ArticleRapid communications in mass spectrometry : RCM2021
MS Amanda 2.0: Advancements in the standalone implementation.
Article in Rapid communications in mass spectrometry : RCM, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Pathogenicity of Cadophora luteo-olivacea on Quercus robur and multi-omics characterization of antagonism by Trichoderma atroviride.Scientific reports · 2026Article
- Prosit-XL: enhanced cross-linked peptide identification by fragment intensity prediction to study protein interactions and structures.Nature communications · 2025Article
- Developing a new cleavable crosslinker reagent for in-cell crosslinking.Communications chemistry · 2025Article
- Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex.Communications chemistry · 2024Article
- Divergent Molecular Responses to Heavy Water inPlants (Basel, Switzerland) · 2024Article
- A Proteomics Approach Identifies RREB1 as a Crucial Molecular Target of Imidazo-Pyrazole Treatment in SKMEL-28 Melanoma Cells.International journal of molecular sciences · 2024Article
- Micropillar arrays, wide window acquisition and AI-based data analysis improve comprehensiveness in multiple proteomic applications.Nature communications · 2024Article
- AI-Assisted Processing Pipeline to Boost Protein Isoform Detection.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Mapping Peptide-Protein Interactions by Amine-Reactive Cleavable Photoaffinity Reagents.ACS omega · 2023Article
- Antibiotic resistance and host immune system-induced metal bactericidal control are key factors for microbial persistence in the developing human preterm infant gut microbiome.Frontiers in microbiology · 2022Article
- Deep-Sea Anemones Are Prospective Source of New Antimicrobial and Cytotoxic Compounds.Marine drugs · 2021Article
- MS Amanda 2.0: Advancements in the standalone implementation.Rapid communications in mass spectrometry : RCM · 2021Article
- HSP70 as a Mediator of Host-Pathogen Interaction in Arabidopsis thaliana During Plasmodiophora brassicae Infection.Physiologia plantarumArticle
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
rationaleDatabase search engines are the preferred method to identify peptides in mass spectrometry data. However, valuable software is in this context not only defined by a powerful algorithm to separate correct from false identifications, but also by constant maintenance and continuous improvements.
methodsIn 2014, we presented our peptide identification algorithm MS Amanda, showing its suitability for identifying peptides in high-resolution tandem mass spectrometry data and its ability to outperform widely used tools to identify peptides. Since then, we have continuously worked on improvements to enhance its usability and to support new trends and developments in this fast-growing field, while keeping the original scoring algorithm to assess the quality of a peptide spectrum match unchanged.
resultsWe present the outcome of these efforts, MS Amanda 2.0, a faster and more flexible standalone version with the original scoring algorithm. The new implementation has led to a 3-5× speedup, is able to handle new ion types and supports standard data formats. We also show that MS Amanda 2.0 works best when using only the most common ion types in a particular search instead of all possible ion types.
conclusionsMS Amanda is available free of charge from https://ms.imp.ac.at/index.php?action=msamanda.
Indexed as
Identifiers
What Socratic holds
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 Socratic graph.