Proteogenomics: concepts, applications and computational strategies

No abstract is available for this paper.

• Publication year

  2014

• Venue

  Nature Methods

• Publication date

  2014-10-30

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1038/nmeth.3144PMID 25357241PMCID PMC4392723
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Space-time wiring specificity supports direction selectivity in the retina

  2014cited by this paper
• Mass-spectrometry-based draft of the human proteome

  2014influential reference
• Strain-specific proteogenomics accelerates the discovery of natural products via their biosynthetic pathways

  2014cited by this paper
• N‐terminomics and proteogenomics, getting off to a good start

  2014cited by this paper
• Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations

  2014cited by this paper
• Proteogenomic database construction driven from large scale RNA-seq data.

  2014cited by this paper
• PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations

  2014cited by this paper
• Discovery of Novel Genes and Gene Isoforms by Integrating Transcriptomic and Proteomic Profiling from Mouse Liver.

  2014cited by this paper
• Onco-proteogenomics: cancer proteomics joins forces with genomics

  2014cited by this paper
• N-terminal Proteomics and Ribosome Profiling Provide a Comprehensive View of the Alternative Translation Initiation Landscape in Mice and Men*

  2014cited by this paper
• Ribosome profiling: new views of translation, from single codons to genome scale

  2014cited by this paper
• Proteogenomic characterization of human colon and rectal cancer

  2014influential reference
• Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics

  2014cited by this paper
• Non-model organisms, a species endangered by proteogenomics.

  2014cited by this paper
• Discovery of novel genes and gene isoforms by integrating transcriptomic and proteomic profiling from mouse liver.

  2014cited by this paper
• ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination

  2014cited by this paper
• The strategy, organization, and progress of the HUPO Human Proteome Project.

  2014cited by this paper
• [RNA editing. The classical cases and the outlook of new technologies].

  2014cited by this paper
• Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences.

  2014cited by this paper
• A draft map of the human proteome

  2014cited by this paper
• Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities

  2013cited by this paper
• Genomics meets proteomics: identifying the culprits in disease

  2013cited by this paper
• Deep Coverage of the Escherichia coli Proteome Enables the Assessment of False Discovery Rates in Simple Proteogenomic Experiments*

  2013cited by this paper
• Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions

  2013influential reference
• The coming age of complete, accurate, and ubiquitous proteomes.

  2013cited by this paper
• Combining Results of Multiple Search Engines in Proteomics*

  2013cited by this paper
• Variation and Genetic Control of Protein Abundance in Humans

  2013cited by this paper
• Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq*

  2013cited by this paper
• An Automated Proteogenomic Method Uses Mass Spectrometry to Reveal Novel Genes in Zea mays*

  2013influential reference
• Systematic evaluation of spliced alignment programs for RNA-seq data

  2013cited by this paper
• Genetics of single-cell protein abundance variation in large yeast populations

  2013cited by this paper
• A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis

  2013cited by this paper
• Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins.

  2013cited by this paper
• Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium.

  2013cited by this paper
• Assessment of transcript reconstruction methods for RNA-seq

  2013cited by this paper
• Moving away from the reference genome: evaluating a peptide sequencing tagging approach for single amino acid polymorphism identifications in the genus Populus.

  2013cited by this paper
• Functional transcriptomics in the post-ENCODE era

  2013cited by this paper
• NONCODEv4: exploring the world of long non-coding RNA genes

  2013cited by this paper
• Evaluating the Impact of Different Sequence Databases on Metaproteome Analysis: Insights from a Lab-Assembled Microbial Mixture

  2013cited by this paper
• Searching for a needle in a stack of needles: challenges in metaproteomics data analysis.

  2013cited by this paper
• Deep Proteome Coverage Based on Ribosome Profiling Aids Mass Spectrometry-based Protein and Peptide Discovery and Provides Evidence of Alternative Translation Products and Near-cognate Translation Initiation Events*

  2013cited by this paper
• Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome

  2013cited by this paper
• customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search

  2013cited by this paper
• HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics

  2013influential reference
• Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts

  2012cited by this paper
• Peptidomic discovery of short open reading frame-encoded peptides in human cells

  2012cited by this paper
• Addressing Statistical Biases in Nucleotide-Derived Protein Databases for Proteogenomic Search Strategies

  2012cited by this paper
• Comparative Proteomics Reveals a Significant Bias Toward Alternative Protein Isoforms with Conserved Structure and Function

  2012cited by this paper
• De novo derivation of proteomes from transcriptomes for transcript and protein identification

  2012cited by this paper
• Protein identification using customized protein sequence databases derived from RNA-Seq data.

  2012cited by this paper
• ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data

  2012cited by this paper
• Overcoming Species Boundaries in Peptide Identification with Bayesian Information Criterion-driven Error-tolerant Peptide Search (BICEPS)*

  2012cited by this paper
• Mass spectrum sequential subtraction speeds up searching large peptide MS/MS spectra datasets against large nucleotide databases for proteogenomics

  2012cited by this paper
• The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

  2012cited by this paper
• A Highly Efficient Multifunctional Tandem Affinity Purification Approach Applicable to Diverse Organisms*

  2012cited by this paper
• Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

  2012cited by this paper
• GENCODE: The reference human genome annotation for The ENCODE Project

  2012cited by this paper
• Long noncoding RNAs are rarely translated in two human cell lines

  2012cited by this paper
• De Novo Sequencing and Homology Searching‡‡*

  2011cited by this paper
• Widespread RNA and DNA Sequence Differences in the Human Transcriptome

  2011cited by this paper
• Coding potential of the products of alternative splicing in human

  2011cited by this paper
• iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates*

  2011cited by this paper
• Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses.

  2011cited by this paper
• Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome.

  2011influential reference
• Discovery and annotation of small proteins using genomics, proteomics, and computational approaches.

  2011cited by this paper
• A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry.

  2011cited by this paper
• Data mining in proteomics : from standards to applications

  2011cited by this paper
• A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics*

  2011influential reference
• Identification of alternatively spliced transcripts using a proteomic informatics approach.

  2011cited by this paper
• The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment

  2010influential reference
• TagRecon: high-throughput mutation identification through sequence tagging.

  2010cited by this paper
• Proteogenomics to discover the full coding content of genomes: a computational perspective.

  2010cited by this paper
• DiScRIBinATE: a rapid method for accurate taxonomic classification of metagenomic sequences

  2010cited by this paper
• Proteogenomic Analysis of Polymorphisms and Gene Annotation Divergences in Prokaryotes using a Clustered Mass Spectrometry-Friendly Database*

  2010cited by this paper
• Expansion of the eukaryotic proteome by alternative splicing

  2010cited by this paper
• A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics.

  2010influential reference
• Computational analysis of unassigned high‐quality MS/MS spectra in proteomic data sets

  2010cited by this paper
• Community proteogenomics reveals insights into the physiology of phyllosphere bacteria

  2009cited by this paper
• Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles.

  2009cited by this paper
• RNA-Seq: a revolutionary tool for transcriptomics

  2009cited by this paper
• Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer.

  2009cited by this paper
• Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes.

  2008cited by this paper
• Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations.

  2008cited by this paper
• Discovery and revision of Arabidopsis genes by proteogenomics

  2008cited by this paper
• Protein identification pipeline for the homology-driven proteomics.

  2008cited by this paper
• Steady progress and recent breakthroughs in the accuracy of automated genome annotation

  2008cited by this paper
• Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

  2008cited by this paper
• Novel peptide identification from tandem mass spectra using ESTs and sequence database compression

  2007influential reference
• Diversity of Translation Start Sites May Define Increased Complexity of the Human Short ORFeome*S

  2007cited by this paper
• A high-quality catalog of the Drosophila melanogaster proteome

  2007cited by this paper
• Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria

  2007cited by this paper
• Improving gene annotation using peptide mass spectrometry.

  2007influential reference
• Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics

  2006cited by this paper
• Dynamic Spectrum Quality Assessment and Iterative Computational Analysis of Shotgun Proteomic Data

  2006influential reference
• The Abundance of Short Proteins in the Mammalian Proteome

  2006cited by this paper
• Interpretation of Shotgun Proteomic Data

  2005cited by this paper
• Identification of post-translational modifications by blind search of mass spectra

  2005cited by this paper
• Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry

  2004cited by this paper
• The Need for Guidelines in Publication of Peptide and Protein Identification Data

  2004cited by this paper
• Proteogenomic mapping as a complementary method to perform genome annotation

  2004cited by this paper

• Proteogenomic discovery of novel small proteins in clinical Mycobacterium tuberculosis strains

  2026influential citation
• Sample-specific haplotype-resolved protein isoform characterization via long-read RNA-seq-based proteogenomics

  2026cites this paper
• Methods for Isolating and Analyzing the HLA Class I Immunopeptidome.

  2026cites this paper
• Quantitative proteomics analysis to identify biomarkers of refractory benign paroxysmal positional vertigo

  2026cites this paper
• Proteogenomic investigation of plant constituents in herbal beverages.

  2026cites this paper
• FiCOPS: Hardware/Software Co-Design of FPGA Computational Framework for Mass Spectrometry-Based Peptide Database Search

  2026cites this paper
• Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics

  2026cites this paper
• Integrative omics-based biotechnological strategies for deciphering plant stress responses

  2026cites this paper
• Identification of Potentially Coding Small ORFs in Plant Transcriptomes.

  2026cites this paper
• Less missing values—evaluation of proteomics workflows for the quantification of (small) proteins

  2026cites this paper
• iPepGen: a modular, immunopeptidogenomic analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates.

  2026cites this paper
• IsoPS-DIA: Dual Functionality of Absolute Targeted Quantification and Global Proteome Profiling.

  2026cites this paper
• Mass Spectrometry‐Based Integrated Multiomics Platforms for Medicinal Plant Analysis

  2026cites this paper
• Recent Characterization of Key Proteins to Combat Tuberculosis.

  2026cites this paper
• Advances in Mass Spectrometry Instrumentation and Methodology for Analysis of Alternative Protein Isoforms.

  2026cites this paper
• Advances in delivery technologies-powered cancer vaccines.

  2026cites this paper
• A Systematic Approach to Selecting the Right Tool for Mass Spectrometry Data Analysis in Protein and Peptide Bioanalysis.

  2026cites this paper
• Ficus benghalensis β-amylase: A potent biofilm-degrading enzyme with broad-Spectrum activity against nosocomial and foodborne pathogens.

  2026cites this paper
• Multi-State Structural Genomics Enables Large-Scale, Mechanistic, and Context-Specific Classification of ABCC6 Genetic Variants Implicated in Calcification Diseases.

  2026cites this paper
• Future Research Directions on Mycobacterium tuberculosis Proteins.

  2026cites this paper
• Brownotate, a Comprehensive Solution to Generate Protein Sequence Databases for Any Species.

  2026cites this paper
• Proteoform medicine: characterizing and targeting protein forms in human disease.

  2026cites this paper
• The splice of life: how alternative splicing shapes regulatory and phenotypic evolution.

  2026cites this paper
• Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer

  2025cites this paper
• Advancing Thoracic Surgical Oncology in the Era of Precision Medicine

  2025cites this paper
• The effect of thermal stress on the X-organ/sinus gland proteome of the estuarine blue crab Callinectes sapidus during the intermolt and premolt stages.

  2025cites this paper
• Discovering Novel Proteoforms Using Proteogenomic Workflows Within the Galaxy Bioinformatics Platform.

  2025cites this paper
• Moving Toward Metaproteogenomics: A Computational Perspective on Analyzing Microbial Samples via Proteogenomics.

  2025cites this paper
• Opportunities for predictive proteogenomic biomarkers of drug treatment sensitivity in epithelial ovarian cancer

  2025cites this paper
• A modular, immunopeptidogenomic (iPepGen) analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates

  2025cites this paper
• Assessing the Performance of Mass Spectrometry Search Strategies in Identifying Translational Errors Using PDX Proteomics Data

  2025cites this paper
• Proteolytic and non-proteolytic mechanisms of keratin degradation in Onygena corvina revealed by a proteogenomic approach

  2025cites this paper
• Introduction to Integrated Proteogenomic Pipeline for Dealing with Pathogenic Missense SNPs.

  2025cites this paper
• Methodological Toolbox for Identifying and Studying Micropeptides: From Genome to Function

  2025cites this paper
• Evolving stratification and biomarker discovery in cancer research with technological advancement of proteomics: 35 years and counting

  2025cites this paper
• PepCentric Enables Fast Repository-Scale Proteogenomics Searches

  2025cites this paper
• Proteogenomic analysis of Cyprinid herpesvirus 2 using high-resolution mass spectrometry

  2025cites this paper
• The hidden bacterial microproteome.

  2025cites this paper
• The ‘non-conventional’ peptidome: A new layer in plant regulatory mechanisms

  2025cites this paper
• Insights from Mass Spectrometry-Based Proteomics on Cryptococcus neoformans

  2025cites this paper
• Benchmarking Software for DDA-PASEF Immunopeptidomics

  2025cites this paper
• An Overview of Analytical Approaches to Cancer Proteogenomics.

  2025cites this paper
• Precise Discovery of Novel N-Terminal Proteoforms beyond the Limitations of Proteogenomics and De Novo Sequencing.

  2025cites this paper
• A Multi-State Structural Genomics Approach Enables Large-Scale, Mechanistic, and Context-Specific Classification of ABCC6 Genetic Variants Implicated in Calcification Diseases

  2025cites this paper
• GeneCAD: Plant Genome Annotation with a DNA Foundation Model

  2025cites this paper
• Limitations of de novo sequencing in resolving sequence ambiguity

  2025cites this paper
• An Automated Workflow to Address Proteome Complexity and the Large Search Space Problem in Proteomics and HLA-I Immunopeptidomics

  2025cites this paper
• Metaproteomics in the One Health framework for unraveling microbial effectors in microbiomes

  2025cites this paper
• Implementing N-terminomics and machine learning to probe Nt-arginylation

  2025cites this paper
• Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment

  2025cites this paper
• Next-generation sequencing: A powerful multi-purpose tool in cell line development for biologics production

  2025cites this paper
• ProHap Explorer: Visualizing Haplotypes in Proteogenomic Datasets

  2025cites this paper
• Proteogenomics for Non-model Ocean-Derived Fungi.

  2025cites this paper
• From Gene to Whole Cell: Modeling, Visualization, and Analysis.

  2025cites this paper
• From reference to reality: identifying noncanonical peptides.

  2025cites this paper
• Integrated plasma metabolomic and proteomic analysis uncover the effects and mechanisms of isotretinoin in severe acne

  2025cites this paper
• Standard Protocols for Characterising Primary and In Vitro‐Generated Human Hepatocytes

  2025cites this paper
• Transcriptomic and proteomic analyses of SH-SY5Y neuroblastoma cells treated with amisulpride

  2025cites this paper
• Transcriptomics and Proteomics Identify Serotonin Transporter as a Promising Therapeutic Target for Essential Tremor

  2025cites this paper
• Unlocking the Therapeutic Power of Panax Species: A Concise Review of Bioactive Compounds, Pharmacological Properties and Clinical Applications

  2025cites this paper
• Uncovering dark mass in population proteomics: Pan-analysis of single amino acid polymorphism relevant to cognition and aging

  2025cites this paper
• Unlocking the secrets of the immunopeptidome: MHC molecules, ncRNA peptides, and vesicles in immune response

  2025cites this paper
• Implementing N-terminomics and machine learning to probe in vivo Nt-arginylation

  2025cites this paper
• Multiomics in cancer biomarker discovery and cancer subtyping.

  2025cites this paper
• Sensitive neoantigen discovery by real-time mutanome-guided immunopeptidomics

  2025cites this paper
• Relational model of all genetic codes

  2025cites this paper
• ProHap enables human proteomic database generation accounting for population diversity

  2024cites this paper
• Addressing Sample Mix‐Ups: Tools and Approaches for Large‐Scale Multi‐Omics Studies

  2024cites this paper
• Proteomics Can Rise to the Challenge of Pseudogenes’ Coding Nature

  2024cites this paper
• Chemoproteogenomic stratification of the missense variant cysteinome

  2024cites this paper
• Proteogenomics offers a novel avenue in neoantigen identification for cancer immunotherapy.

  2024cites this paper
• ProHap enables proteomic database generation accounting for population diversity

  2024cites this paper
• Direct Mapping of Polyclonal Epitopes in Serum by HDX-MS.

  2024cites this paper
• Proteogenomics-guided functional venomics resolves the toxin arsenal and activity of Deinagkistrodon acutus venom.

  2024cites this paper
• Community Resource: Large-Scale Proteogenomics to Refine Wheat Genome Annotations

  2024cites this paper
• Rp3: Ribosome profiling-assisted proteogenomics improves coverage and confidence during microprotein discovery

  2024cites this paper
• Exploring the Alternative Proteome with OpenProt and Mass Spectrometry.

  2024cites this paper
• Predicting peptide properties from mass spectrometry data using deep attention-based multitask network and uncertainty quantification

  2024cites this paper
• Evidence for widespread translation of 5′ untranslated regions

  2024cites this paper
• MSCI: an open-source Python package for information content assessment of peptide fragmentation spectra

  2024cites this paper
• Advances in the Clinical Application of High-throughput Proteomics

  2024cites this paper
• Myoglobin as a molecular biomarker for meat authentication and traceability.

  2024cites this paper
• Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors Into Peptide Identification

  2024cites this paper
• Phenotyping Tumor Heterogeneity through Proteogenomics: Study Models and Challenges

  2024cites this paper
• Evaluation of the antitumor effect of neoantigen peptide vaccines derived from the translatome of lung cancer

  2024cites this paper
• Data-Independent Acquisition: A Milestone and Prospect in Clinical Mass Spectrometry–Based Proteomics

  2024cites this paper
• Systematic identification of exercise-induced anti-aging processes involving intron retention

  2024cites this paper
• Broadening environmental research in the era of accurate protein structure determination and predictions

  2024cites this paper
• Understanding bacterial pathogen diversity: A proteogenomic analysis and use of an array of genome assemblies to identify novel virulence factors of the honey bee bacterial pathogen Paenibacillus larvae

  2024influential citation
• Systematic data analysis pipeline for quantitative morphological cell phenotyping

  2024cites this paper
• Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection

  2024cites this paper
• Plant genome information facilitates plant functional genomics

  2024cites this paper
• Improvement of tumor neoantigen detection by high field asymmetric waveform ion mobility mass spectrometry.

  2024cites this paper
• Multi-omics Identify Serotonin Transporter as a Promising Therapeutic Target for Essential Tremor

  2024cites this paper
• Immunopeptidomics-based identification of naturally presented non-canonical circRNA-derived peptides

  2024cites this paper
• Advancements in the Application of Proteogenomic in Assisting the Discovery of Novel Cancer Antigens

  2024cites this paper
• pXg: Comprehensive Identification of Noncanonical MHC-I–Associated Peptides From De Novo Peptide Sequencing Using RNA-Seq Reads

  2024cites this paper
• AttnPep: A Self-Attention-Based Deep Learning Method for Peptide Identification in Shotgun Proteomics.

  2024cites this paper
• Analysis and visualization of quantitative proteomics data using FragPipe-Analyst

  2024cites this paper
• Intracellular and Extracellular Peptidomes of the Model Plant, Physcomitrium patens.

  2024cites this paper