SearchGUI: a highly adaptable common interface for proteomics search and de novo engines

Mass-spectrometry-based proteomics has become the standard approach for identifying and quantifying proteins. A vital step consists of analyzing experimentally generated mass spectra to identify the underlying peptide sequences for later mapping to the originating proteins. We here present the latest developments in SearchGUI, a common open-source interface for the most frequently used freely available proteomics search and de novo engines that has evolved into a central component in numerous bioinformatics workflows.acceptedVersio

Ultrafast Acousto-Plasmonics in Gold Nanoparticles Superlattice

We report the investigation of the generation and detection of GHz coherent acoustic phonons in plasmonic gold nanoparticles superlattices (NPS). The experiments have been performed from an optical femtosecond pump-probe scheme across the optical plasmon resonance of the superlattice. Our experiments allow to estimate the collective elastic response (sound velocity) of the NPS as well as an estimate of the nano-contact elastic stiffness. It appears that the light-induced coherent acoustic phonon pulse has a typical in-depth spatial extension of about 45 nm which is roughly 4 times the optical skin depth in gold. The modeling of the transient optical reflectivity indicates that the mechanism of phonon generation is achieved through ultrafast heating of the NPS assisted by light excitation of the volume plasmon. These results demonstrate how it is possible to map the photon-electron-phonon interaction in subwavelength nanostructures

Low sensitivity to optical feedback and optical injection of discrete mode lasers

In this paper, we demonstrate the low sensitivity to both external optical feedback and external optical injection of a new type of extremely low cost single-mode lasers, called "discrete mode" (DM) lasers. The DM lasers are obtained from ridge waveguide Fabry Perot (FP) lasers, in which the effective refractive index of the lasing mode has been perturbed. These lasers exhibit a low sensitivity to external optical feedback since the coherence collapse threshold is around 5 dB higher in comparison to a commercial DFB laser

Automated splitting into batches for observational biomedical studies with sequential processing

Experimental design usually focuses on the setting where treatments and/or other aspects of interest can be manipulated. However, in observational biomedical studies with sequential processing, the set of available samples is often fixed, and the problem is thus rather the ordering and allocation of samples to batches such that comparisons between different treatments can be made with similar precision. In certain situations, this allocation can be done by hand, but this rapidly becomes impractical with more challenging cohort setups. Here, we present a fast and intuitive algorithm to generate balanced allocations of samples to batches for any single-variable model where the treatment variable is nominal. This greatly simplifies the grouping of samples into batches, makes the process reproducible, and provides a marked improvement over completely random allocations. The general challenges of allocation and why good solutions can be hard to find are also discussed, as well as potential extensions to multivariable settings.publishedVersio

Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics

With the advent of mass spectrometry based proteomics, the identification of thousands of proteins has become commonplace in biology nowadays. Increasingly, efforts have also been invested toward the detection and localization of posttranslational modifications. It is furthermore common practice to quantify the identified entities, a task supported by a panel of different methods. Finally, the results can also be enriched with functional knowledge gained on the proteins, detecting for instance differentially expressed gene ontology terms or biological pathways. In this study, we review the resources, methods and tools available for the researcher to achieve such a quantitative functional analysis. These include statistics for the post-processing of identification and quantification results, online resources and public repositories. With a focus on free but user-friendly software, preferably also open-source, we provide a list of tools designed to help the researcher manage the vast amount of data generated. We also indicate where such applications currently remain lacking. Moreover, we stress the eventual pitfalls of every step of such studies. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.acceptedVersio

Observation of the nonlinear Wood's anomaly on periodic arrays of nickel nanodimers

Linear and nonlinear magneto-photonic properties of periodic arrays of nickel nanodimers are governed by the interplay of the (local) optical response of individual nanoparticles and (non-local) diffraction phenomena, with a striking example of Wood's anomaly. Angular and magnetic-field dependencies of the second harmonic intensity evidence Wood's anomaly when new diffraction orders emerge. Near-infrared spectroscopic measurements performed at different optical wavelengths and grating constants discriminate between the linear and nonlinear excitation mechanisms of Wood's anomalies. In the nonlinear regime the Wood's anomaly is characterized by an order-of-magnitude larger effect in intensity redistribution between the diffracted beams, as compared to the linear case. The nonlinear Wood's anomaly manifests itself also in the nonlinear magnetic contrast highlighting the prospects of nonlinear magneto-photonics.Comment: 8 pages, 6 figure

PeptideShaker Online: A User-Friendly Web-Based Framework for the Identification of Mass Spectrometry-Based Proteomics Data

Mass spectrometry-based proteomics is a high-throughput technology generating ever-larger amounts of data per project. However, storing, processing, and interpreting these data can be a challenge. A key element in simplifying this process is the development of interactive frameworks focusing on visualization that can greatly simplify both the interpretation of data and the generation of new knowledge. Here we present PeptideShaker Online, a user-friendly web-based framework for the identification of mass spectrometry-based proteomics data, from raw file conversion to interactive visualization of the resulting data. Storage and processing of the data are performed via the versatile Galaxy platform (through SearchGUI, PeptideShaker, and moFF), while the interaction with the results happens via a locally installed web server, thus enabling researchers to process and interpret their own data without requiring advanced bioinformatics skills or direct access to compute-intensive infrastructures. The source code, additional documentation, and a fully functional demo is available at https://github.com/barsnes-group/peptide-shaker-online.publishedVersio