ArticleJournal of the American Society for Mass Spectrometry2016
An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results.
Article in Journal of the American Society for Mass Spectrometry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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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.
The trial behind it
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
7 citing papers in PubMed.
- Spectroscape enables real-time query and visualization of a spectral archive in proteomics.Nature communications · 2023Article
- Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline.Journal of proteome research · 2023Article
- Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite.Journal of proteome research · 2023Article
- Rab1-AMPylation by Legionella DrrA is allosterically activated by Rab1.Nature communications · 2021Article
- Cross-ID: Analysis and Visualization of Complex XL-MS-Driven Protein Interaction Networks.Journal of proteome research · 2019Article
- Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus.Journal of proteome research · 2018Article
- Expanding the Scope of Cross-Link Identifications by Incorporating Collisional Activated Dissociation and Ultraviolet Photodissociation Methods.Analytical chemistry · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Protein-protein interactions are an important element in the understanding of protein function, and chemical cross-linking shotgun mass spectrometry is rapidly becoming a routine approach to identify these specific interfaces and topographical interactions. Protein cross-link data analysis is aided by dozens of algorithm choices, but hindered by a lack of a common format for representing results. Consequently, interoperability between algorithms and pipelines utilizing chemical cross-linking remains a challenge. pepXML is an open, widely-used format for representing spectral search algorithm results that has facilitated information exchange and pipeline development for typical shotgun mass spectrometry analyses. We describe an extension of this format to incorporate cross-linking spectral search results. We demonstrate application of the extension by representing results of multiple cross-linking search algorithms. In addition, we demonstrate adapting existing pepXML-supporting software pipelines to analyze protein cross-linking results formatted in pepXML. Graphical Abstract ᅟ.
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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.