Bioinformatics solutions for confident identification and targeted quantification of proteins using tandem mass spectrometry

Proteins are the structural supports, signal messengers and molecular workhorses that underpin living processes in every cell. Understanding when and where proteins are expressed, and their structure and functions, is the realm of proteomics. Mass spectrometry (MS) is a powerful method for identifying and quantifying proteins, however, very large datasets are produced, so researchers rely on computational approaches to transform raw data into protein information. This project develops new bioinformatics solutions to support the next generation of proteomic MS research. Part I introduces the state of the art in proteomic bioinformatics in industry and academia. The business history and funding mechanisms are examined to fill a notable gap in management research literature, and to explain events at the sponsor, GlaxoSmithKline. It reveals that public funding of proteomic science has yet to come to fruition and exclusively high-tech niche bioinformatics businesses can succeed in the current climate. Next, a comprehensive review of repositories for proteomic MS is performed, to locate and compile a summary of sources of datasets for research activities in this project, and as a novel summary for the community. Part II addresses the issue of false positive protein identifications produced by automated analysis with a proteomics pipeline. The work shows that by selecting a suitable decoy database design, a statistically significant improvement in identification accuracy can be made. Part III describes development of computational resources for selecting multiple reaction monitoring (MRM) assays for quantifying proteins using MS. A tool for transition design, MRMaid (pronounced „mermaid‟), and database of pre-published transitions, MRMaid-DB, are developed, saving practitioners time and leveraging existing resources for superior transition selection. By improving the quality of identifications, and providing support for quantitative approaches, this project brings the field a small step closer to achieving the goal of systems biology.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Center on Disability Studies eNewsletter, September 2022

Welcome to the September 2022 issue of the CDS eNewsletter. Special highlights in this issue include: Featured Artist Lynnell Mateaki RDS Seeks Manuscript Review Board Members Exhibitor Release #PacRim2023 Introducing Deaf in Government Partnership #PacRim2023 Call for Presentation Proposals #PacRim2023 Legislative Forum Dates | Hawaiʻi DD Council Hawaiʻi's Path to Employment First Seminar Recording Now Available 2022-2023 CDS Community Advisory Council Introduction Website Launch Project Hoʻokuʻi V: Kūlia i ka Nuʻu Fall Announcements with Project Hōkūlani eNewsletterSpecial eNewsletter highlights include: Featured Artist Lynnell Mateaki; RDS Seeks Disability Studies Call for Reviewers; Pac Rim Exhibitor Invitation; Pac Rim Call for Proposals; Hawaiʻi State Council on Developmental Disabilities Legislative Forums; Presentation Hawaiʻi's Path to Employment First with Patrick Gartside available; Introducing 2022-2023 Community Advisory Council; Project Hoʻokuʻi V: Kūlia i ka Nuʻu Website Launch; and Project Hōkūlani 2022 Summer eNewsletter Release, Hōkūlani Insider

Bioinformatics solutions for confident identification and targeted quantification of proteins using tandem mass spectrometry

Proteins are the structural supports, signal messengers and molecular workhorses that underpin living processes in every cell. Understanding when and where proteins are expressed, and their structure and functions, is the realm of proteomics. Mass spectrometry (MS) is a powerful method for identifying and quantifying proteins, however, very large datasets are produced, so researchers rely on computational approaches to transform raw data into protein information. This project develops new bioinformatics solutions to support the next generation of proteomic MS research. Part I introduces the state of the art in proteomic bioinformatics in industry and academia. The business history and funding mechanisms are examined to fill a notable gap in management research literature, and to explain events at the sponsor, GlaxoSmithKline. It reveals that public funding of proteomic science has yet to come to fruition and exclusively high-tech niche bioinformatics businesses can succeed in the current climate. Next, a comprehensive review of repositories for proteomic MS is performed, to locate and compile a summary of sources of datasets for research activities in this project, and as a novel summary for the community. Part II addresses the issue of false positive protein identifications produced by automated analysis with a proteomics pipeline. The work shows that by selecting a suitable decoy database design, a statistically significant improvement in identification accuracy can be made. Part III describes development of computational resources for selecting multiple reaction monitoring (MRM) assays for quantifying proteins using MS. A tool for transition design, MRMaid (pronounced „mermaid‟), and database of pre-published transitions, MRMaid-DB, are developed, saving practitioners time and leveraging existing resources for superior transition selection. By improving the quality of identifications, and providing support for quantitative approaches, this project brings the field a small step closer to achieving the goal of systems biology

Example room layout for an interactive workshop.

<p>This bird's-eye view shows the setup for supporting group-based, facilitated activities around a specific topic, problem, or project. The moderator oversees the workshop with the help of facilitators, who are briefed in the aims and methods of the activities. Alternatives include “circuit training” layout, where each table is an activity station and the participants move around the room.</p

Example of a workshop artefact: The output of the “Speed Boat” activity.

<p>The aim of this activity is to identify improvements that need to be made, for instance, to a product or service. The boat and anchors are drawn on paper as a template before the workshop. During the activity, the groups add their ideas in pen: they write the goal of the workshop on the boat and the challenges to achieving this goal by the anchors. We also include “positive forces for change”—things that are moving the project towards the goal—as “wind arrows” flanking the boat. The sticky notes have been added after the activity by the facilitator during the presenting-back stage and group discussion. The sticky notes have been labelled with the letters A to E for reference; note that a labelling scheme may be helpful for the analysis and report. This activity was adapted from p. 206 in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003485#pcbi.1003485-Gray1" target="_blank">[5]</a>; also watch this video for more hints: <a href="http://www.youtube.com/watch?v=xwVbcioYvdM" target="_blank">http://www.youtube.com/watch?v=xwVbcioYvdM</a>.</p

Example of a visual agenda.

<p>This was created for an internal workshop held to gather ideas for a website redesign process. Visual agendas are useful for setting the creative tone needed for successful interactive workshops.</p

Bioinformatics meets user-centred design: a perspective.

Designers have a saying that "the joy of an early release lasts but a short time. The bitterness of an unusable system lasts for years." It is indeed disappointing to discover that your data resources are not being used to their full potential. Not only have you invested your time, effort, and research grant on the project, but you may face costly redesigns if you want to improve the system later. This scenario would be less likely if the product was designed to provide users with exactly what they need, so that it is fit for purpose before its launch. We work at EMBL-European Bioinformatics Institute (EMBL-EBI), and we consult extensively with life science researchers to find out what they need from biological data resources. We have found that although users believe that the bioinformatics community is providing accurate and valuable data, they often find the interfaces to these resources tricky to use and navigate. We believe that if you can find out what your users want even before you create the first mock-up of a system, the final product will provide a better user experience. This would encourage more people to use the resource and they would have greater access to the data, which could ultimately lead to more scientific discoveries. In this paper, we explore the need for a user-centred design (UCD) strategy when designing bioinformatics resources and illustrate this with examples from our work at EMBL-EBI. Our aim is to introduce the reader to how selected UCD techniques may be successfully applied to software design for bioinformatics

CORRESPONDENCE Open Access The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics

The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics de Matos et al. de Matos et al. BMC Bioinformatics 2013, 14:10