Ontology highlight
ABSTRACT: Background
Two-dimensional differential gel electrophoresis (2D-DIGE) provides a powerful technique to separate proteins on their isoelectric point and apparent molecular mass and quantify changes in protein expression. Abundantly available proteins in spots can be identified using mass spectrometry-based approaches. However, identification is often not possible for low-abundant proteins.Results
We present a novel computational approach to prioritize candidate proteins for unidentified spots. Our approach exploits noisy information on the isoelectric point and apparent molecular mass of a protein spot in combination with functional similarities of candidate proteins to already identified proteins to select and rank candidates. We evaluated our method on a 2D-DIGE dataset comparing protein expression in uninfected and HIV-1 infected T-cells. Using leave-one-out cross-validation, we show that the true-positive rate for the top-5 ranked proteins is 43.8%.Conclusions
Our approach shows good performance on a 2D-DIGE dataset comparing protein expression in uninfected and HIV-1 infected T-cells. We expect our method to be highly useful in (re-)mining other 2D-DIGE experiments in which especially the low-abundant protein spots remain to be identified.
SUBMITTER: Nandal UK
PROVIDER: S-EPMC4384356 | biostudies-literature | 2015 Jan
REPOSITORIES: biostudies-literature
Nandal Umesh K UK Vlietstra Wytze J WJ Byrman Carsten C Jeeninga Rienk E RE Ringrose Jeffrey H JH van Kampen Antoine H C AH Speijer Dave D Moerland Perry D PD
BMC bioinformatics 20150128
<h4>Background</h4>Two-dimensional differential gel electrophoresis (2D-DIGE) provides a powerful technique to separate proteins on their isoelectric point and apparent molecular mass and quantify changes in protein expression. Abundantly available proteins in spots can be identified using mass spectrometry-based approaches. However, identification is often not possible for low-abundant proteins.<h4>Results</h4>We present a novel computational approach to prioritize candidate proteins for uniden ...[more]