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Observations from the proteomics bench
Open accessPreprint — published as 10.3390/proteomes12010006
Abstract
Many challenges in proteomics result from the high-throughput nature of the experiments. The paper first presents pre-analytical problems, which still occur, although the call for standardisation in omics has been ongoing for many years. This article also discusses aspects, which affect bioinformatic analysis, based on three sets of reference data measured with different orbitrap instruments. Despite continuous advances in mass spectrometer technology as well as analysis software, data set-wise quality control is still necessary and decoy-based estimation, although challenged by modern instruments, should be utilized. We draw attention to the fact that numerous young researchers perceive proteomics as a mature, readily applicable technology. However, it is important to emphasize that the maximum potential of the technology can only be realized by an educated handling of its limitations.
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Cites
How many human proteoforms are there?
Aebersold, R., Agar, J. N., Amster, I. J., Baker, M. S., Bertozzi, C. R., Boja, E. S., Costello, C. E., Cravatt, B. F., Fenselau, C., Garcia, B. A., et al. (2018) · Nature Chemical Biology · doi:10.1038/nchembio.2576 · Cited by 907
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Metadata
- Authors
- König, S., Schork, K., & Eisenacher, M.
- Affiliations
- University of Münster (DE)
- Ruhr University Bochum (DE)
- Corresponding author
- König, Simone
- Venue
- Proteomes
- Publisher
- MDPI AG
- Published
- 2024-01-05
- Volume
- 12
- Issue
- 1
- Pages
- 6-6
- ISSN
- 2227-7382 (ISSN-L)
- PMC
- PMC10885119
- OpenAlex
- W4391576496
- Cited by
- 4
- References
- 1
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 2
- FWCI
- 0.50
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Proteomes (publishedVersion, cc-by)
- Preprints.org (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- proteomics, Orbitrap mass spectrometer, reference dataset, data quality control, bioinformatics analysis, high-throughput proteomics
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