IProX in 2021: connecting proteomics data sharing with big data.
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ABSTRACT:
SUBMITTER: Chen T
PROVIDER: S-EPMC8728291 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The launch of the US BRAIN and European Human Brain Projects coincides with growing international efforts toward transparency and increased access to publicly funded research in the neurosciences. The need for data-sharing standards and neuroinformatics infrastructure is more pressing than ever. However, 'big science' efforts are not the only drivers of data-sharing needs, as neuroscientists across the full spectrum of research grapple with the overwhelming volume of data being generated daily and a scientific environment that is increasingly focused on collaboration. In this commentary, we consider the issue of sharing of the richly diverse and heterogeneous small data sets produced by individual neuroscientists, so-called long-tail data. We consider the utility of these data, the diversity of repositories and options available for sharing such data, and emerging best practices. We provide use cases in which aggregating and mining diverse long-tail data convert numerous small data sources into big data for improved knowledge about neuroscience-related disorders.
| S-EPMC4728080 | biostudies-literature
Project description:BACKGROUND:In order to tackle the important and challenging problem in proteomics of identifying known and new protein sequences using high-throughput methods, we propose a data-sharing platform that uses fully distributed P2P technologies to share specifications of peer-interaction protocols and service components. By using such a platform, information to be searched is no longer centralised in a few repositories but gathered from experiments in peer proteomics laboratories, which can subsequently be searched by fellow researchers. METHODS:The system distributively runs a data-sharing protocol specified in the Lightweight Communication Calculus underlying the system through which researchers interact via message passing. For this, researchers interact with the system through particular components that link to database querying systems based on BLAST and/or OMSSA and GUI-based visualisation environments. We have tested the proposed platform with data drawn from preexisting MS/MS data reservoirs from the 2006 ABRF (Association of Biomolecular Resource Facilities) test sample, which was extensively tested during the ABRF Proteomics Standards Research Group 2006 worldwide survey. In particular we have taken the data available from a subset of proteomics laboratories of Spain's National Institute for Proteomics, ProteoRed, a network for the coordination, integration and development of the Spanish proteomics facilities. RESULTS AND DISCUSSION:We performed queries against nine databases including seven ProteoRed proteomics laboratories, the NCBI Swiss-Prot database and the local database of the CSIC/UAB Proteomics Laboratory. A detailed analysis of the results indicated the presence of a protein that was supported by other NCBI matches and highly scored matches in several proteomics labs. The analysis clearly indicated that the protein was a relatively high concentrated contaminant that could be present in the ABRF sample. This fact is evident from the information that could be derived from the proposed P2P proteomics system, however it is not straightforward to arrive to the same conclusion by conventional means as it is difficult to discard organic contamination of samples. The actual presence of this contaminant was only stated after the ABRF study of all the identifications reported by the laboratories.
| S-EPMC3298698 | biostudies-literature
Project description:BACKGROUND:To foster responsible data sharing in health research, ethical governance complementary to the EU General Data Protection Regulation is necessary. A governance framework for Big Data-driven research platforms will at least need to consider the conditions as specified a priori for individual datasets. We aim to identify and analyze these conditions for the Innovative Medicines Initiative's (IMI) BigData@Heart platform. METHODS:We performed a unique descriptive case study into the conditions for data sharing as specified for datasets participating in BigData@Heart. Principle investigators of 56 participating databases were contacted via e-mail with the request to send any kind of documentation that possibly specified the conditions for data sharing. Documents were qualitatively reviewed for conditions pertaining to data sharing and data access. RESULTS:Qualitative content analysis of 55 relevant documents revealed overlap on the conditions: (1) only to share health data for scientific research, (2) in anonymized/coded form, (3) after approval from a designated review committee, and while (4) observing all appropriate measures for data security and in compliance with the applicable laws and regulations. CONCLUSIONS:Despite considerable overlap, prespecified conditions give rise to challenges for data sharing. At the same time, these challenges inform our thinking about the design of an ethical governance framework for data sharing platforms. We urge current data sharing initiatives to concentrate on: (1) the scope of the research questions that may be addressed, (2) how to deal with varying levels of de-identification, (3) determining when and how review committees should come into play, (4) align what policies and regulations mean by "data sharing" and (5) how to deal with datasets that have no system in place for data sharing.
| S-EPMC6936121 | biostudies-literature
Project description:Although the privacy issues in human genomic studies are well known, the privacy risks in clinical proteomic data have not been thoroughly studied. As a proof of concept, we reported a comprehensive analysis of the privacy risks in clinical proteomic data. It showed that a small number of peptides carrying the minor alleles (referred to as the minor allelic peptides) at non-synonymous single nucleotide polymorphism (nsSNP) sites can be identified in typical clinical proteomic datasets acquired from the blood/serum samples of individual patient, from which the patient can be identified with high confidence. Our results suggested the presence of significant privacy risks in raw clinical proteomic data. However, these risks can be mitigated by a straightforward pre-processing step of the raw data that removing a very small fraction (0.1%, 7.14 out of 7,504 spectra on average) of MS/MS spectra identified as the minor allelic peptides, which has little or no impact on the subsequent analysis (and re-use) of these datasets.
| S-EPMC5009298 | biostudies-literature
Project description:We present xiSPEC, a standard compliant, next-generation web-based spectrum viewer for visualizing, analyzing and sharing mass spectrometry data. Peptide-spectrum matches from standard proteomics and cross-linking experiments are supported. xiSPEC is to date the only browser-based tool supporting the standardized file formats mzML and mzIdentML defined by the proteomics standards initiative. Users can either upload data directly or select files from the PRIDE data repository as input. xiSPEC allows users to save and share their datasets publicly or password protected for providing access to collaborators or readers and reviewers of manuscripts. The identification table features advanced interaction controls and spectra are presented in three interconnected views: (i) annotated mass spectrum, (ii) peptide sequence fragmentation key and (iii) quality control error plots of matched fragments. Highlighting or selecting data points in any view is represented in all other views. Views are interactive scalable vector graphic elements, which can be exported, e.g. for use in publication. xiSPEC allows for re-annotation of spectra for easy hypothesis testing by modifying input data. xiSPEC is freely accessible at http://spectrumviewer.org and the source code is openly available on https://github.com/Rappsilber-Laboratory/xiSPEC.
| S-EPMC6030980 | biostudies-literature
Project description:The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) has standardized data submission and dissemination of mass spectrometry proteomics data worldwide since 2012. In this paper, we describe the main developments since the previous update manuscript was published in Nucleic Acids Research in 2017. Since then, in addition to the four PX existing members at the time (PRIDE, PeptideAtlas including the PASSEL resource, MassIVE and jPOST), two new resources have joined PX: iProX (China) and Panorama Public (USA). We first describe the updated submission guidelines, now expanded to include six members. Next, with current data submission statistics, we demonstrate that the proteomics field is now actively embracing public open data policies. At the end of June 2019, more than 14 100 datasets had been submitted to PX resources since 2012, and from those, more than 9 500 in just the last three years. In parallel, an unprecedented increase of data re-use activities in the field, including 'big data' approaches, is enabling novel research and new data resources. At last, we also outline some of our future plans for the coming years.
| S-EPMC7145525 | biostudies-literature
Project description:SummaryShotgun proteomics is widely used in many system biology studies to determine the global protein expression profiles of tissues, cultures, and microbiomes. Many non-distributed computer algorithms have been developed for users to process proteomics data on their local computers. However, the amount of data acquired in a typical proteomics study has grown rapidly in recent years, owing to the increasing throughput of mass spectrometry and the expanding scale of study designs. This presents a big data challenge for researchers to process proteomics data in a timely manner. To overcome this challenge, we developed a cloud-based parallel computing application to offer end-to-end proteomics data analysis software as a service (SaaS). A web interface was provided to users to upload mass spectrometry-based proteomics data, configure parameters, submit jobs, and monitor job status. The data processing was distributed across multiple nodes in a supercomputer to achieve scalability for large datasets. Our study demonstrated SaaS for proteomics as a viable solution for the community to scale up the data processing using cloud computing.Availability and implementationThis application is available online at https://sipros.oscer.ou.edu/ or https://sipros.unt.edu for free use. The source code is available at https://github.com/Biocomputing-Research-Group/CloudProteoAnalyzer under the GPL version 3.0 license.
| S-EPMC10942798 | biostudies-literature
Project description:This paper reports carbon, nitrogen, and sulfur stable isotope data obtained from bone collagen of humans from the early medieval cemeteries of Hemmaberg/Gora svete Heme and Oberleiserberg located in Austria. The Hemmaberg/Gora svete Heme cemetery, dating from the 8th to the 11th century, comprises 29 graves, from which 15 individuals were analyzed. The Oberleiserberg cemetery, established in the first half of the 11th century, includes 71 graves as well as several incidental finds of human bones, from which 75 samples were analyzed. Both cemeteries show comparable δ13C data (mean for Oberleiserberg: -17.5 ± 1.2 ‰, 1σ; mean for Hemmaberg: -16.4 ± 1.6‰, 1σ). However, the δ15N values of individuals from Oberleiserberg (mean: +10.4 ± 1.5‰, 1σ) are slightly higher than those of individuals from Hemmaberg/Gora svete Heme (mean: +8.8 ± 1.1‰,1σ). The δ34S values were only obtained on the individuals from Oberleiserberg, and show a mean value of -0.9 ± 2.0 ‰ (1σ). Beyond the isotopic data presented in this article, we lay the foundations for cooperation between the IsoArcH database (https://isoarch.eu) [1] and the THANADOS (https://thanados.net) [2] project. While IsoArcH primarily stores isotope-related datasets for bioarchaeology, THANADOS stores data on archaeologically and anthropologically researched burials. Moving forward, IsoArcH and THANADOS plan to work closely together to integrate their databases. This collaboration presents a promising opportunity for both projects to pool their resources and knowledge, offering a wealth of information for researchers and the general public who are interested in anthropology and archaeology.
| S-EPMC10293964 | biostudies-literature
Project description:The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets.
| S-EPMC8494749 | biostudies-literature
Project description:Amyloidosis is a relatively rare human disease caused by the deposition of abnormal protein fibres in the extracellular space of various tissues, impairing their normal function. Proteomic analysis of patients' biopsies, developed by Dogan and colleagues at the Mayo Clinic, has become crucial for clinical diagnosis and for identifying the amyloid type. Currently, the proteomic approach is routinely used at National Amyloidosis Centre (NAC, London, UK) and Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche (ITB-CNR, Milan, Italy). Both centres are members of the European Proteomics Amyloid Network (EPAN), which was established with the aim of sharing and discussing best practice in the application of amyloid proteomics. One of the EPAN's activities was to evaluate the quality and the confidence of the results achieved using different software and algorithms for protein identification. In this paper, we report the comparison of proteomics results obtained by sharing NAC proteomics data with the ITB-CNR centre. Mass spectrometric raw data were analysed using different software platforms including Mascot, Scaffold, Proteome Discoverer, Sequest and bespoke algorithms developed for an accurate and immediate amyloid protein identification. Our study showed a high concordance of the obtained results, suggesting a good accuracy of the different bioinformatics tools used in the respective centres. In conclusion, inter-centre data exchange is a worthwhile approach for testing and validating the performance of software platforms and the accuracy of results, and is particularly important where the proteomics data contribute to a clinical diagnosis.
| S-EPMC8037974 | biostudies-literature