ReviewMolecular & cellular proteomics : MCP2013
Combining results of multiple search engines in proteomics.
Review in Molecular & cellular proteomics : MCP, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers, 1 of them a synthesis that pooled it.
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
85 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Reproducibility Crossroads: Impact of Statistical Choices on Proteomics Functional Enrichment.International journal of molecular sciences · 2025Pooled it
- Bypassing Androgens: Retina-Targeted 17β-Estradiol Delivery via DHED Eye Drops Ameliorates Orchiectomy-Induced Shifts in the Male Rat Visual Cortex Proteome.Antioxidants (Basel, Switzerland) · 2026Article
- SPROUTS_DB: An Implemented Database of Contaminants for Extracellular Vesicle Proteomics Studies.Proteomics · 2026Article
- Changes in the proteomic profile of athletes' plasma associated with exercise intensity.Scientific reports · 2026Article
- Identification of microbial species and proteins associated with colorectal cancer by reanalyzing CPTAC proteomic datasets.Scientific reports · 2025Article
- Proximity proteomics reveals unique and shared pathological features between multiple system atrophy and Parkinson's disease.Acta neuropathologica communications · 2025Article
- APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control.Genomics, proteomics & bioinformatics · 2024Article
- SEMQuant: Extending Sipros-Ensemble with Match-Between-Runs for Comprehensive Quantitative Metaproteomics.Bioinformatics research and applications : ... international symposium, ISBRA ... proceedings. ISBRA (Conference) · 2024Article
- Bioinformatic Workflows for Metaproteomics.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Metabolomic, Proteomic, and Single-Cell Proteomic Analysis of Cancer Cells Treated with the KRASJournal of proteome research · 2023Article
- Differential Expression of Proteins Associated with Bipolar Disorder as Identified Using the PeptideShaker Software.International journal of molecular sciences · 2023Article
- A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS.Scientific data · 2023Article
- Article
- Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection.Journal of proteome research · 2023Article
- Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite.Journal of proteome research · 2023Article
- MetaProD: A Highly-Configurable Mass Spectrometry Analyzer for Multiplexed Proteomic and Metaproteomic Data.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
- Mass Spectrometry Approaches Empowering Neuropeptide Discovery and Therapeutics.Pharmacological reviews · 2022Review
- Proteomic Comparison of Ivermectin Sensitive and ResistantAntibiotics (Basel, Switzerland) · 2022Article
- Comparative Proteomic Profiling of Secreted Extracellular Vesicles from Breast Fibroadenoma and Malignant Lesions: A Pilot Study.International journal of molecular sciences · 2022Article
25 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
4 authors.
Funding
Abstract
A crucial component of the analysis of shotgun proteomics datasets is the search engine, an algorithm that attempts to identify the peptide sequence from the parent molecular ion that produced each fragment ion spectrum in the dataset. There are many different search engines, both commercial and open source, each employing a somewhat different technique for spectrum identification. The set of high-scoring peptide-spectrum matches for a defined set of input spectra differs markedly among the various search engine results; individual engines each provide unique correct identifications among a core set of correlative identifications. This has led to the approach of combining the results from multiple search engines to achieve improved analysis of each dataset. Here we review the techniques and available software for combining the results of multiple search engines and briefly compare the relative performance of these techniques.
Indexed as
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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.