Neuropeptidomics: expanding proteomics downwards

Abstract

Biological function is mainly carried out by a dynamic population of proteins and peptides which may be used as markers for disease diagnosis, prognosis and as a guide for effective treatment. The study of proteins is called proteomics and it is generally performed by two-dimensional gel electrophoresis and mass spectrometric methods. However, gel-based proteomics is methodologically restricted from the low mass region, which includes important endogenous peptides. The study of endogenous peptides, peptidomics, is complicated by protein fragments produced post-mortem during conventional sample handling. Nanoflow liquid chromatography and MS, together with improved methods for sample preparation, have been used to semi-quantitatively monitor endogenous peptides in brain tissue. When rapidly heat-denatured brain tissue was analysed, these methods enabled simultaneous detection of hundreds of peptides and the identification of several endogenous peptides not previously described in the literature. In an application of the MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) model for Parkinson's disease, the expression of the small protein PEP-19 was compared with controls. The levels were found to be significantly decreased in the striatum of MPTP-treated animals.

Impaired Locomotor Learning and Altered Cerebellar Synaptic Plasticity in pep-19/pcp4-Null Mice

“…In addition to DS, altered levels of PEP-19 have been found in other neurodegenerative/ neurocognitive disorders. For example, reduced expression of PEP-19 is reported in the prefrontal cortex of alcoholics (30) and in the basal ganglia in Huntington's disease (58) and mouse models of Parkinson's disease (52,56), whereas cerebellar PEP-19 levels are increased in Alzheimer's disease (54). Furthermore, overexpression of Pep-19 in PC12 cells (16) and cortical neurons (33) inhibits cell death, suggesting neuroprotective properties.…”

Development and Evaluation of Normalization Methods for Label-free Relative Quantification of Endogenous Peptides

“…Endogenous neuropeptides are peptides used for intracellular signaling that can act as neurotransmitters or neuromodulators in the nervous system. These polypeptides of 3-100 amino acids can be abundantly produced in large neural populations or in trace levels from single neurons (5) and are often generated through the cleavage of precursor proteins. However, unwanted peptides can also be created through post-mortem induced proteolysis (6).…”

“…It has been suggested by us (4,5) and others (9) that comparing the peptidome between samples of e.g. diseased and normal tissue may lead to the discovery of biologically relevant peptides of certain pathological or pharmacological events.…”

Strategies for Reliable and Improved Identification of Peptides

“…These softwares automatically detect peptides in MS raw data files and compare the peptide intensities between the different MS files. Peptide data generated can be directly searched against SwePep for identification [55,56]. For example, DeCyder MS was used by us to study label-free peptidomics by nano-LC-MS with automatic analysis of the experimental data.…”