Combining MALDI-FTMS and bioinformatics for rapid peptidomic comparisons.

Published

Journal Article

Increasing research efforts in large-scale mass spectral analyses of peptides and proteins have led to many advances in technology and method development for collecting data and improving the quality of data. However, the resultant large data sets often pose significant challenges in extracting useful information in a high-throughput manner. Here, we describe one such method where we analyzed a large mass spectral data set collected using decapod crustacean nervous tissue extracts separated via high-performance liquid chromatography (HPLC) coupled to high-resolution matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS). Following their acquisition, the data collected from discrete LC fractions was compiled and analyzed using an in-house developed software package that deisotoped, compressed, calibrated, and matched peaks to a list of known crustacean neuropeptides. By processing these data via bioinformatics tools such as hierarchical clustering, more than 110 neuropeptides that belong to 14 peptide families were mapped in five crustacean species. Overall, we demonstrate the utility of MALDI-FTMS in combination with a bioinformatics software package for the elucidation and comparison of peptidomes of varying crustacean species. This study established an effective methodology and will provide the basis for future investigations into more comprehensive comparative peptidomics with larger collection of species and phyla in order to gain a deeper understanding of the evolution and diversification of peptide families.

Full Text

Duke Authors

Cited Authors

  • Schmidt, JJ; McIlwain, S; Page, D; Christie, AE; Li, L

Published Date

  • March 2008

Published In

Volume / Issue

  • 7 / 3

Start / End Page

  • 887 - 896

PubMed ID

  • 18205299

Pubmed Central ID

  • 18205299

International Standard Serial Number (ISSN)

  • 1535-3893

Digital Object Identifier (DOI)

  • 10.1021/pr070390p

Language

  • eng

Conference Location

  • United States