ArticleAnalytical chemistry2011
On the accuracy and limits of peptide fragmentation spectrum prediction.
Article in Analytical chemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Peptide ratios for post-mortem interval estimation using targeted liquid chromatography triple quadrupole mass spectrometry.International journal of legal medicine · 2026Article
- Applications and Prospects of Artificial Intelligence in ProteomicsCurrent protein & peptide science · 2026Review
- TopLib: Building and Searching Top-Down Mass Spectral Libraries for Proteoform Identification.Analytical chemistry · 2025Article
- Decoding Neuropeptide Complexity: Advancing Neurobiological Insights from Invertebrates to Vertebrates through Evolutionary Perspectives.ACS chemical neuroscience · 2025Review
- Mass Spectral Library for DNA Adductomics.Chemical research in toxicology · 2024Article
- Accurate Prediction of y Ions in Beam-Type Collision-Induced Dissociation Using Deep Learning.Analytical chemistry · 2022Article
- Deep learning neural network tools for proteomics.Cell reports methods · 2021Review
- Quantum Chemistry Calculations for Metabolomics.Chemical reviews · 2021Review
- CIDer: A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation.Journal of proteome research · 2021Article
- Deep Learning in Proteomics.Proteomics · 2020Review
- A Fast and Memory-Efficient Spectral Library Search Algorithm Using Locality-Sensitive Hashing.Proteomics · 2020Article
- NAguideR: performing and prioritizing missing value imputations for consistent bottom-up proteomic analyses.Nucleic acids research · 2020Article
- A Frequency-Based Approach to Predict the Low-Energy Collision-Induced Dissociation Fragmentation Spectra.ACS omega · 2020Article
- Software-aided detection and structural characterization of cyclic peptide metabolites in biological matrix by high-resolution mass spectrometry.Journal of pharmaceutical analysis · 2020Article
- Full-Spectrum Prediction of Peptides Tandem Mass Spectra using Deep Neural Network.Analytical chemistry · 2020Article
- In silico spectral libraries by deep learning facilitate data-independent acquisition proteomics.Nature communications · 2020Article
- MS2CNN: predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks.BMC genomics · 2019Article
- Impact of Amidination on Peptide Fragmentation and Identification in Shotgun Proteomics.Journal of proteome research · 2016Article
- Technical Challenges in Mass Spectrometry-Based Metabolomics.Mass spectrometry (Tokyo, Japan) · 2016Article
- Building high-quality assay libraries for targeted analysis of SWATH MS data.Nature protocols · 2015Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
We estimated the reproducibility of tandem mass spectra for the widely used collision-induced dissociation (CID) of peptide ions. Using the Pearson correlation coefficient as a measure of spectral similarity, we found that the within-experiment reproducibility of fragment ion intensities is very high (about 0.85). However, across different experiments and instrument types/setups, the correlation decreases by more than 15% (to about 0.70). We further investigated the accuracy of current predictors of peptide fragmentation spectra and found that they are more accurate than the ad-hoc models generally used by search engines (e.g., SEQUEST) and, surprisingly, approaching the empirical upper limit set by the average across-experiment spectral reproducibility (especially for charge +1 and charge +2 precursor ions). These results provide evidence that, in terms of accuracy of modeling, predicted peptide fragmentation spectra provide a viable alternative to spectral libraries for peptide identification, with a higher coverage of peptides and lower storage requirements. Furthermore, using five data sets of proteome digests by two different proteases, we find that PeptideART (a data-driven machine learning approach) is generally more accurate than MassAnalyzer (an approach based on a kinetic model for peptide fragmentation) in predicting fragmentation spectra but that both models are significantly more accurate than the ad-hoc models.
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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.