PAnalyzer: A software tool for protein inference in shotgun proteomics

Background Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA) approaches have emerged as an alternative to the traditional data dependent acquisition (DDA) in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data. Results In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS) software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file) files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server. Conclusions We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an easy to use multiplatform and free software tool.

Transverse target single-spin asymmetry in inclusive electroproduction of charged pions and kaons

Single-spin asymmetries were investigated in inclusive electroproduction of charged pions and kaons from transversely polarized protons at the HERMES experiment. The asymmetries were studied as a function of the azimuthal angle psi about the beam direction between the target-spin direction and the hadron production plane, the transverse hadron momentum P-T relative to the direction of the incident beam, and the Feynman variable x(F). The sin psi* amplitudes are positive for pi(+) and K+ slightly negative for pi(-) and consistent with zero for K-, with particular P-T but weak x(F) dependences. Especially large asymmetries are observed for two small subsamples of events, where also the scattered electron was recorded by the spectrometer. (C) 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Evaluación y predicción del riesgo de mala evolución de la neumonía adquirida en la comunidad

206 p.