Protein and peptide identification and quantitation are essential tasks in proteomics research and involve a series of steps in analyzing mass spectrometry data. Trans-Proteomic Pipeline (TPP) provides a wide range of useful tools through its web interfaces for analyses such as sequence database search, statistical validation, and quantitation. To utilize the powerful functionality of TPP without the need for manual intervention to launch each step, we developed a software tool, called WinProphet, to create and automatically execute a pipeline for proteomic analyses. It seamlessly integrates with TPP and other external command-line programs, supporting various functionalities, including database search for protein and peptide identification, spectral library construction and search, data-independent acquisition (DIA) data analysis, and isobaric labeling and label-free quantitation. WinProphet is a standalone, installation-free tool with graphical interfaces for users to configure, manage, and automatically execute pipelines. The constructed pipelines can be exported as XML files with all of the parameter settings for reusability and portability. The executable files, user manual, and sample data sets of WinProphet are freely available at http://ms.iis.sinica.edu.tw/COmics/Software_WinProphet.html .
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1021/acs.analchem.9b01556 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Who is coming in? Evaluation of physician performance within multi-physician emergency departments.
Am J Emerg Med
January 2025
Department of Emergency Medicine, Yale University School of Medicine, New Haven, CT, USA; Center for Outcomes Research and Evaluation, Yale University, New Haven, CT, USA.
Background: This study aimed to examine how physician performance metrics are affected by the speed of other attendings (co-attendings) concurrently staffing the ED.
Methods: A retrospective study was conducted using patient data from two EDs between January-2018 and February-2020. Machine learning was used to predict patient length of stay (LOS) conditional on being assigned a physician of average speed, using patient- and departmental-level variables.
Nurse Leader Perspectives on Precepting in a Graduate Nursing Administration Practicum.
J Nurs Adm
December 2024
Author Affiliations: Assistant Professor (Dr Hickman), Assistant Professor (Dr Petri), and Coordinator (Connors), University of Maryland School of Nursing, Baltimore.
Objective: To describe practicum experiences as perceived by nurse leader preceptors of graduate students in a nursing administration practicum.
Background: Practicum experiences in graduate nursing administration programs provide students with exposure to the real-life experiences of nurse leaders, bridging the gap between academic knowledge gained and the application of that information to the workplace. The literature lacks best practices for graduate nursing administration practicum experiences.
A Preliminary Qualitative Exploration of the Lived Experiences of Presenteeism Among Taiwanese Nursing Staff.
J Nurs Adm
December 2024
Authors Affiliations: PhD Candidate (Hung) and Professor (Dr Jeng), School of Nursing, Taipei Medical University; Head Nurse (Hung) and Director (Dr Ming), Department of Nursing, Taipei Veterans General Hospital; Adjunct Assistant Professor (Dr Ming), School of Nursing, College of Nursing, National Yang Ming Chiao Tung University, Taipei City; and Professor (Dr Tsao), Nursing Department and Graduate School, National Taipei University of Nursing and Health Sciences, Taiwan.
Objective: The aim of this study was to explore the lived experiences of presenteeism among Taiwanese nursing staffs.
Background: Presenteeism is a subjective and multifaceted experience, but nurses have rarely been invited to provide their own views of presenteeism.
Methods: A qualitative study based on content analysis was conducted.
What has brain diffusion magnetic resonance imaging taught us about chronic primary pain: a narrative review.
Pain
February 2025
Department of Anesthesiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada.
Chronic pain is a pervasive and debilitating condition with increasing implications for public health, affecting millions of individuals worldwide. Despite its high prevalence, the underlying neural mechanisms and pathophysiology remain only partly understood. Since its introduction 35 years ago, brain diffusion magnetic resonance imaging (MRI) has emerged as a powerful tool to investigate changes in white matter microstructure and connectivity associated with chronic pain.
View Article and Find Full Text PDFEnergy-poverty-inequality SDGs: A large-scale household analysis and forecasting in China.
Proc Natl Acad Sci U S A
January 2025
Department of Biology, Stanford University, Stanford, CA 94305.
Affordable and clean energy, eliminating poverty, and reducing inequality are important goals of the United Nations Sustainable Development Goals (SDGs). This paper examines the role of access to clean cooking fuels in promoting income growth and reducing income inequality. Using data from Chinese households, we show that a 10% increase in the adoption of clean cooking fuels would result in an increase in total annual household income of US$37 billion nationwide.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!