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Characterization of Protein Glycosylation Using Chip-Based Nanoelectrospray with Precursor Ion Scann - http://jbt.abrf.org/cgi/content/full/16/3/209

Category: Molecular Biology Protocols: Carbohydrate Protocols

Characterization of Protein Glycosylation Using Chip-Based Nanoelectrospray with Precursor Ion Scanning Quadrupole Linear Ion Trap Mass Spectrometry. Sheng Zhang1 and Brian L. Williamson. Journal of Biomolecular Techniques, 16:209-219 2005. - [Read Characterization of Protein Glycosylation Using Chip-Based Nanoelectrospray with Precursor Ion Scann]

Coomasie and SYPRO Destaining Method - http://www.cbs.umn.edu/msp/protocols/destaining.shtml

Category: Proteomic Protocols

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

Determination of Neopterin and Biopterin by Liquid Chromatography Protocol - http://www.natureprotocols.com/2006/10/13/determination_of_neopterin_and.php

Category: Chromatography Protocols: Liquid Chromatography Protocols

Protocol for determination of neopterin and biopterin by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) in rat and human plasma, cell extracts and tissue homogenates. - [Read Determination of Neopterin and Biopterin by Liquid Chromatography Protocol]

In-Gel Digestion of Proteins Separated by Polyacrylamide Gel Electrophoresis - http://web.archive.org/web/20010906052645/http://www.pharma.ethz.ch/bmm/protocols/ingeldig.html

Category: Proteomic Protocols: 2-D Gel Electrophoresis

In gel trypsin digestion for Mass spectrometry. (According to EMBL Protein and Peptide Group, 1997) - [Read In-Gel Digestion of Proteins Separated by Polyacrylamide Gel Electrophoresis]

In-gel digestion of proteins to be analyzed by mass spectrometry - http://www.narrador.embl-heidelberg.de/GroupPages/PageLink/activities/protocols/ingeldigest.html

Category: Proteomic Protocols

In-Gel Digestion Protocol. Excision of protein bands (spots) from polyacrylamide gels Reduction and alkylation . Reduction and alkylation . MALDI analysis of the supernatant after in-gel digestion. Extraction of Peptides.Matthias Wilm EMBL Bioanalytical R - [Read In-gel digestion of proteins to be analyzed by mass spectrometry]

Mass spectrometry analysis and identification of proteins - http://www.healthsystem.virginia.edu/internet/biomolec/mass_spectrometry.cfm

Category: Mass Spectrometry Protocols

Protein sequencing by mass spectrometry. Mass analysis of peptides and proteins. Identification of modifications in proteins. Good information.Univ. Virginia. Dr. Nicholas Sherman - [Read Mass spectrometry analysis and identification of proteins]

Mass spectrometry compatible silver staining of gels protocol - http://www.narrador.embl-heidelberg.de/GroupPages/PageLink/activities/protocols/silverstain.html

Category: Mass Spectrometry Protocols

Mass spectrometry compatible silver staining of gels protocol. EMBL Bioanalytical Research Group. Wilm. - [Read Mass spectrometry compatible silver staining of gels protocol]

Millipore ZipTip detailed protocol. MSCLS - http://www.cbs.umn.edu/msp/protocols/ziptip.shtml

Category: Proteomic Protocols

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

Monosaccharide Composition Analysis: Alditol Acetates Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4246

Category: Chromatography Protocols: Gas Chromatography Protocols

Protocol describes how to determine the monosaccharide composition of glycans, glycoproteins, or proteoglycans by hydrolyzing the sample to monosaccharides and converting them to alditols, then performing acetylation to make them volatile compounds and analysis by gas chromatography (GC) or gas chromatography coupled with mass spectrometry (GC-MS). - [Read Monosaccharide Composition Analysis: Alditol Acetates Protocol]

Overview of Affinity Purification in Combination with Mass Spectrometry Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/30/pdb.top3

Category: Chromatography Protocols: Affinity Chromatography Protocols

Protein complexes can be isolated by several different approaches. For example, a protein can be tagged with an epitope such as Flag or TAP and then overexpressed in a target cell, allowing the interacting proteins to be purified. Similarly, epitope tags can be homologously recombined into the endogenous locus ("knocked-in"), allowing protein complexes containing the tagged proteins to be isolated at their natural expression level. - [Read Overview of Affinity Purification in Combination with Mass Spectrometry Protocol]

Preparation and Enrichment of Phosphopeptides from Phosphotyrosine Protocol - http://www.signaling-gateway.org/data/cgi-bin/ProtocolFile.cgi/afcs_PP00000193.pdf?pid=PP00000193

Category: Chromatography Protocols: Immobilized Metal Ion Affinity Chromatography Protocols

Protocol is specifically for the further enrichment of phosphopeptides from a phosphotyrosine pull-down. This is the final step for the preparation and enrichment of phosphopeptides using immobilized metal affinity chromatography (IMAC) for the identification of the phosphopeptides by liquid chromatography tandem mass spectrometry (LC-MS/MS). - [Read Preparation and Enrichment of Phosphopeptides from Phosphotyrosine Protocol]

Protein microarray technology and ultraviolet crosslinking combined - http://www.molgen.mpg.de/~functional_protein_analysis/15265736.pdf

Category: Protein Microarray Protocols

Protein microarray technology and ultraviolet crosslinking combined with mass spectrometry for the analysis of proteinâ€“DNA interactions. Gobom. - [Read Protein microarray technology and ultraviolet crosslinking combined]

Protocols for Mass Spectrometry Analysis Preparation - http://www.st-andrews.ac.uk/~bmsmspf/protocols.htm#manual

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]

Silver Staining of Gels for Mass Spectrometry - http://www.healthsystem.virginia.edu/internet/biomolec/Silverstains.cfm

Category: Mass Spectrometry Protocols

Silver Staining of Gels for Mass Spectrometry. Desiderio procedure: R.R. Becklin. Univ. Virginia. - [Read Silver Staining of Gels for Mass Spectrometry]

Silver Staining Protocol - http://www.lamondlab.com/pdf/silver_staining.pdf

Category: Proteomic Protocols: Silver Staining Protocols

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

Stable Isotope Labeling by Amino Acids in Cell Culture SILAC Protocol - http://www.natureprotocols.com/2007/01/11/a_practical_recipe_for_stable.php

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]

The Use of Mass Spectrometry in Proteomics: Database Searching - http://www.cshprotocols.org/cgi/content/extract/2006/27/pdb.ip5

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]

Tips for Sample Preparation for MALDI mass spectrometry - http://www.cfgbiotech.com/proteomics/sample_prep.htm

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]

Tissue subcellular fractionation and protein extraction for use in mass-spectrometry-based proteomic - http://www.nature.com/nprot/journal/v1/n4/abs/nprot.2006.273.html

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]

Understanding Protein Trafficking in Plant Cells Through Proteomics - http://www.cepceb.ucr.edu/resources/pdf/pan/ERP-review2_781_2005.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]