ArticleNature protocols2016
Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0.
Article in Nature protocols, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 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.
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
112 citing papers in PubMed.
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- Fungal Extracellular Vesicles are Recoverable Across Variable Ultracentrifugation Speeds but Display Species-specific Profiles of Sedimentation.The Journal of membrane biology · 2026Article
- Suppression of astrocyte BMP signaling improves molecular signatures and functional deficits in a fragile X syndrome mouse model.Nature communications · 2026Article
- Proangiogenic Properties of Extracellular Vesicles Secreted by Endothelial Cells Reversibly Primed for Anoikis: A Possible Autocrine Mechanism Induced by Astrocytoma Extracellular Matrix.International journal of molecular sciences · 2026Article
- Transposable elements hitchhike on Starships across fungal genomes.Nature communications · 2026Article
- Spectral Cruncher: A Visualization Tool Integrating Manual Curation, Ion-Intensity Prediction, and De Novo Tag Generation.Journal of the American Society for Mass Spectrometry · 2026Article
- Core-sheath coupling controls flagellar curvature and motility inbioRxiv : the preprint server for biology · 2026Article
- Methanogenesis from tetramethylammonium and choline inFrontiers in microbiology · 2026Article
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- Endosymbiosis in trypanosomatids: the bacterium regulates the intermediate and oxidative metabolism of the host cell.mSphere · 2025Article
- The flippases Apt1 and Apt2 differentially influence extracellular vesicle cargo and polysaccharide secretion in Cryptococcus neoformans.Journal of proteomics · 2025Article
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- Comet Fragment-Ion Indexing for Enhanced Peptide Sequencing.Journal of proteome research · 2025Article
- ProteoPlotter: An Executable Proteomics Visualization Tool Compatible with Perseus.Journal of proteome research · 2025Article
- An insight into the salivary gland content of the human body louse, Pediculus humanus.Scientific reports · 2025Article
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- Proteomic Characterization of Extracellular Vesicles from Human Neural Precursor Cells: A Promising Advanced Therapy for Neurodegenerative Diseases.International journal of nanomedicine · 2025Article
- Phosphoketolase and KDPG aldolase metabolisms modulate photosynthetic carbon yield in cyanobacteria.The Plant cell · 2024Article
52 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
PatternLab for proteomics is an integrated computational environment that unifies several previously published modules for the analysis of shotgun proteomic data. The contained modules allow for formatting of sequence databases, peptide spectrum matching, statistical filtering and data organization, extracting quantitative information from label-free and chemically labeled data, and analyzing statistics for differential proteomics. PatternLab also has modules to perform similarity-driven studies with de novo sequencing data, to evaluate time-course experiments and to highlight the biological significance of data with regard to the Gene Ontology database. The PatternLab for proteomics 4.0 package brings together all of these modules in a self-contained software environment, which allows for complete proteomic data analysis and the display of results in a variety of graphical formats. All updates to PatternLab, including new features, have been previously tested on millions of mass spectra. PatternLab is easy to install, and it is freely available from http://patternlabforproteomics.org.
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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.