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Methods: Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes
- Nitin Gupta,
- Jamal Benhamida,
- Vipul Bhargava,
- Daniel Goodman,
- Elisabeth Kain,
- Ian Kerman,
- Ngan Nguyen,
- Noah Ollikainen,
- Jesse Rodriguez,
- Jian Wang,
- Mary S. Lipton,
- Margaret Romine,
- Vineet Bafna,
- Richard D. Smith,
- and Pavel A. Pevzner
Genome Res. July 2008 18: 1133-1142; Published in Advance April 21, 2008, doi:10.1101/gr.074344.107
...of the traditional “single proteome” approach in mass spectrometry. In particular, we show how comparative proteogenomics addresses the notoriously difficult problem of “one-hit-wonders” in proteomics, improves on the existing gene prediction tools in genomics, and allows identification of rare post-translational...
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LETTER: Mass spectrometry of the M. smegmatis proteome: Protein expression levels correlate with function, operons, and codon bias
- Rong Wang,
- John T. Prince,
- and Edward M. Marcotte
Genome Res. August 2005 15: 1118-1126; doi:10.1101/gr.3994105
...The physical and metabolic changes in mycobacteria during exponential and stationary phase are largely unknown. As comparative proteomics has the potential to detect changes in the proteome, for example, changes in abundance as well as post-translational modifications such as phosphorylation and glycosylation...
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Method: Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome
- Ulrich Omasits,
- Maxime Quebatte,
- Daniel J. Stekhoven,
- Claudia Fortes,
- Bernd Roschitzki,
- Mark D. Robinson,
- Christoph Dehio,
- and Christian H. Ahrens
Genome Res. November 2013 23: 1916-1927; Published in Advance July 22, 2013, doi:10.1101/gr.151035.112
...modifications, subcellular localization information, and identification of interaction partners of proteins. Due to enormous advances in mass spectrometry instrumentation, biochemical fractionation methods, and computational approaches, proteomics hasmatured into a statewhere the description of complete...
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Resource: PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations
- Bo Wen,
- Xiaojing Wang,
- and Bing Zhang
Genome Res. March 2019 29: 485-493; Published in Advance January 4, 2019, doi:10.1101/gr.235028.118
..., Petralia F, et al. 2016. Proteogenomics connects somatic mutations to signalling in breast cancer. Nature 534: 55–62. doi:10.1038/nature18003 ↵Nesvizhskii AI. 2006. Protein identification by tandem mass spectrometry and sequence database searching. In Mass spectrometry data analysis in proteomics (ed...
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Resource: GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes
- Yi Shao,
- Chunyan Chen,
- Hao Shen,
- Bin Z. He,
- Daqi Yu,
- Shuai Jiang,
- Shilei Zhao,
- Zhiqiang Gao,
- Zhenglin Zhu,
- Xi Chen,
- Yan Fu,
- Hua Chen,
- Ge Gao,
- Manyuan Long,
- and Yong E. Zhang
Genome Res. April 2019 29: 682-696; Published in Advance March 12, 2019, doi:10.1101/gr.238733.118
...that our approach and findings may have wider implications.Inference of the protein-coding potential of new genes requires both evolutionary and proteomic approachesBoth selective constraints and proteogenomics (Branca et al. 2014; Kim et al. 2014; Wright et al. 2016) have been used to annotate proteins...
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Perspective: Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship
- Marie A. Brunet,
- Sébastien A. Levesque,
- Darel J. Hunting,
- Alan A. Cohen,
- and Xavier Roucou
Genome Res. May 2018 28: 609-624; Published in Advance April 6, 2018, doi:10.1101/gr.230938.117
..., consideration of proteomic complexity is usually restricted to one protein (and its splicing-derived isoforms) per gene. Protein complexity can arise from multiple sources, such as RNA splicing and editing, post-translational modifications, alternative initiation (internal ribosome entry site), stop codon read...
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Method: An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics
- Ulrich Omasits,
- Adithi R. Varadarajan,
- Michael Schmid,
- Sandra Goetze,
- Damianos Melidis,
- Marc Bourqui,
- Olga Nikolayeva,
- Maxime Québatte,
- Andrea Patrignani,
- Christoph Dehio,
- Juerg E. Frey,
- Mark D. Robinson,
- Bernd Wollscheid,
- and Christian H. Ahrens
Genome Res. December 2017 27: 2083-2095; Published in Advance November 15, 2017, doi:10.1101/gr.218255.116
...).Proteogenomics, a research field at the interface of proteomics and genomics (Ahrens et al. 2010; Nesvizhskii 2014), is one attractive approach to address these problems. The direct protein expression evidence provided by tandem mass spectrometry (MS) for CDSs missed in annotations differs from ribosome...
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Methods: Ortho-proteogenomics: Multiple proteomes investigation through orthology and a new MS-based protocol
- Sébastien Gallien,
- Emmanuel Perrodou,
- Christine Carapito,
- Caroline Deshayes,
- Jean-Marc Reyrat,
- Alain Van Dorsselaer,
- Olivier Poch,
- Christine Schaeffer,
- and Odile Lecompte
Genome Res. January 2009 19: 128-135; Published in Advance October 27, 2008, doi:10.1101/gr.081901.108
...-terminal peptides . Nat. Biotechnol. 21 : 566 – 569 . ↵ Gupta, N. , Tanner, S. , Jaitly, N. , Adkins, J.N. , Lipton, M. , Edwards, R. , Romine, M. , Osterman, A. , Bafna, V. , Smith, R.D. , et al. ( 2007 ) Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry...
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Methods: Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations
- Gennifer E. Merrihew,
- Colleen Davis,
- Brent Ewing,
- Gary Williams,
- Lukas Käll,
- Barbara E. Frewen,
- William Stafford Noble,
- Phil Green,
- James H. Thomas,
- and Michael J. MacCoss
Genome Res. October 2008 18: 1660-1669; Published in Advance July 24, 2008, doi:10.1101/gr.077644.108
..., N. , Adkins, J.N. , Lipton, M. , Edwards, R. , Romine, M. , Osterman, A. , Bafna, V. , Smith, R.D. , et al. ( 2007 ) Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation . Genome Res. 17 : 1362 – 1377 . ↵ Jaffe, J.D. , Berg, H...
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Resource: A platform for curated products from novel open reading frames prompts reinterpretation of disease variants
- Matthew D.C. Neville,
- Robin Kohze,
- Chaitanya Erady,
- Narendra Meena,
- Matthew Hayden,
- David N. Cooper,
- Matthew Mort,
- and Sudhakaran Prabakaran
Genome Res. February 2021 31: 327-336; Published in Advance January 19, 2021, doi:10.1101/gr.263202.120
...for each CDS, “ATG” as the only start codon, and conservative definitions of Kozak sequences (Plaza et al. 2017; Brunet et al. 2018). There have also been recent advances in the sensitivity of proteomics methods such as ribosome profiling and mass spectrometry (MS), the ability to sequence s...

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