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An important part of proteomics is to study changes in protein levels between samples from different cells or tissues where ideally all proteins present in the sample are monitored. There are two main methods that allow for both global scanning for significantly varying proteins, and targeted profiling of proteins of interest. One is based on 2D gel electrophoresis and image analysis of labeled proteins. The other method is based on LC-MS/MS analysis of either unlabeled peptides or peptides derived from isotopically labeled proteins or peptides. In this study, the non-labeling approach was used, involving DeCyder MS Differential Analysis Software (DeCyder MS), for automated detection and relative quantitation of LC-MS data acquired from trypsin-digested proteins.
The study method aimed to identify and quantitate differentially regulated proteins following administration of recombinant human growth hormone (rhGH). Two groups of hypophysectomized male Sprague Dawley rats were daily subcutaneously injected during 8 d with rhGH and saline, respectively. The total soluble protein content of nucleus accumbens was extracted, digested with trypsin, and analyzed by 2D LC-MS/MS. In the first dimension, the peptides were separated by micropreparative cation exchange chromatography using an Ettan LC System. Collected fractions were analyzed in the second dimension using nanoscale RPC on Ettan NanoLC connected to an ion-trap mass spectrometer.
Acquired LC-MS data were evaluated using DeCyder MS, resulting in the detection of more than 5000 peptides, of which several were found to be significantly regulated. Several of these peptides could be correlated to proteins involved in synaptic plasticity as a response to growth factors.