Simple, efficient and thorough shotgun proteomic analysis with PatternLab V.

Shotgun proteomics aims to identify and quantify the thousands of proteins in complex mixtures such as cell and tissue lysates and biological fluids. This approach uses liquid chromatography coupled with tandem mass spectrometry and typically generates hundreds of thousands of mass spectra that require specialized computational environments for data analysis. PatternLab for proteomics is a unified computational environment for analyzing shotgun proteomic data. PatternLab V (PLV) is the most comprehensive and crucial update so far, the result of intensive interaction with the proteomics community over several years. All PLV modules have been optimized and its graphical user interface has been completely updated for improved user experience. Major improvements were made to all aspects of the software, ranging from boosting the number of protein identifications to faster extraction of ion chromatograms. PLV provides modules for preparing sequence databases, protein identification, statistical filtering and in-depth result browsing for both labeled and label-free quantitation. The PepExplorer module can even pinpoint de novo sequenced peptides not already present in the database. PLV is of broad applicability and therefore suitable for challenging experimental setups, such as time-course experiments and data handling from unsequenced organisms. PLV interfaces with widely adopted software and community initiatives, e.g., Comet, Skyline, PEAKS and PRIDE. It is freely available at http://www.patternlabforproteomics.org .

A new species of Haliclona (Demospongiae: Haplosclerida: Chalinidae) from southeastern Brazil and the first record of Haliclona vansoesti from the Brazilian coast.

In this paper we describe two species of the cosmopolitan sponge genus Haliclona from Rio de Janeiro State, SE Brazil, one of which is new to science and the other a new record to Brazil. Haliclona (Rhizoniera) fugidia sp. nov. is brownish-pink, salmon or cream, thickly encrusting, without oscular tubes and tangential ectosomal reticulation. Choanosomal skeleton is a mostly unispicular ladder-like reticulation of oxeas, very organized near the sponge surface and denser and more disorganized in the interior of the sponge. Haliclona (Halichoclona) vansoesti de Weerdt et al., 1999 was originally described from the Caribbean. It has a very loose connection between ectosome and choanosome, a whitish translucent ectosome combined with a purplish choanosome, a cavernous structure and a friable or crispy consistency. The conspecificity of SE Brazilian and Caribbean populations of H. (Halich.) vansoesti was verified through phylogenetic analysis of small subunit 18S rRNA (18S) and mitochondrial cytochrome oxidase subunit I (COI) gene sequences. A maximum likelihood phylogenetic tree constructed with 18S sequences indicates that specimens of H. (Halich.) vansoesti from Rio de Janeiro were phylogenetically closer to the same species from the Caribbean than to other species of Haliclona. Although not available for H. (Halich.) vansoesti from the Caribbean, COI sequences of our specimens were also quite distinct from those of other Haliclona species. Molecular identification based on DNA sequences is a useful complement to traditional morphology-based taxonomy, especially in highly plastic sponges such as Haliclona spp. and other haplosclerids.