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 To use the CNRU Mass Spectrometry Core Facility for your research you must first get started.
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MASS SPECTROMETRY ANALYSESAt the CNRU Mass Spectrometry Facility we have a variety of mass spectrometry systems. Below are general guidelines for selecting a mass analyzer to suit an application. These are guidelines only and we often use more than one analytical platform to ensure we obtain comprehensive information about your sample.
The proteomics workflow primarily relies on the ability of mass spectrometers such as ion traps to fragment peptides by collisionally-induced dissociation, the known dominant peptide fragmentation pathways, and comprehensive protein and nucleotide databases to identify proteins in a complex mixture. Protein identification using mass spectrometry can include: 
Identifying a single protein band from a gel
Identifying proteins co-precipitating with a protein of interest
Identifying all proteins in a cell that show quantitative changes when compared with another cellular state.
We can either try to identify the intact protein or, more typical, use an enzyme such as trypsin to cleave the protein into smaller peptides. The benefits of generating the peptides are that their mass-to-charge ratio is within the measurement range of most mass spectrometers and they fragment more easily and completely than proteins do. After fragmenting the peptide ions in an ion trap mass analyzer, we use Spectrum Mill and Mascot, two database searching algorithms, to deduce the peptide sequence from the fragmentation pattern. Peptide sequences are then linked to protein sequences to provide a protein identification. The CNRU Mass Spectrometry Core Facility offers protein identification services employing peptide fragmentation, typically using our LC/MS/MS nanoflow system or our new HPLC-Chip. We also have available an AP-MALDI source interfaced with an ion trap for fragmentation of MALDI-generated peptides. In addition, we have a MALDI-TOF for rapid screening of peptide digests, usually from large 2D gel projects. Please follow the links for: In gel digestion protocol In solution digestion protocol Description of LC and nanoLC Description of MALDI and AP-MALDI Tutorial on peptide fragmentation Understanding Spectrum Mill results |
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