A Perl procedure for protein identification by Peptide Mass Fingerprinting

<p>Abstract</p> <p>Background</p> <p>One of the topics of major interest in proteomics is protein identification. Protein identification can be achieved by analyzing the mass spectrum of a protein sample through different approaches. One of them, called Peptide Mass Fingerprinting (PMF), combines mass spectrometry (MS) data with searching strategies in a suitable database of known protein to provide a list of candidate proteins ranked by a score. To this aim, several algorithms and software tools have been proposed. However, the scoring methods and mainly the statistical evaluation of the results can be significantly improved.</p> <p>Results</p> <p>In this work, a Perl procedure for protein identification by PMF, called MsPI (Mass spectrometry Protein Identification), is presented. The implemented scoring methods were derived from the literature. MsPI implements a strategy to remove the contaminant masses present in the acquired spectra. Moreover, MsPI includes a statistical method to assign to each candidate protein, in addition to the scoring value, a p-value. Results obtained by MsPI on a dataset of 10 protein samples were compared with those achieved using two other software tools, i.e. Piums and Mascot. Piums implements one of the scoring methods available in MsPI, while Mascot is one of the most frequently used software tools in the protein identification field. MsPI scripts are available for downloading on the web site <url>http://aimed11.unipv.it/MsPI</url>.</p> <p>Conclusion</p> <p>The performances of MsPI seem to be better than those of Piums and Mascot. In fact, on the considered dataset, MsPI includes in its candidate proteins list, the "true" proteins nine times over ten, whereas Piums includes in its list the "true" proteins only four time over ten. Even if Mascot also correctly includes in the candidates list the "true" proteins nine times over ten, it provides longer candidate lists, therefore increasing the number of false positives when the molecular weight of the proteins in the sample is approximatively known (e.g. by the 1-D/2-D electrophoresis gel). Moreover, being MsPI a Perl tool, it can be easily extended and customized by the final users.</p

A multi-center validation study on the discrimination of Legionella pneumophila sg.1, Legionella pneumophila sg. 2-15 and Legionella non-pneumophila isolates from water by FT-IR spectroscopy

This study developed and validated a method, based on the coupling of Fourier-transform infrared spectroscopy (FT-IR) and machine learning, for the automated serotyping of Legionella pneumophila serogroup 1, Legionella pneumophila serogroups 2-15 as well as their successful discrimination from Legionella non-pneumophila. As Legionella presents significant intra- and inter-species heterogeneities, careful data validation strategies were applied to minimize late-stage performance variations of the method across a large microbial population. A total of 244 isolates were analyzed. In details, the method was validated with a multi-centric approach with isolates from Italian thermal and drinking water (n = 82) as well as with samples from German, Italian, French, and British collections (n = 162). Specifically, robustness of the method was verified over the time-span of 1 year with multiple operators and two different FT-IR instruments located in Italy and Germany. Moreover, different production procedures for the solid culture medium (in-house or commercial) and different culture conditions (with and without 2.5% CO2) were tested. The method achieved an overall accuracy of 100, 98.5, and 93.9% on the Italian test set of Legionella, an independent batch of Legionella from multiple European culture collections, and an extra set of rare Legionella non-pneumophila, respectively

Prediction of Peptide Reactivity with Human IVIg through a Knowledge-Based Approach

The prediction of antibody-protein (antigen) interactions is very difficult due to the huge variability that characterizes the structure of the antibodies. The region of the antigen bound to the antibodies is called epitope. Experimental data indicate that many antibodies react with a panel of distinct epitopes (positive reaction). The Challenge 1 of DREAM5 aims at understanding whether there exists rules for predicting the reactivity of a peptide/epitope, i.e., its capability to bind to human antibodies. DREAM 5 provided a training set of peptides with experimentally identified high and low reactivities to human antibodies. On the basis of this training set, the participants to the challenge were asked to develop a predictive model of reactivity. A test set was then provided to evaluate the performance of the model implemented so far

Norma DIN 476, su uso para desarrollar algunos temas de matemática de un programa de segundo año

Se presenta una propuesta de enseñanza, utilizando un material concreto que nos permite desarrollar algunos temas del programa de Matemática correspondiente al 2do año de la Escuela Industrial Superior de la ciudad de Santa Fe. La selección del material tiene que ver con una búsqueda de relaciones con otras asignaturas del mismo nivel (u otros) porque creemos que la enseñanza y aprendizaje de los contenidos de nuestra área tienen mejor recepción en los alumnos cuando se la contextualiza, cuando se evidencia su necesidad, valor o colaboración en otras áreas de estudio. El abordaje transdisciplinario requiere de mentes creativas, abiertas y capaces de resolver situaciones problemáticas específicas desde muchas perspectivas. Esto indica que el docente debe diseñar estrategias de enseñanza basadas en una concepción cognitiva del aprendizaje, favoreciendo el tratamiento de los contenidos disciplinares desde una perspectiva crítica y reflexiva; en la cual el joven pueda poner en juego sus propias capacidades y posibilidades para participar activamente del proceso y construir el conocimiento.Facultad de Humanidades y Ciencias de la Educació

The IXPE View of GRB 221009A

We present the IXPE observation of GRB 221009A, which includes upper limits on the linear polarization degree of both prompt and afterglow emission in the soft X-ray energy band. GRB 221009A is an exceptionally bright gamma-ray burst (GRB) that reached Earth on 2022 October 9 after traveling through the dust of the Milky Way. The Imaging X-ray Polarimetry Explorer (IXPE) pointed at GRB 221009A on October 11 to observe, for the first time, the 2–8 keV X-ray polarization of a GRB afterglow. We set an upper limit to the polarization degree of the afterglow emission of 13.8% at a 99% confidence level. This result provides constraints on the jet opening angle and the viewing angle of the GRB, or alternatively, other properties of the emission region. Additionally, IXPE captured halo-rings of dust-scattered photons that are echoes of the GRB prompt emission. The 99% confidence level upper limit to the prompt polarization degree depends on the background model assumption, and it ranges between ∼55% and ∼82%. This single IXPE pointing provides both the first assessment of X-ray polarization of a GRB afterglow and the first GRB study with polarization observations of both the prompt and afterglow phases

The LOFT mission concept: a status update

The Large Observatory For x-ray Timing (LOFT) is a mission concept which was proposed to ESA as M3 and M4 candidate in the framework of the Cosmic Vision 2015-2025 program. Thanks to the unprecedented combination of effective area and spectral resolution of its main instrument and the uniquely large field of view of its wide field monitor, LOFT will be able to study the behaviour of matter in extreme conditions such as the strong gravitational field in the innermost regions close to black holes and neutron stars and the supra-nuclear densities in the interiors of neutron stars. The science payload is based on a Large Area Detector (LAD, >8m2 effective area, 2-30 keV, 240 eV spectral resolution, 1 degree collimated field of view) and a Wide Field Monitor (WFM, 2-50 keV, 4 steradian field of view, 1 arcmin source location accuracy, 300 eV spectral resolution). The WFM is equipped with an on-board system for bright events (e.g., GRB) localization. The trigger time and position of these events are broadcast to the ground within 30 s from discovery. In this paper we present the current technical and programmatic status of the mission