title: A proteomic study of microgravity cardiac effects: feature maps of label-free LC-MALDI data for differential expression analysis.
abstract: We present a computational analysis of Mass Spectrometry (MS) data based on a proteomic study of mice cardiac tissue samples whose measured changes in peptide and protein abundance were obtained under normal (control or CTRL) and simulated microgravity conditions (hind-limb unloading or HLU). A pipeline consisting of experimental and computational steps has been designed to achieve, respectively, pre-fractionation to simplify mouse heart protein extracts and data synthesis by feature consensus maps. Both acid and neutral protein fractions obtained from differential solubility have been digested, and peptide mixtures have been resolved by LC-MALDI. The computational tools employed to analyze the MS data and reduce their complex dimensionality have included spectra alignment, denoising and normalization to obtain good-quality peak detection performance. In turn, features could be identified and further refined by searching patterns across repeated measurements obtained under differential conditions (HLU-CTRL, acid-neutral protein extracts). The assessment of reproducibility aspects for evaluating the efficacy of label-free comparative proteomic analysis, combined with the goal of identifying from HLU-CTRL consensus maps candidate proteins with differential expression, led to a computationally efficient approach delivering proteins related to the basic heart functions, cardiac stress and energy supply.
authors.affiliation: Clinical Physiology Institute-CNR, Via Moruzzi 1, 56124 Pisa, Italy.
authors.forename: Silvia
authors.initials: S
authors.lastname: Rocchiccioli
authors.forename: Enrico
authors.initials: E
authors.lastname: Congiu
authors.forename: Claudia
authors.initials: C
authors.lastname: Boccardi
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Citti
authors.forename: Luciano
authors.initials: L
authors.lastname: Callipo
authors.forename: Aldo
authors.initials: A
authors.lastname: Laganà
authors.forename: Enrico
authors.initials: E
authors.lastname: Capobianco
mesh_terms: D000818:Animals; D002138:Calibration; D002853:Chromatography, Liquid; D019417:Hindlimb Suspension; D051379:Mice; D009206:Myocardium / Q000378:metabolism*; D010455:Peptides / Q000032:analysis; D011506:Proteins / Q000032:analysis / Q000737:chemistry / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D013194:Staining and Labeling; D014893:Weightlessness
chemical_list: D010455:Peptides; D011506:Proteins