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Vizcaino, J. A.

Publications and source records attributed to Vizcaino, J. A..

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Universal Spectrum Identifier for mass spectra

Mass spectra provide the ultimate evidence for supporting the findings of mass spectrometry (MS) proteomics studies in publications, and it is therefore crucial to be able to trace the conclusions back to the spectra. The Universal Spectrum Identifier (USI) provides a standardized mechanism for encoding a virtual path to any mass spectrum contained in datasets deposited to public proteomics repositories. USIs enable greater transparency for providing spectral evidence in support of key findings in publications, with more than 1 billion USI identifications from over 3 billion spectra already available through ProteomeXchange repositories.

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BioContainers Registry: searching for bioinformatics tools, packages and containers

1BioContainers is an open-source project that aims to create, store, and distribute bioinformatics software containers and packages. The BioContainers community has developed a set of guidelines to standardize the software containers including the metadata, versions, licenses, and/or software dependencies. BioContainers supports multiple packaging and containers technologies such as Conda, Docker, and Singularity. Here, we introduce the BioContainers Registry and Restful API to make containerized bioinformatics tools more findable, accessible, interoperable, and reusable (FAIR). BioContainers registry provides a fast and convenient way to find and retrieve bioinformatics tools packages and containers. By doing so, it will increase the use of bioinformatics packages and containers while promoting replicability and reproducibility in research.

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An integrated landscape of protein expression in human cancer

Using public proteomics datasets, mostly available through the PRIDE database, we assembled a proteomics resource for 191 cancer cell lines and 246 clinical tumour samples, across 13 cancer lineages. We found that baseline protein abundance in cell lines was generally representative of tumours. However, when considering differences in protein expression between tumour subtypes, as exemplified in the breast lineage, many of these changes were no longer recapitulated in the cell line models. Integration of proteomics and transcriptomics data suggested that the level of transcriptional control in cell lines changed significantly depending on their lineage. Additionally, in agreement with previous studies, variation in mRNA levels was often a poor predictor of changes in protein abundance. To our knowledge, this work constitutes the first meta-analysis study including cancer-related proteomics datasets. We anticipate this aggregated dataset will be of significant aid to future studies requiring a reference to baseline protein expression in cancer.

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Proteomics Standards Initiative Extended FASTA Format (PEFF)

Mass spectrometry-based proteomics enables the high-throughput identification and quantification of proteins, including sequence variants and post-translational modifications (PTMs), in biological samples. However, most workflows require that such variations be included in the search space used to analyze the data, and doing so remains challenging with most analysis tools. In order to facilitate the search for known sequence variants and PTMs, the Proteomics Standards Initiative (PSI) has designed and implemented the PSI Extended FASTA Format (PEFF). PEFF is based on the very popular FASTA format but adds a uniform mechanism for encoding substantially more metadata about the sequence collection as well as individual entries, including support for encoding known sequence variants, PTMs, and proteoforms. The format is very nearly backwards compatible, and as such, existing FASTA parsers will require little or no changes to be able to read PEFF files as FASTA files, although without supporting any of the extra capabilities of PEFF. PEFF is defined by a full specification document, controlled vocabulary terms, a set of example files, software libraries, and a file validator. Popular software and resources are starting to support PEFF, including the sequence search engine Comet and the knowledge bases neXtProt and UniProtKB. Widespread implementation of PEFF is expected to further enable proteogenomics and top-down proteomics applications by providing a standardized mechanism for encoding protein sequences and their known variations. All the related documentation, including the detailed file format specification and example files, are available at http://www.psidev.info/peff.

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Quantifying the impact of public omics data

The amount of omics data in the public domain is increasing every year [1, 2]. Public availability of datasets is growing in all disciplines, because it is considered to be a good scientific practice (e.g. to enable reproducibility), and/or it is mandated by funding agencies, scientific journals, etc. Science is now a data intensive discipline and therefore, new and innovative ways for data management, data sharing, and for discovering novel datasets are increasingly required [3, 4]. However, as data volumes grow, quantifying its impact becomes more and more important. In this context, the FAIR (Findable, Accessible, Interoperable, Reusable) principles have been developed to promote good scientific practises for scientific data and data resources [5]. In fact, recently, several resources [1, 2, 6] have been created to facilitate the Findability (F) and Accessibility (A) of biomedical datasets. These principles put a specific emphasis on enhancing the ability of both individuals and software to discover and re-use digital objects in an automated fashion throughout their entire life cycle [5]. While data resources typically assign an equal relevance to all datasets (e.g. as results of a query), the usage patterns of the data can vary enormously, similarly to other \"research products\" such as publications. How do we know which datasets are getting more attention? More generally, how can we quantify the scientific impact of datasets?

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The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.

On behalf of The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI), we are here introducing two novel standard data formats, proBAM and proBed, that have been developed to address the current challenges of integrating mass spectrometry based proteomics data with genomics and transcriptomics information in proteogenomics studies. proBAM and proBed are adaptations from the well-defined, widely used file formats SAM/BAM and BED respectively, and both have been extended to meet specific requirements entailed by proteomics data. Therefore, existing popular genomics tools such as SAMtools and Bedtools, and several very popular genome browsers, can be used to manipulate and visualize these formats already out-of-the-box. We also highlight that a number of specific additional software tools, properly supporting the proteomics information available in these formats, are now available providing functionalities such as file generation, file conversion, and data analysis. All the related documentation to the formats, including the detailed file format specifications, and example files are accessible at http://www.psidev.info/probam and http://www.psidev.info/probed.

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Accurate And Fast Feature Selection Workflow For High-Dimensional Omics Data

We are moving into the age of Big Data in biomedical research and bioinformatics. This trend could be encapsulated in this simple formula: D = S x F, where the volume of data generated (D) increases in both dimensions: the number of samples (S) and the number of sample features (F). Frequently, a typical bioinformatics problem (e.g. classification) includes redundant and irrelevant features that can result, in the worst-case scenario, in false positive results. Then, Feature Selection (FS) constitutes an enormous challenge. Despite the number and diversity of algorithms available, the proper choice of an approach for facing a specific problem often falls in a grey zone. In this study, we select a subset of FS methods to develop an efficient workflow and an R package for bioinformatics machine learning problems. We cover relevant issues concerning FS, ranging from domains problems to algorithm solutions and computational tools. Finally, we use seven different proteomics and gene expression datasets to evaluate the workflow and guide the FS process.

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