A plethora of software suites and multiple classes of spectral libraries have been developed to enhance the depth and robustness of data-independent acquisition (DIA) data processing. However, how the combination of a DIA software tool and a spectral library impacts the outcome of DIA proteomics and phosphoproteomics data analysis has been rarely investigated using benchmark data that mimics biological complexity. In this study, we create DIA benchmark data sets simulating the regulation of thousands of proteins in a complex background, which are collected on both an Orbitrap and a timsTOF instruments. We evaluate four commonly used software suites (DIA-NN, Spectronaut, MaxDIA and Skyline) combined with seven different spectral libraries in global proteome analysis. Moreover, we assess their performances in analyzing phosphopeptide standards and TNF-α-induced phosphoproteome regulation. Our study provides a practical guidance on how to construct a robust data analysis pipeline for different proteomics studies implementing the DIA technique.
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http://dx.doi.org/10.1038/s41467-022-35740-1 | DOI Listing |
Sci Rep
January 2025
Center for Health Technology and Services Research (CINTESIS@RISE), School of Health Sciences, University of Aveiro, Aveiro, Portugal.
This study describes the process of designing and developing the user interface of a digital solution aiming to promote physical and cognitive training (DanceMove) and testing for its usability by community-dwelling older adults. This study is subdivided into four phases: (i) concept and ideation, (ii) design and development of the prototype, (iii) testing of the functional mock-ups, and (iv) testing of the prototype in the laboratory and in the real context of use. Through the different phases of the study technological and healthcare professionals and users were involved.
View Article and Find Full Text PDFJMIR Med Inform
January 2025
Department of Medical Informatics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
Background: The field of digital health solutions (DHS) has grown tremendously over the past years. DHS include tools for self-management, which support individuals to take charge of their own health. The usability of DHS, as experienced by patients, is pivotal to adoption.
View Article and Find Full Text PDFOrphanet J Rare Dis
January 2025
Ionis Pharmaceuticals, Inc, 2855 Gazelle Court, Carlsbad, CA, 92010, USA.
Background: Hereditary angioedema (HAE) is a rare, autosomal dominant disorder causing swelling attacks in various parts of the body, resulting in impacts on health-related quality of life (HRQoL). The symptoms of HAE and its impacts on HRQoL have been well-documented in adults; however, relatively little is known about the experiences of adolescents with HAE. The objective of this study was to use qualitative interviews to investigate how adolescents experience HAE symptoms and how HAE impacts their HRQoL.
View Article and Find Full Text PDFCureus
December 2024
Radiology, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS) Saveetha University, Chennai, IND.
Introduction Cosmetic surgery has advanced significantly, with wound closure techniques crucial for determining aesthetic and healing outcomes. Recently, cyanoacrylate glue and subcuticular sutures have gained attention for their unique benefits in cosmetic procedures. Cyanoacrylate glue, a non-invasive tissue adhesive, facilitates faster wound closure with minimal trauma, while subcuticular sutures offer durable, concealed closures, particularly suited for areas under mechanical stress.
View Article and Find Full Text PDFBrief Bioinform
November 2024
National Center, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng Road, Hangzhou 310052, P. R. China.
The unique cyclic structure of cyclic peptides grants them remarkable stability and bioactivity, making them powerful candidates for treating various diseases. However, the lack of standardized tools for cyclic peptide data has hindered their potential in today's artificial intelligence-driven efficient drug design landscape. To bridge this gap, here we introduce a Python package named cyclicpeptide specifically for cyclic peptide drug design.
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