ArticleJournal of proteome research2023
The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data.
Article in Journal of proteome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 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
7 citing papers in PubMed.
- Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment.Nature methods · 2025Article
- Open-Source and FAIR Research Software for Proteomics.Journal of proteome research · 2025Review
- Limelight: An Open, Web-Based Tool for Visualizing, Sharing, and Analyzing Mass Spectrometry Data from DDA Pipelines.Journal of proteome research · 2025Article
- Quetzal: Comprehensive Peptide Fragmentation Annotation and Visualization.Journal of proteome research · 2025Article
- Query Mix-Max Method for FDR Estimation Supported by Entrapment Queries.Journal of proteome research · 2025Article
- MS-PyCloud: A Cloud Computing-Based Pipeline for Proteomic and Glycoproteomic Data Analyses.Analytical chemistry · 2024Article
- 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
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
The Crux tandem mass spectrometry data analysis toolkit provides a collection of algorithms for analyzing bottom-up proteomics tandem mass spectrometry data. Many publications have described various individual components of Crux, but a comprehensive summary has not been published since 2014. The goal of this work is to summarize the functionality of Crux, focusing on developments since 2014. We begin with empirical results demonstrating our recently implemented speedups to the Tide search engine. Other new features include a new score function in Tide, two new confidence estimation procedures, as well as three new tools: Param-medic for estimating search parameters directly from mass spectrometry data, Kojak for searching cross-linked mass spectra, and DIAmeter for searching data independent acquisition data against a sequence database.
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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.