Protein Identification by LC-MS/MS (<50 proteins)

Service description

LC MS/MS is an efficient approach either for the exhaustive characterization of a protein sequence or for a general characterization of the proteins in a protein extract or a full proteome. The sample is digested with trypsin and the peptide digests loaded into a capillary chromatography system coupled to the mass spectrometer through a microelectrospray interface (also called nanospray interface). Peptides are separated by reversed phase chromatography using an acetonitrile gradient and directly eluted and ionized into the mass spectrometer. The mass spectrometer perform scan cycles consisting of a full scan from where it determines the mass of the peptide eluting at a given moment, followed by 5-10 consecutive MS/MS scans on the corresponding 5-10 more intense peptide signals detected in the MS scan. The identification of the peptides on the digest and hence of the original protein, is carried out from the MS/MS data using a search engine such as Sequest or Mascot. Note: When the sequence data obtained cannot be matched against the corresponding database (partially annotated species, presence of unexpected modifications), you may want to perform a de novo analysis of the data using PEAKS software.