In the "post-genome" era, mass spectrometry (MS) has become an important method for the analysis of proteome data. The rapid advancement of this technique in combination with other methods used in proteomics results in an increasing number of high-throughput projects. This leads to an increasing amount of data that needs to be archived and analyzed. To cope with the need for automated data conversion, storage, and analysis in the field of proteomics, the open source system ProDB was developed. The system handles data conversion from different mass spectrometer software, automates data analysis, and allows the annotation of MS spectra (e.g. assign gene names, store data on protein modifications). The system is based on an extensible relational database to store the mass spectra together with the experimental setup. It also provides a graphical user interface (GUI) for managing the experimental steps which led to the MS data. Furthermore, it allows the integration of genome and proteome data. Data from an ongoing experiment was used to compare manual and automated analysis. First tests showed that the automation resulted in a significant saving of time. Furthermore, the quality and interpretability of the results was improved in all cases.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/j.jbiotec.2003.08.009 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Leveraging molecular dynamics, physicochemical, and structural analysis to explore OMP33-36 protein as a drug target in Acinetobacter baumannii: An approach against nosocomial infection.
J Mol Graph Model
January 2025
Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Gomtinagar Extension, Lucknow, 226028, India; Research Cell, Amity University Uttar Pradesh, Lucknow Campus, India. Electronic address:
The Acinetobacter baumannii is a member of the "ESKAPE" bacteria responsible for many serious multidrug-resistant (MDR) illnesses. This bacteria swiftly adapts to environmental cues leading to the emergence of multidrug-resistant variants, particularly in hospital/medical settings. In this work, we have demonstrated the outer membrane protein 33-36 (Omp33-36) porin as a potential therapeutic target in A.
View Article and Find Full Text PDFA study on how to improve students' continuance intention in landscape architecture conservation course within a virtual learning environment based on SVVR.
Acta Psychol (Amst)
January 2025
Department of Culture and Arts Management, Honam University, 62399 Gwangju, South Korea. Electronic address:
With the rapid pace of global urbanization, preserving natural landscapes has become increasingly critical. However, urbanization presents significant environmental risks worsened by decreased ecological consciousness. This has led to a pressing demand for education in landscape conservation.
View Article and Find Full Text PDFInvestigating the relationship between goal orientation, self-efficacy, positive emotionality, and affective engagement among Chinese students.
Acta Psychol (Amst)
January 2025
School of Marxism, Southwest Jiaotong University Hope College, Chengdu 610400, China; Health and Rehabilitation College, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, China. Electronic address:
This study delved into the complex interplay between self-efficacy, achievement goals, positive emotions, and affective engagement among university students in China. To achieve this, a stratified random sampling technique was employed, resulting in a sample of 391 students from four geographically distinct universities across China. The data collection relied on self-reported questionnaires that measured academic self-efficacy, goal orientation (specifically focusing on mastery versus performance goals), positive emotions, and various aspects of affective engagement, including enjoyment, satisfaction, and interest in learning.
View Article and Find Full Text PDFHeterogeneous distribution of the reported prevalence of Dirofilaria immitis infections in Australian canids - A systematic review and meta-analysis.
Prev Vet Med
January 2025
The University of Adelaide - Roseworthy Campus, Mudla Wirra Rd, Roseworthy, SA 5371, Australia; The University of Sydney, Regimental Dr, Camperdown, NSW 2050, Australia. Electronic address:
Reports of Dirofilaria immitis infection vary by location in the USA and Europe, with an occurrence gradient increasing towards the equator and warmer climates. In Australia, heartworm preventative guidelines are not climate specific, implying homogenous risk of infection across the continent. We systematically reviewed the published literature to assess if the distribution of D.
View Article and Find Full Text PDFMelatonin protects aged oocytes from depalmitoylation-mediated quality reduction by promoting PPT1 degradation and antioxidation.
Redox Biol
January 2025
Department of Reproductive Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210002, China; State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, China; Department of Reproductive Medicine, Affiliated Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, 210002, China. Electronic address:
Oocyte aging is closely related to a decline in female fertility, accompanied by increased reactive oxygen species levels and changes in protein posttranslational modifications. However, the role of protein palmitoylation in oocyte aging has not been investigated. In the present study, a new association between redox and palmitoylation in aging oocytes was found.
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!