ArticleBioinformatics (Oxford, England)2008
Comparison of algorithms for pre-processing of SELDI-TOF mass spectrometry data.
Article in Bioinformatics (Oxford, England), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Reproductomics: Exploring the Applications and Advancements of Computational Tools.Physiological research · 2024Review
- SPA-STOCSY: an automated tool for identifying annotated and non-annotated metabolites in high-throughput NMR spectra.Bioinformatics (Oxford, England) · 2023Article
- SPA-STOCSY: An Automated Tool for Identification of Annotated and Non-Annotated Metabolites in High-Throughput NMR Spectra.bioRxiv : the preprint server for biology · 2023Article
- Bacterial species identification using MALDI-TOF mass spectrometry and machine learning techniques: A large-scale benchmarking study.Computational and structural biotechnology journal · 2021Article
- Cumulative learning enables convolutional neural network representations for small mass spectrometry data classification.Nature communications · 2020Article
- Computational Convolution of SELDI Data for the Diagnosis of Alzheimer's Disease.High-throughput · 2018Article
- Signal Partitioning Algorithm for Highly Efficient Gaussian Mixture Modeling in Mass Spectrometry.PloS one · 2015Article
- Radiation-induced changes in serum lipidome of head and neck cancer patients.International journal of molecular sciences · 2014Article
- Sensitive and specific peak detection for SELDI-TOF mass spectrometry using a wavelet/neural-network based approach.PloS one · 2012Article
- A simpler method of preprocessing MALDI-TOF MS data for differential biomarker analysis: stem cell and melanoma cancer studies.Clinical proteomics · 2011Article
- A high performance profile-biomarker diagnosis for mass spectral profiles.BMC systems biology · 2011Article
- Reproducible cancer biomarker discovery in SELDI-TOF MS using different pre-processing algorithms.PloS one · 2011Article
- Automatic selection of preprocessing methods for improving predictions on mass spectrometry protein profiles.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2010Article
- Quadratic variance models for adaptively preprocessing SELDI-TOF mass spectrometry data.BMC bioinformatics · 2010Article
- Mass spectrometry data processing using zero-crossing lines in multi-scale of Gaussian derivative wavelet.Bioinformatics (Oxford, England) · 2010Article
- A novel preprocessing method using Hilbert Huang Transform for MALDI-TOF and SELDI-TOF mass spectrometry data.PloS one · 2010Article
- Interdependence of signal processing and analysis of urine 1H NMR spectra for metabolic profiling.Analytical chemistry · 2009Article
- Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets.Proteome science · 2009Article
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6 authors.
Funding
Abstract
motivationSurface-enhanced laser desorption and ionization (SELDI) time of flight (TOF) is a mass spectrometry technology. The key features in a mass spectrum are its peaks. In order to locate the peaks and quantify their intensities, several pre-processing steps are required. Though different approaches to perform pre-processing have been proposed, there is no systematic study that compares their performance.
resultsIn this article, we present the results of a systematic comparison of various popular packages for pre-processing of SELDI-TOF data. We evaluate their performance in terms of two of their primary functions: peak detection and peak quantification. Regarding peak quantification, the performance of the algorithms is measured in terms of reproducibility. For peak detection, the comparison is based on sensitivity and false discovery rate. Our results show that for spectra generated with low laser intensity, the software developed by Ciphergen Biosystems (ProteinChip Software 3.1 with the additional tool Biomarker Wizard) produces relatively good results for both peak quantification and detection. On the other hand, for the data produced with either medium or high laser intensity, none of the methods show uniformly better performances under both criteria. Our analysis suggests that an advantageous combination is the use of the packages MassSpecWavelet and PROcess, the former for peak detection and the latter for peak quantification.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.