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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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Research: A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry
- Raghothama Chaerkady,
- Dhanashree S. Kelkar,
- Babylakshmi Muthusamy,
- Kumaran Kandasamy,
- Sutopa B. Dwivedi,
- Nandini A. Sahasrabuddhe,
- Min-Sik Kim,
- Santosh Renuse,
- Sneha M. Pinto,
- Rakesh Sharma,
- Harsh Pawar,
- Nirujogi Raja Sekhar,
- Ajeet Kumar Mohanty,
- Derese Getnet,
- Yi Yang,
- Jun Zhong,
- Aditya P. Dash,
- Robert M. MacCallum,
- Bernard Delanghe,
- Godfree Mlambo,
- Ashwani Kumar,
- T.S. Keshava Prasad,
- Mobolaji Okulate,
- Nirbhay Kumar,
- and Akhilesh Pandey
Genome Res. November 2011 21: 1872-1881; Published in Advance July 27, 2011, doi:10.1101/gr.127951.111
..., A Mohanty, Ajeet Kumar Kumar, A Pinto Sneha M. Dhanashree Kelkar 10.1101/gr.127951.111 genome;gr.127951.111 1088-9051 A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry Research A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier...
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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
...for proteogenomic annotation . Genome Res. 17 : 1362 – 1377 . ↵ Gupta, N. , Benhamida, J. , Bhargava, V. , Goodman, D. , Kain, E. , Kerman, I. , Nguyen, N. , Ollikainen, N. , Rodriguez, J. , Wang, J. , et al. ( 2008 ) Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze...
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Method: Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes
- T.S. Keshava Prasad,
- Ajeet Kumar Mohanty,
- Manish Kumar,
- Sreelakshmi K. Sreenivasamurthy,
- Gourav Dey,
- Raja Sekhar Nirujogi,
- Sneha M. Pinto,
- Anil K. Madugundu,
- Arun H. Patil,
- Jayshree Advani,
- Srikanth S. Manda,
- Manoj Kumar Gupta,
- Sutopa B. Dwivedi,
- Dhanashree S. Kelkar,
- Brantley Hall,
- Xiaofang Jiang,
- Ashley Peery,
- Pavithra Rajagopalan,
- Soujanya D. Yelamanchi,
- Hitendra S. Solanki,
- Remya Raja,
- Gajanan J. Sathe,
- Sandip Chavan,
- Renu Verma,
- Krishna M. Patel,
- Ankit P. Jain,
- Nazia Syed,
- Keshava K. Datta,
- Aafaque Ahmed Khan,
- Manjunath Dammalli,
- Savita Jayaram,
- Aneesha Radhakrishnan,
- Christopher J. Mitchell,
- Chan-Hyun Na,
- Nirbhay Kumar,
- Photini Sinnis,
- Igor V. Sharakhov,
- Charles Wang,
- Harsha Gowda,
- Zhijian Tu,
- Ashwani Kumar,
- and Akhilesh Pandey
Genome Res. January 2017 27: 133-144; Published in Advance November 15, 2016, doi:10.1101/gr.201368.115
...peptides selected at random across the various proteogenomic categories. These peptides were then analyzed using the same instrument parameters on the mass spectrometer that was used for proteomic analysis of the tissues from An. stephensi. MS/MS fragmentation patterns of these synthetic peptides were...
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Research: Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models
- Nadine Borchert,
- Christoph Dieterich,
- Karsten Krug,
- Wolfgang Schütz,
- Stephan Jung,
- Alfred Nordheim,
- Ralf J. Sommer,
- and Boris Macek
Genome Res. June 2010 20: 837-846; Published in Advance March 17, 2010, doi:10.1101/gr.103119.109
...of the filarial nematode parasite Brugia malayi. Science 317: 1756–1760. Gupta N, Benhamida J, Bhargava V, Goodman D, Kain E, Kerman I, Nguyen N, Ollikainen N, Rodriguez J, Wang J, et al. 2008. Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple s. Genome Res 18...
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Methods: Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation
- Nitin Gupta,
- Stephen Tanner,
- Navdeep Jaitly,
- Joshua N. Adkins,
- Mary Lipton,
- Robert Edwards,
- Margaret Romine,
- Andrei Osterman,
- Vineet Bafna,
- Richard D. Smith,
- and Pavel A. Pevzner
Genome Res. September 2007 17: 1362-1377; Published in Advance August 9, 2007, doi:10.1101/gr.6427907
...Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation Nitin Gupta 1 , 7 , 8 , Stephen Tanner 1 , 7 , Navdeep Jaitly 2 , Joshua N. Adkins 2 , Mary Lipton 2...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...), further substantiating its potential as a bona fide neoantigen candidate.View larger version: In this window In a new window Figure 8. TE-chimeric transcript–derived peptides as neoantigens. (A) Annotation of 12,234 HLA-bound peptides identified by mass spectrometry (MS) from AsPC-1 cells across multiple...
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Method: Discovery and annotation of small proteins using genomics, proteomics, and computational approaches
- Xiaohan Yang,
- Timothy J. Tschaplinski,
- Gregory B. Hurst,
- Sara Jawdy,
- Paul E. Abraham,
- Patricia K. Lankford,
- Rachel M. Adams,
- Manesh B. Shah,
- Robert L. Hettich,
- Erika Lindquist,
- Udaya C. Kalluri,
- Lee E. Gunter,
- Christa Pennacchio,
- and Gerald A. Tuskan
Genome Res. April 2011 21: 634-641; Published in Advance March 2, 2011, doi:10.1101/gr.109280.110
...451709, and HP451711–HP451725. Mass spectrometry data have been uploaded to the Proteome Commons Tranche repository ( https://proteomecommons.org/tranche/ ).] Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10...
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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
...continuously identify new genomic alterations that may lead to novel protein sequences, which are attractive candidates for disease biomarkers and therapeutic targets after proteomic validation. Integrative proteogenomic methods have been developed to use mass spectrometry (MS)-based proteomics data...
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Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
- Alejandro Ceron-Noriega,
- Miguel V. Almeida,
- Michal Levin,
- and Falk Butter
Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
...of nematodes is believed to date back to ∼650–750 million years, generating a large and phylogenetically diverse group to be explored. However, for most species high-quality gene annotations are incomprehensive or missing. Combining short-read RNA sequencing with mass spectrometry–based proteomics and machine...

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