel Digestion Protocols for Silver Stained and Coomassie Stained Gels]

Category: Mass Spectrometry Protocols

Peptide Mapping Analysis Techniques. Dr.Aebersold, Vrije Universiteit Amsterdam - [Read In-gel digestion of proteins for peptide fingerprint mapping]

Category: DNA Protocols: EMSA DNA-Protein Protocols

A non-radioactive electrophoretic mobility which works quite well using biotin and streptavidin detection. Non-specific and specific competititor, oligo labeling, Binding Reaction. Pierce - [Read Introduction to the EMSA (Gel Shift) Technique]

Category: Proteomic Protocols

ZipTip Protocol detailed protocol. MSCLS Center for Mass Spectrometry and Proteomics - [Read Millipore ZipTip detailed protocol. MSCLS]

Category: Plant Biology Protocols: Arabidopsis Tissue Culture

Protocol for the evaluation of cell wall preparations for proteomics: a new procedure for purifying cell walls from Arabidopsis hypocotyls. - [Read Procedure for Purifying Cell Walls from Arabidopsis Hypocotyls]

Category: Primary Cell Isolation and Culture Protocols: Laser Capture Microdissection Protocols

The methodology and buffers utilized for processing microdissected samples for protein-based studies is variable depending on the downstream molecular analysis method. - [Read Processing of Microdissected Tissue for Molecular Analysis Proteomics-based Studies]

Category: Protein Protocols: Protein Extraction From Tissue

Protein extraction from whole tissues for isoelectric focusing. University of Missouri - Columbia Proteomics Center. SDS extraction followed by acetone precipitation. Also has Phenol extraction followed by methanolic ammonium acetate precipitation. - [Read Protein extraction from whole tissues for isoelectric focusing]

Category: Primary Cell Isolation and Culture Protocols

Protocols for protein staining. Includes: Coomassie Blue Staining; Silver Nitrate Staining; Zinc Imidazole Negative Staining. - [Read Protein Staining Protocols]

Category: Proteomic Protocols

Proteomic Protocols for Sample Submission to Mass Spec. Gel Staining, In gel trypsin digestion, Coomassie Blue staining and TCA precipitation. CFG U. Albany. - [Read Proteomic Protocols for Sample Submission to Mass Spec]

Category: Peptide Protocols

Protocol for Manual Peptide Synthesis. Resin Swelling And Coupling Of Activated Amino Acid Esters. Deblocking and cleaving peptide from solid support. Synthesis of Peptides. The University of Nebraska-Lincoln Protein Core Facility - [Read Protocol for Manual Peptide Synthesis]

Category: Protein Protocols: Protein Extraction Protocols

Protocol for Protein Extraction Using Proteomics. Extraction of proteins from plant cells that are rich in compounds that interfere with the 2-Dimensional electrophoretic separation methods such as salts, organic acids, phenolics, pigments, terpenes, among others. A common protocol used in our lab for extraction proteins from plant tissues consists in the homogenization of mortar-grounded material in liquid nitrogen with an extraction buffer. - [Read Protocol for Protein Extraction Using Proteomics]

Category: Mass Spectrometry Protocols

Protocols for Mass Spectrometry Analysis Preparation. Preparing gel slices for PMF or MS/MS , mass spec data interpretation, Submitting proteins in solution, Interpretation of LC-MS/MS data. BMS MASS SPECTROMETRY AND PROTEOMICS FACILITY - [Read Protocols for Mass Spectrometry Analysis Preparation]

Category: Cell Biology and Cell Culture: Apoptosis Protocols

Quantitative Flow Cytometry for Apoptosis Detection. Flow Cytometry Facility, U.Illinois. - [Read Quantitative Flow Cytometry for Apoptosis]

Category: Protein Staining Protocols

Protocol for silver nitrate staining. - [Read Silver Nitrate Staining Protocol]

Category: Bioinformatics

Searches are not constrained for only tryptic peptides, and indexed databases (databases only containing tryptic peptides) are not used. In cases where there are very complex mixtures, such as cell lysates, nonspecific cleavages can occur. Therefore, nontryptic peptides would be missed in the database search. - [Read The Use of Mass Spectrometry in Proteomics: Database Searching]

Category: Mass Spectrometry Protocols

Tips for Sample Preparation for MALDI mass spectrometry. Sample quantity, Solvent, Protein/Peptide sample handling. U. Albany. CFG - [Read Tips for Sample Preparation for MALDI mass spectrometry]