ArticleJournal of proteome research2016
Dinosaur: A Refined Open-Source Peptide MS Feature Detector.
Article in Journal of proteome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 1 of them a synthesis that pooled it.
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Who cites it
34 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Comprehensive proteomics and meta-analysis of COVID-19 host response.Nature communications · 2023Pooled it
- Targeting infection-specific peptides in immunopeptidomics studies for vaccine target discovery.The Journal of experimental medicine · 2025Article
- On the question of correct use of replicates in quantitative label-free proteomics.Analytical and bioanalytical chemistry · 2025Article
- MassCube improves accuracy for metabolomics data processing from raw files to phenotype classifiers.Nature communications · 2025Article
- SWAPS: A Modular Deep-Learning Empowered Peptide Identity Propagation Framework Beyond Match-Between-Run.Journal of proteome research · 2025Article
- Increasing Proteome Coverage Through a Reduction in Analyte Complexity in Single-Cell Equivalent Samples.Journal of proteome research · 2025Article
- Metabolic labeling based methylome profiling enables functional dissection of histidine methylation in C3H1 zinc fingers.Nature communications · 2024Article
- The quantification of zebrafish ocular-associated proteins provides hints for sex-biased visual impairments and perception.Heliyon · 2024Article
- AlphaPept: a modern and open framework for MS-based proteomics.Nature communications · 2024Article
- DeepRTAlign: toward accurate retention time alignment for large cohort mass spectrometry data analysis.Nature communications · 2023Article
- Data-Driven Optimization of DIA Mass Spectrometry by DO-MS.Journal of proteome research · 2023Article
- Data-Driven Optimization of DIA Mass Spectrometry by DO-MS.bioRxiv : the preprint server for biology · 2023Article
- TopFD: A Proteoform Feature Detection Tool for Top-Down Proteomics.Analytical chemistry · 2023Article
- Strategies for Increasing the Depth and Throughput of Protein Analysis by plexDIA.Journal of proteome research · 2023Review
- Integrating Identification and Quantification Uncertainty for Differential Protein Abundance Analysis with Triqler.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Deep Learning Based MS2 Feature Detection for Data-Independent Shotgun Proteomics.Proceedings. IEEE International Conference on Bioinformatics and Biomedicine · 2022Article
- Coisolation of Peptide Pairs for Peptide Identification and MS/MS-Based Quantification.Analytical chemistry · 2022Article
- Multiomic Profiling Identified EGF Receptor Signaling as a Potential Inhibitor of Type I Interferon Response in Models of Oncolytic Therapy by Vesicular Stomatitis Virus.International journal of molecular sciences · 2022Article
- A de novo MS1 feature detector for the Bruker timsTOF Pro.PloS one · 2022Article
- Leaf Apoplast of Field-Grown Potato Analyzed by Quantitative Proteomics and Activity-Based Protein Profiling.International journal of molecular sciences · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
In bottom-up mass spectrometry (MS)-based proteomics, peptide isotopic and chromatographic traces (features) are frequently used for label-free quantification in data-dependent acquisition MS but can also be used for the improved identification of chimeric spectra or sample complexity characterization. Feature detection is difficult because of the high complexity of MS proteomics data from biological samples, which frequently causes features to intermingle. In addition, existing feature detection algorithms commonly suffer from compatibility issues, long computation times, or poor performance on high-resolution data. Because of these limitations, we developed a new tool, Dinosaur, with increased speed and versatility. Dinosaur has the functionality to sample algorithm computations through quality-control plots, which we call a plot trail. From the evaluation of this plot trail, we introduce several algorithmic improvements to further improve the robustness and performance of Dinosaur, with the detection of features for 98% of MS/MS identifications in a benchmark data set, and no other algorithm tested in this study passed 96% feature detection. We finally used Dinosaur to reimplement a published workflow for peptide identification in chimeric spectra, increasing chimeric identification from 26% to 32% over the standard workflow. Dinosaur is operating-system-independent and is freely available as open source on https://github.com/fickludd/dinosaur .
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Registered trials
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.