ReviewCurrent opinion in biotechnology2013
Current algorithmic solutions for peptide-based proteomics data generation and identification.
Review in Current opinion in biotechnology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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.
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
19 citing papers in PubMed.
- Designing a Comparative Proteomics Experiment: Retention-Time Alignment and Imputation Algorithms Affect Statistical Comparisons between Samples.Journal of proteome research · 2025Article
- Assessing Multiple Evidence Streams to Decide on Confidence for Identification of Post-Translational Modifications, within and Across Data Sets.Journal of proteome research · 2023Article
- How to use open-pFind in deep proteomics data analysis?- A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data.Biophysics reports · 2021Article
- Total Retention Liquid Chromatography-Mass Spectrometry to Achieve Maximum Protein Sequence Coverage.Analytical chemistry · 2021Article
- The Power of Three in Cannabis Shotgun Proteomics: Proteases, Databases and Search Engines.Proteomes · 2020Article
- Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era.Plants (Basel, Switzerland) · 2020Review
- Computational Oncology in the Multi-Omics Era: State of the Art.Frontiers in oncology · 2020Review
- Article
- Multifunctional sequence-defined macromolecules for chemical data storage.Nature communications · 2018Article
- Identification of RNA-binding domains of RNA-binding proteins in cultured cells on a system-wide scale with RBDmap.Nature protocols · 2017Article
- In-Depth Proteomic Analysis of the Porcine Retina by Use of a four Step Differential Extraction Bottom up LC MS Platform.Molecular neurobiology · 2017Article
- Proteomic Profiling of Serial Prediagnostic Serum Samples for Early Detection of Colon Cancer in the U.S. Military.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2017Article
- Phosphoproteome Discovery in Human Biological Fluids.Proteomes · 2016Review
- Proteomics, biomarkers, and HIV-1: A current perspective.Proteomics. Clinical applications · 2016Review
- Article
- Bioinformatics-Aided Venomics.Toxins · 2015Review
- Making proteomics data accessible and reusable: current state of proteomics databases and repositories.Proteomics · 2015Review
- Bioinformatic analysis of proteomics data.BMC systems biology · 2014Review
- Evaluating the impact of different sequence databases on metaproteome analysis: insights from a lab-assembled microbial mixture.PloS one · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Peptide-based proteomic data sets are ever increasing in size and complexity. These data sets provide computational challenges when attempting to quickly analyze spectra and obtain correct protein identifications. Database search and de novo algorithms must consider high-resolution MS/MS spectra and alternative fragmentation methods. Protein inference is a tricky problem when analyzing large data sets of degenerate peptide identifications. Combining multiple algorithms for improved peptide identification puts significant strain on computational systems when investigating large data sets. This review highlights some of the recent developments in peptide and protein identification algorithms for analyzing shotgun mass spectrometry data when encountering the aforementioned hurdles. Also explored are the roles that analytical pipelines, public spectral libraries, and cloud computing play in the evolution of peptide-based proteomics.
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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.