ArticleNature methods2017
Informed-Proteomics: open-source software package for top-down proteomics.
Article in Nature methods, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 91 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
91 citing papers in PubMed.
- ProteoformTracker: an interactive tool for planning proteoform detectability in top-down and middle-down proteomics.bioRxiv : the preprint server for biology · 2026Article
- A Unified Mass Spectrometry Workflow Integrating Bottom-Up and Native Top-Down Proteomics via Nanodroplet Enzymatic Digestion.Analytical chemistry · 2026Article
- Automating Middle-Down Mass Spectrometry Analysis for Extensive Antibody Characterization.Analytical chemistry · 2026Article
- Advances in Mass Spectrometry Instrumentation and Methodology for Analysis of Alternative Protein Isoforms.Journal of mass spectrometry : JMS · 2026Review
- Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome.Journal of cardiovascular development and disease · 2026Review
- An Overview of Mass Spectrometry-Based Methods to Analyze Post-Translational Modifications.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Proteoform Identification Using Multiplexed Top-Down Mass Spectra.Proteomics · 2025Article
- Article
- Circadian clock control of ribosome composition promotes rhythmic translation and termination fidelity.Cell reports · 2025Article
- Evaluation of Protein Ion Relative Ratio Quantification in Top-down Electrospray Ionization-Mass Spectrometry Using Site-Specific Acetylated Recombinant Histone H3 Proteoforms.Journal of the American Society for Mass Spectrometry · 2025Article
- ResNeXt-Based Rescoring Model for Proteoform Characterization in Top-Down Mass Spectra.Interdisciplinary sciences, computational life sciences · 2025Article
- A Fast Neural Network for Isotopic Charge State Assignment.Journal of the American Chemical Society · 2025Article
- TopLib: Building and Searching Top-Down Mass Spectral Libraries for Proteoform Identification.Analytical chemistry · 2025Article
- Spatial top-down proteomics for the functional characterization of human kidney.Clinical proteomics · 2025Article
- FAST MS: Software for the Automated Analysis of Top-Down Mass Spectra of Polymeric Molecules Including RNA, DNA, and Proteins.Journal of the American Society for Mass Spectrometry · 2025Article
- Improving Top-Down Sequence Coverage with Targeted Fragment Matching.Journal of the American Society for Mass Spectrometry · 2024Article
- Top-down mass spectrometry of native proteoforms and their complexes: a community study.Nature methods · 2024Article
- FLASHQuant: A Fast Algorithm for Proteoform Quantification in Top-Down Proteomics.Analytical chemistry · 2024Article
- pyMS-Vis, an Open-Source Python Application for Visualizing and Investigating Deconvoluted Top-Down Mass Spectrometric Experiments: A Histone Proteoform Case Study.Analytical chemistry · 2024Article
- Recent Contributions of Proteomics to Our Understanding of Reversible NJournal of proteome research · 2024Review
31 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
18 authors.
Funding
Abstract
Top-down proteomics, the analysis of intact proteins in their endogenous form, preserves valuable information about post-translation modifications, isoforms and proteolytic processing. The quality of top-down liquid chromatography-tandem MS (LC-MS/MS) data sets is rapidly increasing on account of advances in instrumentation and sample-processing protocols. However, top-down mass spectra are substantially more complex than conventional bottom-up data. New algorithms and software tools for confident proteoform identification and quantification are needed. Here we present Informed-Proteomics, an open-source software suite for top-down proteomics analysis that consists of an LC-MS feature-finding algorithm, a database search algorithm, and an interactive results viewer. We compare our tool with several other popular tools using human-in-mouse xenograft luminal and basal breast tumor samples that are known to have significant differences in protein abundance based on bottom-up analysis.
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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.