mass Protocols

Category: Proteomic Protocols: Silver Staining Protocols

Silver Staining Protocol. Compatible with mass spectrometry, excellent signal-to-noise ratio. Lammond Lab. - [Read Silver Staining Protocol]

Category: Chromatography Protocols: Liquid Chromatography Protocols

Protocol for stable isotope labeling by amino acids in cell culture (SILAC). Protocol describes how to apply SILAC and the use of nano-scale liquid chromatography coupled to electrospray ionization mass spectrometry for protein identification and quantification.  This procedure can be completed in 8 days. - [Read Stable Isotope Labeling by Amino Acids in Cell Culture SILAC Protocol]

Category: Protein Protocols: Protein Precipitation Procols

TCA Acetone precipitation protocol DOC. Matt Shipman. 2006. Adapted and modified from Gruehler et al., 2005. - [Read TCA Acetone precipitation protocol DOC]

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]

Category: Protein Protocols: Protein Extraction From Tissue

Tissue subcellular fractionation and protein extraction for use in mass-spectrometry-based proteomics. Although many methods exist for fractionating proteins, the method described here can capture the majority of subcellular fractions simultaneously at reasonable purity. The scalability of this method makes it amenable to small samples, such as embryonic tissues, in addition to larger tissues. The protocol described is for the general fractionation and extraction of proteins from organs / tissue - [Read Tissue subcellular fractionation and protein extraction for use in mass-spectrometry-based proteomic]

Category: Protein Protocols: Protein Electrophoresis

Tricine–SDS-PAGE Protocol and background. Nature. PDF file. Tricine–SDS-PAGE is commonly used to separate proteins in the mass range 1–100 kDa. It is the preferred electrophoretic system for the resolution of proteins smaller than 30 kDa. –SDS-PAGE is also used preferentially for doubled SDS-PAGE (dSDS-PAGE), a proteomic tool used to isolate extremely hydrophobic proteins for mass spectrometric identification. - [Read Tricine–SDS-PAGE Protocol PDF]

Category: Protein Protocols: Protein Trafficking

Background and methods to study plant transport. Includes new methods to study protein trafficking in plant cells, includes: Identification of protein sorting pathways in non purified samples; Localization of organelle proteins by isotype tagging/isotype-coded affinity tag; Coupling of chemical genomics and proteomics; Top down mass spectrometry; Compartment-specific markers to aid in the purification of organelles. - [Read Understanding Protein Trafficking in Plant Cells Through Proteomics]