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A predicted novel protein isoform of HOXA9. Leuk Res 2019; 82:7-10. [PMID: 31112908 DOI: 10.1016/j.leukres.2019.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/15/2019] [Accepted: 05/03/2019] [Indexed: 11/20/2022]
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Vanichkina DP, Schmitz U, Wong JJL, Rasko JE. Challenges in defining the role of intron retention in normal biology and disease. Semin Cell Dev Biol 2018; 75:40-49. [DOI: 10.1016/j.semcdb.2017.07.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/19/2017] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
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3
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Kroll JE, da Silva VL, de Souza SJ, de Souza GA. A tool for integrating genetic and mass spectrometry-based peptide data: Proteogenomics Viewer. Bioessays 2017; 39. [DOI: 10.1002/bies.201700015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- José Eduardo Kroll
- Institute of Bioinformatics and Biotechnology; Natal − RN Brazil
- Brain Institute; Universidade Federal do Rio Grande do Norte; Natal − RN Brazil
- Bioinformatics Multidisciplinary Environment; Instituto Metrópole Digital; UFRN, Natal-RN Brazil
| | - Vandeclécio Lira da Silva
- Brain Institute; Universidade Federal do Rio Grande do Norte; Natal − RN Brazil
- Bioinformatics Multidisciplinary Environment; Instituto Metrópole Digital; UFRN, Natal-RN Brazil
| | - Sandro José de Souza
- Brain Institute; Universidade Federal do Rio Grande do Norte; Natal − RN Brazil
- Bioinformatics Multidisciplinary Environment; Instituto Metrópole Digital; UFRN, Natal-RN Brazil
| | - Gustavo Antonio de Souza
- Brain Institute; Universidade Federal do Rio Grande do Norte; Natal − RN Brazil
- Bioinformatics Multidisciplinary Environment; Instituto Metrópole Digital; UFRN, Natal-RN Brazil
- Department of Immunology and Centre for Immune Regulation, Oslo University Hospital HF Rikshospitalet; University of Oslo; Oslo Norway
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Sheynkman GM, Shortreed MR, Cesnik AJ, Smith LM. Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:521-45. [PMID: 27049631 PMCID: PMC4991544 DOI: 10.1146/annurev-anchem-071015-041722] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Mass spectrometry-based proteomics has emerged as the leading method for detection, quantification, and characterization of proteins. Nearly all proteomic workflows rely on proteomic databases to identify peptides and proteins, but these databases typically contain a generic set of proteins that lack variations unique to a given sample, precluding their detection. Fortunately, proteogenomics enables the detection of such proteomic variations and can be defined, broadly, as the use of nucleotide sequences to generate candidate protein sequences for mass spectrometry database searching. Proteogenomics is experiencing heightened significance due to two developments: (a) advances in DNA sequencing technologies that have made complete sequencing of human genomes and transcriptomes routine, and (b) the unveiling of the tremendous complexity of the human proteome as expressed at the levels of genes, cells, tissues, individuals, and populations. We review here the field of human proteogenomics, with an emphasis on its history, current implementations, the types of proteomic variations it reveals, and several important applications.
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Affiliation(s)
- Gloria M Sheynkman
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215;
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706; ,
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706; ,
| | - Anthony J Cesnik
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706; ,
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706; ,
- Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706;
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Tay AP, Pang CNI, Twine NA, Hart-Smith G, Harkness L, Kassem M, Wilkins MR. Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data. J Proteome Res 2015; 14:3541-54. [PMID: 25961807 DOI: 10.1021/pr5011394] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Human proteome analysis now requires an understanding of protein isoforms. We recently published the PG Nexus pipeline, which facilitates high confidence validation of exons and splice junctions by integrating genomics and proteomics data. Here we comprehensively explore how RNA-seq transcriptomics data, and proteomic analysis of the same sample, can identify protein isoforms. RNA-seq data from human mesenchymal (hMSC) stem cells were analyzed with our new TranscriptCoder tool to generate a database of protein isoform sequences. MS/MS data from matching hMSC samples were then matched against the TranscriptCoder-derived database, along with Ensembl and the neXtProt database. Querying the TranscriptCoder-derived or Ensembl database could unambiguously identify ∼450 protein isoforms, with isoform-specific proteotypic peptides, including candidate hMSC-specific isoforms for the genes DPYSL2 and FXR1. Where isoform-specific peptides did not exist, groups of nonisoform-specific proteotypic peptides could specifically identify many isoforms. In both the above cases, isoforms will be detectable with targeted MS/MS assays. Unfortunately, our analysis also revealed that some isoforms will be difficult to identify unambiguously as they do not have peptides that are sufficiently distinguishing. We covisualize mRNA isoforms and peptides in a genome browser to illustrate the above situations. Mass spectrometry data is available via ProteomeXchange (PXD001449).
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Affiliation(s)
- Aidan P Tay
- Systems Biology Initiative, The University of New South Wales , Sydney, New South Wales 2052, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Chi Nam Ignatius Pang
- Systems Biology Initiative, The University of New South Wales , Sydney, New South Wales 2052, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Natalie A Twine
- Systems Biology Initiative, The University of New South Wales , Sydney, New South Wales 2052, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Gene Hart-Smith
- Systems Biology Initiative, The University of New South Wales , Sydney, New South Wales 2052, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Linda Harkness
- Endocrine Research Laboratory (KMEB), Department of Endocrinology and Metabolism, Odense University Hospital & University of Southern Denmark , Odense 5230, Denmark
| | - Moustapha Kassem
- Endocrine Research Laboratory (KMEB), Department of Endocrinology and Metabolism, Odense University Hospital & University of Southern Denmark , Odense 5230, Denmark
| | - Marc R Wilkins
- Systems Biology Initiative, The University of New South Wales , Sydney, New South Wales 2052, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia
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