ArticleGenome medicine2017
Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines.
Article in Genome medicine, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 60 citations in OpenAlex.
- Uncovering dark mass in population proteomics: Pan-analysis of single amino acid polymorphism relevant to cognition and aging.Cell genomics · 2025Article
- PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics - catching the (un)usual suspects.Computational and structural biotechnology journal · 2024Article
- Assessment of Data-Independent Acquisition Mass Spectrometry (DIA-MS) for the Identification of Single Amino Acid Variants.Proteomes · 2024Article
- Chemoproteogenomic stratification of the missense variant cysteinome.Nature communications · 2024Article
- Data-Independent Acquisition and Label-Free Quantification for Quantitative Proteomics Analysis of Human Cerebrospinal Fluid.Current protocols · 2024Article
- Multi-omic stratification of the missense variant cysteinome.bioRxiv : the preprint server for biology · 2023Article
- Re-evaluating the impact of alternative RNA splicing on proteomic diversity.Frontiers in genetics · 2023Review
- Statistical Methodology for Ribosomal Frameshift Detection.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2022Article
- Uncovering the impacts of alternative splicing on the proteome with current omics techniques.Wiley interdisciplinary reviews. RNA · 2022Review
- An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics.Genome biology · 2022Article
- Multiaspect Examinations of Possible Alternative Mappings of Identified Variant Peptides: A Case Study on the HEK293 Cell Line.ACS omega · 2022Article
- Cancer Conformational Landscape Shapes Tumorigenesis.Journal of proteome research · 2022Article
- Targeted Detection of SARS-CoV-2 Nucleocapsid Sequence Variants by Mass Spectrometric Analysis of Tryptic Peptides.Journal of proteome research · 2022Article
- Computational and Mass Spectrometry-Based Approach Identify Deleterious Non-Synonymous Single Nucleotide Polymorphisms (nsSNPs) in JMJD6.Molecules (Basel, Switzerland) · 2021Article
- Selecting Target Antigens for Cancer Vaccine Development.Vaccines · 2020Review
- Article
- Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform.Proteomes · 2020Article
- CusVarDB: A tool for building customized sample-specific variant protein database from next-generation sequencing datasets.F1000Research · 2020Article
- PrecisionMolecular & cellular proteomics : MCP · 2019Article
- Clinical potential of mass spectrometry-based proteogenomics.Nature reviews. Clinical oncology · 2019Review
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
Abstract
backgroundOnco-proteogenomics aims to understand how changes in a cancer's genome influences its proteome. One challenge in integrating these molecular data is the identification of aberrant protein products from mass-spectrometry (MS) datasets, as traditional proteomic analyses only identify proteins from a reference sequence database.
methodsWe established proteomic workflows to detect peptide variants within MS datasets. We used a combination of publicly available population variants (dbSNP and UniProt) and somatic variations in cancer (COSMIC) along with sample-specific genomic and transcriptomic data to examine proteome variation within and across 59 cancer cell-lines.
resultsWe developed a set of recommendations for the detection of variants using three search algorithms, a split target-decoy approach for FDR estimation, and multiple post-search filters. We examined 7.3 million unique variant tryptic peptides not found within any reference proteome and identified 4771 mutations corresponding to somatic and germline deviations from reference proteomes in 2200 genes among the NCI60 cell-line proteomes.
conclusionsWe discuss in detail the technical and computational challenges in identifying variant peptides by MS and show that uncovering these variants allows the identification of druggable mutations within important cancer genes.
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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.