ArticleJournal of proteome research2014
MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra.
Article in Journal of proteome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 253 papers.
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Who cites it
253 citing papers in PubMed.
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- A Parallel Accumulation-Mobility Aligned Fragmentation Strategy Utilizing High-Resolution Ion Mobility for High-Performance Proteomics Analysis.Molecular & cellular proteomics : MCP · 2026Article
- Proteome-wide quantification of inositol pyrophosphate-protein interactions.Nature communications · 2026Article
- P4HA3 is dispensable for prolyl 4-hydroxylation of type I collagen during mouse development.The Journal of biological chemistry · 2026Article
- The coordinated action of UFMylation and the RQC pathways clears arrested polypeptides at the ER.The EMBO journal · 2026Article
- Kinase KEY1 controls pyrenoid condensate size throughout the cell cycle by disrupting phase separation interactions.Nature cell biology · 2026Article
- Factor VIII restores bone parameters and modulates muscle proteo-metabolome in Factor VIII knockout male mice.Bone research · 2026Article
- Automatic Selection of Search Parameter Values for Mass Spectrometry-Based Search Engines.Journal of proteome research · 2026Article
- A multivalent adaptor mechanism drives the nuclear import of proteasomes.Nature communications · 2026Article
- EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery.bioRxiv : the preprint server for biology · 2026Article
- Mass Spectrometry-Based Biomarkers in Drug Development.Advances in experimental medicine and biology · 2026Review
- Article
- Recurrent evolution of selfishness from an essential tRNA synthetase in Caenorhabditis tropicalis.Nature ecology & evolution · 2025Article
- Germ granule localization of nematode Argonaute WAGO-4 ensures fidelity in small RNA loading.The EMBO journal · 2025Article
- Breaking barriers in crosslinking mass spectrometry with enhanced throughput and sensitivity using Orbitrap Astral.Nature communications · 2025Article
- Kinase KEY1 controls pyrenoid condensate size throughout the cell cycle by disrupting phase separation interactions.bioRxiv : the preprint server for biology · 2025Article
- WNK kinase regulates plasma membrane levels of the WNT inhibitor RNF43: A WNK-RNF43 circuit regulates WNT signal suppression.bioRxiv : the preprint server for biology · 2025Article
193 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Today's highly accurate spectra provided by modern tandem mass spectrometers offer considerable advantages for the analysis of proteomic samples of increased complexity. Among other factors, the quantity of reliably identified peptides is considerably influenced by the peptide identification algorithm. While most widely used search engines were developed when high-resolution mass spectrometry data were not readily available for fragment ion masses, we have designed a scoring algorithm particularly suitable for high mass accuracy. Our algorithm, MS Amanda, is generally applicable to HCD, ETD, and CID fragmentation type data. The algorithm confidently explains more spectra at the same false discovery rate than Mascot or SEQUEST on examined high mass accuracy data sets, with excellent overlap and identical peptide sequence identification for most spectra also explained by Mascot or SEQUEST. MS Amanda, available at http://ms.imp.ac.at/?goto=msamanda , is provided free of charge both as standalone version for integration into custom workflows and as a plugin for the Proteome Discoverer platform.
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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.