Genomics, Proteomics & Bioinformatics

Aims and Scope The goals of Genomics,Proteomics＆Bioinformatics（GPB）are to disseminate new frontiers of its focused research fields,to publish high-quality discoveries in a fast-pace,and to promote open access and prompt online publication for efficient publishing.GPB publishes high-quality papers from the frontier research in the fields of genomics.

YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research

We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database（YPED） that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a singlelaboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry（LC–MS/MS） database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring（MRM）/selective reaction monitoring（SRM） assay development. We have linked YPED＇s database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.

A proteomics study to explore the role of adsorbed serum proteins for PC12 cell adhesion and growth on chitosan and collagen/chitosan surfaces

The aim of this article is to apply proteomics in the comparison of the molecular mechanisms of PC12 cell adhesion and growth mediated by the adsorbed serum proteins on the surfaces of chitosan and collagen/chitosan films.First,the chitosan and the collagen/chitosan films were prepared by spin coating;and their surface morphologies were characterized by scanning electron microscopy,X-ray energy dispersive spectroscopy,contact angle measurement and Fourier transform infrared spectroscopy.Subsequently,cell proliferation experiments on two materials were performed and the dynamic curves of protein adsorption on their surfaces were measured.Then,proteomics and bioinformatics were used to analyze and compare the adsorbed serum proteins on the surfaces of two biomaterials;and their effects on cell adhesion were discussed.The results showed that the optimum concentration of chitosan film was 2%w/v.When compared with chitosan film,collagen/chitosan film promoted the growth and proliferation of PC12 cells more significantly.Although the dynamic curves showed no significant difference in the total amount of the adsorbed proteins on both surfaces,proteomics and bioinformatics analyses revealed a difference in protein types:the chitosan surface adsorbed more vitronectin whereas collagen/chitosan surface adsorbed more fibronectin 1 and contained more cell surface receptor binding sites and more Leu-Asp-Val sequences in its surface structure;the collagen/chitosan surface were more conducive to promoting cell adhesion and growth.

Special Issue on“Biomarkers for Diseases”

The journal Genomics Proteomics＆Bioinformatics（GPB）is now inviting submissions for a special issue（to be published in the fall 2015）on the topic of “Biomarkers for Diseases”. As an emerging index,disease biomarkers have demonstrated the potential application in diagnosis and prognosis.

Special Issue on “Biomarkers for Autoimmune Diseases”

The journal Genomics Proteomics＆Bioinformatics（GPB）is now inviting submissions for a special issue（to be published in the summer of 2015）on the topic of “Biomarkers for Autoimmune Diseases”.Autoimmune diseases（AIDs）are the third most common category of disease after cancer and heart disease and affect more than 5%of the general population.

Special Issue on “Metagenomics of Marine Environments”

We are pleased to announce a special issue on“Metagenomics of Marine Environments”of the journal Genomics,Proteomics＆Bioinformatics（GPB）,aiming to provide a platform for high-quality papers focusing on the topic and we invite submissions for this special issue（to be published in August of 2015）.