ArticleNature methods2011
Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra.
Article in Nature methods, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
54 citing papers in PubMed.
- MS/MS Mass Spectrometry Filtering Tree for Bile Acid Regio- and Stereoisomer Annotation.Analytical chemistry · 2026Article
- Article
- MS-RT: A Method for Evaluating MS/MS Clustering Performance for Metabolomics Data.Journal of proteome research · 2025Article
- MS/MS Mass Spectrometry Filtering Tree for Bile Acid Isomer Annotation.bioRxiv : the preprint server for biology · 2025Article
- The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF.Analytical chemistry · 2024Article
- The microbiome diversifiesbioRxiv : the preprint server for biology · 2024Article
- Fast mass spectrometry search and clustering of untargeted metabolomics data.Nature biotechnology · 2024Article
- The Comprehensive Profiling of the Chemical Components in the Raw and Processed Roots ofMolecules (Basel, Switzerland) · 2024Article
- SpecEncoder: deep metric learning for accurate peptide identification in proteomics.Bioinformatics (Oxford, England) · 2024Article
- A Portable and Reusable Database Infrastructure for Mass Spectrometry, and Its Associated Toolkit (The DIMSpec Project).Journal of the American Society for Mass Spectrometry · 2024Article
- Article
- Spectroscape enables real-time query and visualization of a spectral archive in proteomics.Nature communications · 2023Article
- Wood Degradation byJournal of fungi (Basel, Switzerland) · 2023Article
- Application of a Novel Hybrid CNN-GNN for Peptide Ion Encoding.Journal of proteome research · 2023Article
- The critical role that spectral libraries play in capturing the metabolomics community knowledge.Metabolomics : Official journal of the Metabolomic Society · 2022Review
- Article
- Article
- A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics.Journal of proteome research · 2022Article
- Optimization of LC-MSMetabolites · 2022Article
- Data Processing of Product Ion Spectra: Quality Improvement by Averaging Multiple Similar Spectra of Small Molecules.Mass spectrometry (Tokyo, Japan) · 2022Article
Corrections and comments
- Commented on by
Authors and funding
9 authors.
Funding
Abstract
Tandem mass spectrometry (MS/MS) experiments yield multiple, nearly identical spectra of the same peptide in various laboratories, but proteomics researchers typically do not leverage the unidentified spectra produced in other labs to decode spectra they generate. We propose a spectral archives approach that clusters MS/MS datasets, representing similar spectra by a single consensus spectrum. Spectral archives extend spectral libraries by analyzing both identified and unidentified spectra in the same way and maintaining information about peptide spectra that are common across species and conditions. Thus archives offer both traditional library spectrum similarity-based search capabilities along with new ways to analyze the data. By developing a clustering tool, MS-Cluster, we generated a spectral archive from ∼1.18 billion spectra that greatly exceeds the size of existing spectral repositories. We advocate that publicly available data should be organized into spectral archives rather than be analyzed as disparate datasets, as is mostly the case today.
Indexed as
Identifiers
What OpenQuestion 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 OpenQuestion graph.