ArticleJournal of proteome research2013
Peppy: proteogenomic search software.
Article in Journal of proteome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 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
31 citing papers in PubMed.
- Variant biomarker discovery using mass spectrometry-based proteogenomics.Frontiers in aging · 2023Review
- Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach.PLoS genetics · 2021Article
- Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey.IEEE access : practical innovations, open solutions · 2021Article
- Identification of Non-Canonical Translation Products inFrontiers in genetics · 2021Article
- Software Options for the Analysis of MS-Proteomic Data.Methods in molecular biology (Clifton, N.J.) · 2021Article
- CIRFESS: An Interactive Resource for Querying the Set of Theoretically Detectable Peptides for Cell Surface and Extracellular Enrichment Proteomic Studies.Journal of the American Society for Mass Spectrometry · 2020Article
- Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes.BMC genomics · 2019Article
- Proteome and allergenome of the European house dust mite Dermatophagoides pteronyssinus.PloS one · 2019Article
- Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity.BMC genomics · 2018Article
- FSPP: A Tool for Genome-Wide Prediction of smORF-Encoded Peptides and Their Functions.Frontiers in genetics · 2018Article
- An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics.Genome research · 2017Article
- An Accessible Proteogenomics Informatics Resource for Cancer Researchers.Cancer research · 2017Article
- Integrating Next-Generation Genomic Sequencing and Mass Spectrometry To Estimate Allele-Specific Protein Abundance in Human Brain.Journal of proteome research · 2017Article
- Proteogenomics from a bioinformatics angle: A growing field.Mass spectrometry reviews · 2017Review
- Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines.Genome medicine · 2017Article
- Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes.Genome research · 2017Article
- Flexible Data Analysis Pipeline for High-Confidence Proteogenomics.Journal of proteome research · 2016Article
- GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes.Molecular & cellular proteomics : MCP · 2016Article
- JUMPg: An Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells.Journal of proteome research · 2016Article
- Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation.Annual review of analytical chemistry (Palo Alto, Calif.) · 2016Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Proteogenomic searching is a useful method for identifying novel proteins, annotating genes and detecting peptides unique to an individual genome. The approach, however, can be laborious, as it often requires search segmentation and the use of several unintegrated tools. Furthermore, many proteogenomic efforts have been limited to small genomes, as large genomes can prove impractical due to the required amount of computer memory and computation time. We present Peppy, a software tool designed to perform every necessary task of proteogenomic searches quickly, accurately and automatically. The software generates a peptide database from a genome, tracks peptide loci, matches peptides to MS/MS spectra and assigns confidence values to those matches. Peppy automatically performs a decoy database generation, search and analysis to return identifications at the desired false discovery rate threshold. Written in Java for cross-platform execution, the software is fully multithreaded for enhanced speed. The program can run on regular desktop computers, opening the doors of proteogenomic searching to a wider audience of proteomics and genomics researchers. Peppy is available at http://geneffects.com/peppy .
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.