Public proteomics data: How the field has evolved from sceptical inquiry to the promise of in silico proteomics.
Ontology highlight
ABSTRACT:
SUBMITTER: Martens L
PROVIDER: S-EPMC5988554 | biostudies-literature | 2016 Jun
REPOSITORIES: biostudies-literature
Publications
Public proteomics data: How the field has evolved from sceptical inquiry to the promise of <i>in silico</i> proteomics.
EuPA open proteomics 20160328
Similar Datasets
Project description:Inquiry activities have become increasingly common in Ecology and Evolution courses, but the rapid shift to remote instruction for many faculty members in response to the COVID-19 pandemic has created new challenges for maintaining these student-centered activities in a distance learning format. Moving forward, many instructors will be asked to create flexible course structures that allow for a mix of different teaching modalities and will be looking for resources to support student inquiry in both online and in-person settings. Here, we propose the use of data-driven inquiry activities as a flexible option for offering students experiences to build career-relevant skills and learn fundamental ecological concepts. We share lessons learned from our experiences teaching a two-semester course-based research experience in global change ecology that leverages publicly available datasets to engage students in broadly relevant scientific inquiry.
| S-EPMC7679546 | biostudies-literature
Project description:Glioblastoma (GB) is a rare but extremely aggressive brain tumor that significantly impacts patient outcomes, affecting both duration and quality of life. The protocol established by Stupp and colleagues in 2005, based on radiotherapy and chemotherapy with Temozolomide, following maximum safe surgical resection remains the gold standard for GB treatment; however, it is evident nowadays that the extreme intratumoral and intertumoral heterogeneity, as well as the invasiveness and tendency to recur, of GB are not compatible with a routine and unfortunately ineffective treatment. This review article summarizes the main challenges in the search for new valuable therapies for GB and focuses on the impact that extracellular vesicle (EV) research and exploitation may have in the field. EVs are natural particles delimited by a lipidic bilayer and filled with functional cellular content that are released and uptaken by cells as key means of cell communication. Furthermore, EVs are stable in body fluids and well tolerated by the immune system, and are able to cross physiological, interspecies, and interkingdom barriers and to target specific cells, releasing inherent or externally loaded functionally active molecules. Therefore, EVs have the potential to be ideal allies in the fight against GB and to improve the prognosis for GB patients. The present work describes the main preclinical results obtained so far on the use of EVs for GB treatment, focusing on both the EV sources and molecular cargo used in the various functional studies, primarily in vivo. Finally, a SWOT analysis is performed, highlighting the main advantages and pitfalls of developing EV-based GB therapeutic strategies. The analysis also suggests the main directions to explore to realize the possibility of exploiting EVs for the treatment of GB.
| S-EPMC10886570 | biostudies-literature
Project description:In a global effort for scientific transparency, it has become feasible and good practice to share experimental data supporting novel findings. Consequently, the amount of publicly available MS-based proteomics data has grown substantially in recent years. With some notable exceptions, this extensive material has however largely been left untouched. The time has now come for the proteomics community to utilize this potential gold mine for new discoveries, and uncover its untapped potential. In this review, we provide a brief history of the sharing of proteomics data, showing ways in which publicly available proteomics data are already being (re-)used, and outline potential future opportunities based on four different usage types: use, reuse, reprocess, and repurpose. We thus aim to assist the proteomics community in stepping up to the challenge, and to make the most of the rapidly increasing amount of public proteomics data.
| S-EPMC4738454 | biostudies-literature
Project description:High density lipoprotein (HDL) is recognized as the major negative risk factor of cardiovascular disease and number of anti-atherogenic functions has been ascribed to HDL. HDL is an assembly of a neutral lipid core and an outer shell consisting of polar lipids and proteins. It has been defined many different ways based on various distinct properties including density flotation, protein composition, molecular size, and electrophoretic migration. Overall the studies characterizing HDL clearly demonstrate that it is a complex heterogeneous mixture of particles. Furthermore several studies convincingly demonstrated that certain populations of HDL particles have a distinct functionality suggesting that HDL may serve as a platform for assembly of protein complexes with very specific biological functions. Indeed recent proteomics studies described over 100 proteins associated with HDL. Here we review approaches to isolation and proteomic analysis of HDL and discuss potential problems associated with isolation methods which may confound our understanding of the relation of the HDL composition and its biological function.
| S-EPMC3685576 | biostudies-literature
Project description:We present PepQuery2, which leverages a new tandem mass spectrometry (MS/MS) data indexing approach to enable ultrafast, targeted identification of novel and known peptides in any local or publicly available MS proteomics datasets. The stand-alone version of PepQuery2 allows directly searching more than one billion indexed MS/MS spectra in the PepQueryDB or any public datasets from PRIDE, MassIVE, iProX, or jPOSTrepo, whereas the web version enables users to search datasets in PepQueryDB with a user-friendly interface. We demonstrate the utilities of PepQuery2 in a wide range of applications including detecting proteomic evidence for genomically predicted novel peptides, validating novel and known peptides identified using spectrum-centric database searching, prioritizing tumor-specific antigens, identifying missing proteins, and selecting proteotypic peptides for targeted proteomics experiments. By putting public MS proteomics data directly into the hands of scientists, PepQuery2 opens many new ways to transform these data into useful information for the broad research community.
| S-EPMC10113256 | biostudies-literature
Project description:The volume of public proteomics data is rapidly increasing, causing a computational challenge for large-scale reanalysis. Here, we introduce quantms ( https://quant,ms.org/ ), an open-source cloud-based pipeline for massively parallel proteomics data analysis. We used quantms to reanalyze 83 public ProteomeXchange datasets, comprising 29,354 instrument files from 13,132 human samples, to quantify 16,599 proteins based on 1.03 million unique peptides. quantms is based on standard file formats improving the reproducibility, submission and dissemination of the data to ProteomeXchange.
| S-EPMC11399091 | biostudies-literature
Project description:PurposeEpistaxis represents the most frequent ear, nose, throat-related emergency symptom. Seasonal variation in epistaxis incidence, with peaks during winter months, is widely accepted, although the literature itself remains inconclusive. The objective of this study was to evaluate public inquiry into nose bleeding, by considering Google-based search query frequency on "Epistaxis"-related search terms and to assess possible seasonal variations globally.MethodsEpistaxis-related search terms were systematically collected and compared using Google Trends (GT). Relative search volumes for the most relevant epistaxis-related terms, covering a timeframe from 2004 to 2019 were analysed using cosinor time series analysis for the United States of America, Germany, the United Kingdom, Italy, Canada, Australia, and New Zealand.ResultsGraphical representation revealed seasonal variations with peaks during winter months in the majority of countries included. Subsequent cosinor analysis revealed these variations to be significant (all p < 0.001).ConclusionPublic interest in seeking epistaxis-related information through the Internet displayed seasonal patterns in countries from both hemispheres, with the highest interest during winter months. Further studies exploring causality with environmental factors are warranted.
| S-EPMC7286850 | biostudies-literature
Project description:Data-independent acquisition (DIA) is an emerging technology for quantitative proteomic analysis of large cohorts of samples. However, sample-specific spectral libraries built by data-dependent acquisition (DDA) experiments are required prior to DIA analysis, which is time-consuming and limits the identification/quantification by DIA to the peptides identified by DDA. Herein, we propose DeepDIA, a deep learning-based approach to generate in silico spectral libraries for DIA analysis. We demonstrate that the quality of in silico libraries predicted by instrument-specific models using DeepDIA is comparable to that of experimental libraries, and outperforms libraries generated by global models. With peptide detectability prediction, in silico libraries can be built directly from protein sequence databases. We further illustrate that DeepDIA can break through the limitation of DDA on peptide/protein detection, and enhance DIA analysis on human serum samples compared to the state-of-the-art protocol using a DDA library. We expect this work expanding the toolbox for DIA proteomics.
| S-EPMC6952453 | biostudies-literature
Project description:The PRIDE database, developed and maintained at the European Bioinformatics Institute (EBI), is one of the most prominent data repositories dedicated to high throughput MS-based proteomics data. Peptidome, developed by the National Center for Biotechnology Information (NCBI) as a sibling resource to PRIDE, was discontinued due to funding constraints in April 2011. A joint effort between the two teams was started soon after the Peptidome closure to ensure that data were not "lost" to the wider proteomics community by exporting it to PRIDE. As a result, data in the low terabyte range have been migrated from Peptidome to PRIDE and made publicly available under experiment accessions 17 900-18 271, representing 54 projects, ~53 million mass spectra, ~10 million peptide identifications, ~650,000 protein identifications, ~1.1 million biologically relevant protein modifications, and 28 species, from more than 30 different labs.
| S-EPMC3717177 | biostudies-literature
Project description:ADP-ribosylation is a post-translational modification where single units (mono-ADP-ribosylation) or polymeric chains (poly-ADP-ribosylation) of ADP-ribose are conjugated to proteins by ADP-ribosyltransferases. This post-translational modification and the ADP-ribosyltransferases (also known as PARPs) responsible for its synthesis have been found to play a role in nearly all major cellular processes, including DNA repair, transcription, translation, cell signaling, and cell death. Furthermore, dysregulation of ADP-ribosylation has been linked to diseases including cancers, diabetes, neurodegenerative disorders, and heart failure, leading to the development of therapeutic PARP inhibitors, many of which are currently in clinical trials. The study of this therapeutically important modification has recently been bolstered by the application of mass spectrometry-based proteomics, arguably the most powerful tool for the unbiased analysis of protein modifications. Unfortunately, progress has been hampered by the inherent challenges that stem from the physicochemical properties of ADP-ribose, which as a post-translational modification is highly charged, heterogeneous (linear or branched polymers, as well as monomers), labile, and found on a wide range of amino acid acceptors. In this Perspective, we discuss the progress that has been made in addressing these challenges, including the recent breakthroughs in proteomics techniques to identify ADP-ribosylation sites, and future developments to provide a proteome-wide view of the many cellular processes regulated by ADP-ribosylation.
| S-EPMC4486045 | biostudies-literature