ArticleJournal of proteome research2015
Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer.
Article in Journal of proteome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed, 38 citations in OpenAlex.
- Computational identification and characterization of noncoding RNA-encoded peptides: tools, databases, and in silico strategies.Amino acids · 2026Review
- Advances in Mass Spectrometry Instrumentation and Methodology for Analysis of Alternative Protein Isoforms.Journal of mass spectrometry : JMS · 2026Review
- PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics - catching the (un)usual suspects.Computational and structural biotechnology journal · 2024Article
- Chemoproteogenomic stratification of the missense variant cysteinome.Nature communications · 2024Article
- Biological factors and statistical limitations prevent detection of most noncanonical proteins by mass spectrometry.PLoS biology · 2023Article
- SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics.Nature communications · 2023Article
- Multi-omic stratification of the missense variant cysteinome.bioRxiv : the preprint server for biology · 2023Article
- Functional Impact of Protein-RNA Variation in Clinical Cancer Analyses.Molecular & cellular proteomics : MCP · 2023Article
- Accurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant.Journal of proteome research · 2021Article
- Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis.Nature communications · 2020Article
- Recent advances in mass spectrometry based clinical proteomics: applications to cancer research.Clinical proteomics · 2020Review
- Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements.Journal of proteome research · 2019Article
- ProteinExplorer: A Repository-Scale Resource for Exploration of Protein Detection in Public Mass Spectrometry Data Sets.Journal of proteome research · 2018Article
- Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship.Genome research · 2018Review
- Brute-Force Approach for Mass Spectrometry-Based Variant Peptide Identification in Proteogenomics without Personalized Genomic Data.Journal of the American Society for Mass Spectrometry · 2018Article
- The Antibody Repertoire of Colorectal Cancer.Molecular & cellular proteomics : MCP · 2017Article
- Methods, Tools and Current Perspectives in Proteogenomics.Molecular & cellular proteomics : MCP · 2017Review
- The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.Nucleic acids research · 2017Article
- JUMPg: An Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells.Journal of proteome research · 2016Article
- Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.Nature communications · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Aiming toward an improved understanding of the regulation of proteins in cancer, recent studies from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) have focused on analyzing cancer tissue using proteomic technologies and workflows. Although many proteogenomics approaches for the study of cancer samples have been proposed, serious methodological challenges remain, especially in the identification of multiple mutational variants or structural variations such as fusion gene events. In addition, although immune system genes play an important role in cancer, identification of IgG peptides remains challenging in proteomic data sets. Here, we describe an integrative proteogenomic method that extends the limit of proteogenomic searches to identify multiple variant peptides as well as immunoglobulin gene variations/rearrangements using customized mining of RNA-seq data. Our results also provide the first extensive characterization of tumor immune response and demonstrate the potential of this method to improve the molecular characterization of tumor subtypes.
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.