ArticleNature methods2015
Mass spectrometrists should search only for peptides they care about.
Article in Nature methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 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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Who cites it
37 citing papers in PubMed.
- Biochanin A improves nitrogen utilization efficiency by regulating ruminal microbial community in dairy goats.Microbiome · 2025Article
- Designing a Comparative Proteomics Experiment: Retention-Time Alignment and Imputation Algorithms Affect Statistical Comparisons between Samples.Journal of proteome research · 2025Article
- SorCS2 Is Important for Astrocytic Function in Neurovascular Signaling.Acta physiologica (Oxford, England) · 2025Article
- PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics - catching the (un)usual suspects.Computational and structural biotechnology journal · 2024Article
- Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry.ACS measurement science au · 2024Review
- Contigs directed gene annotation (ConDiGA) for accurate protein sequence database construction in metaproteomics.Microbiome · 2024Article
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- Article
- Generalized precursor prediction boosts identification rates and accuracy in mass spectrometry based proteomics.Communications biology · 2023Article
- MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.PLoS computational biology · 2023Article
- Identification of Alternative Splicing in Proteomes of Human Melanoma Cell Lines without RNA Sequencing Data.International journal of molecular sciences · 2023Article
- MetaPep: A core peptide database for faster human gut metaproteomics database searches.Computational and structural biotechnology journal · 2023Article
- An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics.Genome biology · 2022Article
- Building Spectral Libraries from Narrow-Window Data-Independent Acquisition Mass Spectrometry Data.Journal of proteome research · 2022Article
- IntroSpect: Motif-Guided Immunopeptidome Database Building Tool to Improve the Sensitivity of HLA I Binding Peptide Identification by Mass Spectrometry.Biomolecules · 2022Article
- Discovery and Visualization of Uncharacterized Drug-Protein Adducts Using Mass Spectrometry.Analytical chemistry · 2022Article
- Activity- and Enrichment-Based Metaproteomics Insights into Active Urease from the Rumen Microbiota of Cattle.International journal of molecular sciences · 2022Article
- Accurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant.Journal of proteome research · 2021Article
- Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection.Journal of proteome research · 2021Article
- Evaluation of open search methods based on theoretical mass spectra comparison.BMC bioinformatics · 2021Article
Corrections and comments
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Authors and funding
1 author.
Funding
Abstract
Analysis pipelines that assign peptides to shotgun proteomics mass spectra often discard identified spectra deemed irrelevant to the scientific hypothesis being tested. To improve statistical power, I propose that researchers remove irrelevant peptides from the database prior to searching rather than assigning these peptides to spectra and then discarding the matches.
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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.