MOTIVATION: Targeted data extraction methods are attractive ways to obtain quantitative peptide information from a proteomics experiment. Sequential Window Acquisition of all Theoretical Spectra (SWATH) and Data Independent Acquisition (DIA) methods increase reproducibility of acquired data because the classical precursor selection is omitted and all present precursors are fragmented. However, especially for targeted data extraction, MS coordinates (retention time information precursor and fragment masses) are required for the particular entities (peptide ions). These coordinates are usually generated in a so-called discovery experiment earlier on in the project if not available in public spectral library repositories. The quality of the assay panel is crucial to ensure appropriate downstream analysis. For that, a method is needed to create spectral libraries and to export customizable assay panels. RESULTS: Here, we present a versatile set of functions to generate assay panels from spectral libraries for use in targeted data extraction methods (SWATH/DIA) in the area of proteomics. AVAILABILITY AND IMPLEMENTATION: specL is implemented in the R language and available under an open-source license (GPL-3) in Bioconductor since BioC 3.0 (R-3.1) http://www.bioconductor.org (Trachsel et al., 2015). A vignette with a complete tutorial describing data import/export and analysis is included in the package and can also be found as supplement material of this article. CONTACT: [email protected] or [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

BACKGROUND: Recent development of novel technologies paved the way for quantitative proteomics. One of the most important among them is iTRAQ, employing isobaric tags for relative or absolute quantitation. Despite large progress in technology development, still many challenges remain for derivation and interpretation of quantitative results. One of these challenges is the consistent assignment of peptides to proteins. RESULTS: We have developed Peptide Profiling Guided Identification of Proteins (PPINGUIN), a statistical analysis workflow for iTRAQ data addressing the problem of ambiguous peptide quantitations. Motivated by the assumption that peptides uniquely derived from the same protein are correlated, our method employs clustering as a very early step in data processing prior to protein inference. Our method increases experimental reproducibility and decreases variability of quantitations of peptides assigned to the same protein. Giving further support to our method, application to a type 2 diabetes dataset identifies a list of protein candidates that is in very good agreement with previously performed transcriptomics meta analysis. Making use of quantitative properties of signal patterns identified, PPINGUIN can reveal new isoform candidates. CONCLUSIONS: Regarding the increasing importance of quantitative proteomics we think that this method will be useful in practical applications like model fitting or functional enrichment analysis. We recommend to use this method if quantitation is a major objective of research.

This paper demonstrates B-Fabric, an all-in-one solution for two major purposes in life sciences. On the one hand, it is a system for the integrated management of experimental data and scientific annotations. On the other hand, it is a system infrastructure supporting on-the fly coupling of user applications, and thus serving as extensible platform for fast-paced, cutting-edge, collaborative research.

Companies trading stocks need to store information on stock prices over specific time intervals, which results in very large databases. Large quantities of numerical data (thousands of records) are virtually impossible to understand quickly and require the use of a visual model, since that is the fastest way for a human brain to absorb those enormous collections of data. However, little work has been done on verifying which visualizations are more suitable to represent these data sets. Such work is of crucial importance, since it enables us to identify those useful visual models and, in addition, opens our minds to new research possibilities. This paper presents an empirical study of different visualizations, that have been employed for stock market data, by comparing the results obtained by all studied techniques in typical exploratory data analysis tasks. This work provides several research contributions to the design of advanced visual data exploration interfaces.

The feature vector approach is one of the most popular schemes for managing multimedia data. For many data types such as audio, images, or 3D models, an abundance of different feature vector extractors are available. The automatic (unsupervised) identification of the best suited feature extractor for a given multimedia database is a difficult and largely unsolved problem. We here address the problem of comparative unsupervised feature space analysis. We propose two interactive approaches for the visual analysis of certain feature space characteristics contributing to estimated discrimination power provided in the respective feature spaces. We apply the approaches on a database of 3D objects represented in different feature spaces, and we experimentally show the methods to be useful (a) for unsupervised comparative estimation of discrimination power and (b) for visually analyzing important properties of the components (dimensions) of the respective feature spaces. The results of the analysis are useful for feature selection and engineering

In many applications, data is collected and indexed by geo-spatial location. Discovering interesting patterns through visualization is an important way of gaining insight about such data. A previously proposed approach is to apply local placement functions such as PixelMaps that transform the input data set into a solution set that preserves certain constraints while making interesting patterns more obvious and avoid data loss from overplotting. In experience, this family of spatial transformations can reveal fine structures in large point sets, but it is sometimes difficult to relate those structures to basic geographic features such as cities and regional boundaries. Recent information visualization research has addressed other types of transformation functions that make spatially-transformed maps with recognizable shapes. These types of spatial-transformation are called global shape functions. In particular, cartogram-based map distortion has been studied. On the other hand, cartogram-based distortion does not handle point sets readily. In this study, we present a framework that allows the user to specify a global shape function and a local placement function. We combine cartogram-based layout (global shape) with PixelMaps (local placement), obtaining some of the benefits of each toward improved exploration of dense geo-spatial data sets.

In today’s world, e-mail has become one of the most important means of communication in business and private lives due to its efficiency. However, the problems start as soon as mail volumes go beyond the scope of human information processing capabilities. Firstly, time does not allow for leaving certain messages unanswered for a long time, and in certain cases, for reading all messages. Secondly, the dilemma of electronic filters leaves a choice of too many junk mails getting through versus a risk of solicited mails being dumped. In this paper we present a new interactive visual data mining approach for analyzing individual e-mail communication. It combines classical visual analytics (help to identify pattern such as peaks and trends over time) with geo-spatial map distortions (help to understand the routes of e-mails). Experiments show that our visual e-mail explorer produces useful and interesting visualizations of large collections of e-mail and is practical for exploring temporal and geo-spatial patterns hidden in the e-mail data.

Multimedia objects are often described by high-dimensional feature vectors which can be used for retrieval and clustering tasks. We have built an interactive retrieval system for 3D model databases that implements a variety of different feature transforms. Recently, we have enhanced the functionality of our system by integrating a SOM-based visualization module. In this poster demo, we show how 2D maps can be used to improve the effectiveness of retrieval, clustering, and over-viewing tasks in a 3D multimedia system.

Cartograms are a well-known technique for showing geography-related statistical information, such as population demographics and epidemiological data. The basic idea is to distort a map by resizing its regions according to a statistical parameter, but in a way that keeps the map recognizable. In this study, we formally define a family of cartogram drawing problems. We show that even simple variants are unsolvable in the general case. Because the feasible variants are NP-complete, heuristics are needed to solve the problem. Previously proposed solutions suffer from problems with the quality of the generated drawings. For a cartogram to be recognizable, it is important to preserve the global shape or outline of the input map, a requirement that has been overlooked in the past. To address this, our objective function for cartogram drawing includes both global and local shape preservation. To measure the degree of shape preservation, we propose a shape similarity function, which is based on a Fourier transformation of the polygons' curvatures. Also, our application is visualization of dynamic data, for which we need an algorithm that recalculates a cartogram in a few seconds. None of the previous algorithms provides adequate performance with an acceptable level of quality for this application. In this paper, we therefore propose an efficient iterative scanline algorithm to reposition edges while preserving local and global shapes. Scanlines may be generated automatically or entered interactively to guide the optimization process more closely. We apply our algorithm to several example data sets and provide a detailed comparison of the two variants of our algorithm and previous approaches.

PixelMaps are a new pixel-oriented visual data mining technique for large spatial datasets. They combine kernel-density-based clustering with pixel-oriented displays to emphasize clusters while avoiding overlap in locally dense point sets on maps. Because a full evaluation of density functions is prohibitively expensive, we also propose an efficient approximation, Fast-PixelMap, based on a synthesis of the quadtree and gridfile data structures.