The application of mass spectrometry (MS) to the analysis of proteomes has enabled the high-throughput identification and abundance measurement of hundreds to thousands of proteins per experiment. ...However, the formidable informatics challenge associated with analyzing MS data has required a wide variety of data file formats to encode the complex data types associated with MS workflows. These formats encompass the encoding of input instruction for instruments, output products of the instruments, and several levels of information and results used by and produced by the informatics analysis tools. A brief overview of the most common file formats in use today is presented here, along with a discussion of related topics.
Abstract
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.
The ProteomeXchange (PX) Consortium of proteomics resources (http://www.proteomexchange.org) was formally started in 2011 to standardize data submission and dissemination of mass spectrometry ...proteomics data worldwide. We give an overview of the current consortium activities and describe the advances of the past few years. Augmenting the PX founding members (PRIDE and PeptideAtlas, including the PASSEL resource), two new members have joined the consortium: MassIVE and jPOST. ProteomeCentral remains as the common data access portal, providing the ability to search for data sets in all participating PX resources, now with enhanced data visualization components.We describe the updated submission guidelines, now expanded to include four members instead of two. As demonstrated by data submission statistics, PX is supporting a change in culture of the proteomics field: public data sharing is now an accepted standard, supported by requirements for journal submissions resulting in public data release becoming the norm. More than 4500 data sets have been submitted to the various PX resources since 2012. Human is the most represented species with approximately half of the data sets, followed by some of the main model organisms and a growing list of more than 900 diverse species. Data reprocessing activities are becoming more prominent, with both MassIVE and PeptideAtlas releasing the results of reprocessed data sets. Finally, we outline the upcoming advances for ProteomeXchange.
Exploring and identifying a good feature representation to describe high-dimensional datasets is a challenge of prime importance. However, plenty of feature selection techniques and distance metrics ...exist, which entails an intricacy for identifying the one best suited to the task. This paper provides an algorithm to design high-order distance metrics over a sparse selection of features dedicated to classification. Our approach is based on Conditional Random Field (CRF) energy minimization and Dual Decomposition, which allow efficiency and great flexibility in the considered features. The optimization technique ensures the tractability of high-dimensionality problems using hundreds of features and samples. Our approach is evaluated on synthetic data as well as on Covid-19 patient stratification. Comparisons with state-of-the-art baselines and our proposed method on different classification results prove the learned metric’s relevance.
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•Novel higher-order metric learning algorithm with Conditional Random Fields.•Leverage graph and hyper-graph structures.•Semi-supervised feature selection and weighting.•Dedicated classification principle.
SummaryImmunotherapy is radically changing the clinical management of patients affected by an increasingly wide array of tumours. However, not all patients achieve long-term clinical benefits from ...immunotherapy as a standalone treatment, calling for the development of regimens that combine various interventions. Radiotherapy stands out as a particularly promising candidate in this setting, not only because of its established safety profile, but also because radiotherapy has the potential ability to mediate robust immunostimulatory effects that could synergise with immunotherapy in systemic tumour control. However, optimal radioimmunotherapy regimens might call for the redefinition of conventional radiotherapy doses and fractionation schedules. In this Series paper, we discuss current approaches to improve the efficacy and reduce the toxicity of radioimmunotherapy for the management of cancer.
A crucial part of a successful systems biology experiment is an assay that provides reliable, quantitative measurements for each of the components in the system being studied. For proteomics to be a ...key part of such studies, it must deliver accurate quantification of all the components in the system for each tested perturbation without any gaps in the data. This will require a new approach to proteomics that is based on emerging targeted quantitative mass spectrometry techniques. The PeptideAtlas Project comprises a growing, publicly accessible database of peptides identified in many tandem mass spectrometry proteomics studies and software tools that allow the building of PeptideAtlas, as well as its use by the research community. Here, we describe the PeptideAtlas Project, its contents and components, and show how together they provide a unique platform to select and validate mass spectrometry targets, thereby allowing the next revolution in proteomics.
Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) was ...originally set up to standardize data submission and dissemination of public MS proteomics data. It is now 10 years since the initial data workflow was implemented. In this manuscript, we describe the main developments in PX since the previous update manuscript in Nucleic Acids Research was published in 2020. The six members of the Consortium are PRIDE, PeptideAtlas (including PASSEL), MassIVE, jPOST, iProX and Panorama Public. We report the current data submission statistics, showcasing that the number of datasets submitted to PX resources has continued to increase every year. As of June 2022, more than 34 233 datasets had been submitted to PX resources, and from those, 20 062 (58.6%) just in the last three years. We also report the development of the Universal Spectrum Identifiers and the improvements in capturing the experimental metadata annotations. In parallel, we highlight that data re-use activities of public datasets continue to increase, enabling connections between PX resources and other popular bioinformatics resources, novel research and also new data resources. Finally, we summarise the current state-of-the-art in data management practices for sensitive human (clinical) proteomics data.
Ionizing radiation has historically been used to treat cancer by killing tumour cells, in particular by inducing DNA damage. This view of radiotherapy (RT) as a simple cytotoxic agent has ...dramatically changed in recent years, and it is now widely accepted that RT can deeply reshape the tumour environment by modulating the immune response. Such evidence gives a strong rationale for the use of immunomodulators to boost the therapeutic value of RT, introducing the era of ‘immunoradiotherapy’. The increasing amount of preclinical and clinical data concerning the combination of RT with immunomodulators, in particular with immune checkpoint inhibitors such as anti‐PD‐1/PD‐L1 and anti‐CTLA4, reflects the interest of the scientific and medical community concerning immunoradiotherapy. The expectations are enormous since the rationale for performing such combinations is strong, with the possibility to use a local treatment such as RT to amplify a systemic antitumour response, as illustrated by the case of the abscopal effect. Nevertheless, several points remain to be addressed such as the need to find biomarkers to identify patients who will benefit from immunoradiotherapy, the identification of the best sequences/schedules for combination with immunomodulators and mechanisms to overcome resistance. Additionally, the effects of immunoradiotherapy on healthy tissues and related toxicity remain largely unexplored. To answer these critical questions and make immunoradiotherapy keep its promising qualities, large efforts are needed from both the pharmaceutical industry and academic/governmental research. Moreover, because of the work of both these entities, the arsenal of available immunomodulators is quickly expanding, thus opening the field to increasing combinations with RT. We thus forecast that the field of immunoradiotherapy will further expand in the coming years, and it needs to be supported by appropriate investment plans.
This review briefly summarizes the results obtained so far using the combination of immunomodulators with radiotherapy (immunoradiotherapy), both preclinically and clinically, and discusses the perspectives and challenges, including the still limited exploration of the effects of immunoradiotherapy on healthy tissues and related toxicity.
Discover the practical, real-world advantages of the Oliver Wight master planning and scheduling methodology. The newly revised Fourth Edition of Master Planning and Scheduling: An Essential Guide to ...Competitive Manufacturing delivers a masterful exploration of today's master planning and scheduling techniques, as well as an insightful discussion of the future of the master planning and scheduling processes and profession. Written in the context of an ever-evolving digital environment and augmented with new and critical information required to implement best practices, the book is a guide for practitioners and leaders on the principles of master planning and scheduling and its application in modern and future work environments. In this book, readers will learn: Insights regarding top-down, bottom-up, and side-to-side integration of business practices in support of a company's strategic direction and tactical deployment The critical link between time-phased integrated business planning, master planning, master scheduling, capacity planning, and material planning "How-to" details and examples to support master planning and scheduling implementation and enhancements within the company's demand and supply organizations Master Planning and Scheduling is an indispensable guide for supply chain professionals, planners and schedulers in all functional domains of a business. It also belongs on the bookshelves of any executive or manager who seeks to improve their understanding of best practice planning and scheduling processes and how those processes enable a business to outperform the competition through alignment, integration and synchronization across all functions in an organization.
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