ArticlePloS one2016
Performance Investigation of Proteomic Identification by HCD/CID Fragmentations in Combination with High/Low-Resolution Detectors on a Tribrid, High-Field Orbitrap Instrument.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed, 28 citations in OpenAlex.
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- PCI-DB: a novel primary tissue immunopeptidome database to guide next-generation peptide-based immunotherapy development.Journal for immunotherapy of cancer · 2025Article
- IS-PRM-Based Peptide Targeting Informed by Long-Read Sequencing for Alternative Proteome Detection.Journal of the American Society for Mass Spectrometry · 2024Article
- IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection.bioRxiv : the preprint server for biology · 2024Article
- Pseudomonassin, a New Bioactive Ribosomally Synthesised and Post-Translationally Modified Peptide fromMicroorganisms · 2023Article
- Recent advances in mass spectrometry analysis of neuropeptides.Mass spectrometry reviews · 2023Review
- MS-based glycomics: An analytical tool to assess nervous system diseases.Frontiers in neuroscience · 2022Review
- Online Nanoflow Two-Dimension Comprehensive Active Modulation Reversed Phase-Reversed Phase Liquid Chromatography High-Resolution Mass Spectrometry for Metaproteomics of Environmental and Microbiome Samples.Journal of proteome research · 2021Article
- Review of Methodological Approaches to Human Milk Small Extracellular Vesicle Proteomics.Biomolecules · 2021Review
- The Binary Toxin ofFrontiers in microbiology · 2021Article
- The Power of Three in Cannabis Shotgun Proteomics: Proteases, Databases and Search Engines.Proteomes · 2020Article
- Comparative Evaluation of Data Dependent and Data Independent Acquisition Workflows Implemented on an Orbitrap Fusion for Untargeted Metabolomics.Metabolites · 2020Article
- Proteomic Pathway Analysis of Monocyte-Derived Exosomes during Surgical Sepsis Identifies Immunoregulatory Functions.Surgical infections · 2020Article
- Surfactant and Chaotropic Agent Assisted Sequential Extraction/On-Pellet Digestion (SCAD) for Enhanced Proteomics.Journal of proteome research · 2018Article
- Peptide identifications and false discovery rates using different mass spectrometry platforms.Talanta · 2018Article
- Expanding Proteome Coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) Combined with Broad Specificity Proteolysis.Journal of proteome research · 2017Article
- GlycCompSoft: Software for Automated Comparison of Low Molecular Weight Heparins Using Top-Down LC/MS Data.PloS one · 2016Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The recently-introduced Orbitrap Fusion mass spectrometry permits various types of MS2 acquisition methods. To date, these different MS2 strategies and the optimal data interpretation approach for each have not been adequately evaluated. This study comprehensively investigated the four MS2 strategies: HCD-OT (higher-energy-collisional-dissociation with Orbitrap detection), HCD-IT (HCD with ion trap, IT), CID-IT (collision-induced-dissociation with IT) and CID-OT on Orbitrap Fusion. To achieve extensive comparison and identify the optimal data interpretation method for each technique, several search engines (SEQUEST and Mascot) and post-processing methods (score-based, PeptideProphet, and Percolator) were assessed for all techniques for the analysis of a human cell proteome. It was found that divergent conclusions could be made from the same dataset when different data interpretation approaches were used and therefore requiring a relatively fair comparison among techniques. Percolator was chosen for comparison of techniques because it performs the best among all search engines and MS2 strategies. For the analysis of human cell proteome using individual MS2 strategies, the highest number of identifications was achieved by HCD-OT, followed by HCD-IT and CID-IT. Based on these results, we concluded that a relatively fair platform for data interpretation is necessary to avoid divergent conclusions from the same dataset, and HCD-OT and HCD-IT may be preferable for protein/peptide identification using Orbitrap Fusion.
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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.