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Lights and shadows of proteomic technologies for the study of protein species including isoforms, splicing variants and protein post-translational modifications

Authors

  • Juan Casado-Vela,

    Corresponding author
    1. Translational Oncology Unit, Instituto de Investigaciones Biomédicas “Alberto Sols”, Spanish National Research Council (CSIC), Madrid, Spain
    • Translational Oncology Unit, Instituto de Investigaciones Biomédicas “Alberto Sols”, Spanish National Research Council (CSIC), Arturo Duperier, 4, 28029 Madrid, Spain Fax: +34-915854401
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  • Arancha Cebrián,

    1. Translational Oncology Unit, Instituto de Investigaciones Biomédicas “Alberto Sols”, Spanish National Research Council (CSIC), Madrid, Spain
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  • Maria Teresa Gómez del Pulgar,

    1. Translational Oncology Unit, Instituto de Investigaciones Biomédicas “Alberto Sols”, Spanish National Research Council (CSIC), Madrid, Spain
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  • Elsa Sánchez-López,

    1. Translational Oncology Unit, Instituto de Investigaciones Biomédicas “Alberto Sols”, Spanish National Research Council (CSIC), Madrid, Spain
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  • Marta Vilaseca,

    1. Mass Spectrometry Core Facility, Institut de Recerca Biomèdica (IRB Barcelona), Barcelona, Spain
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  • Laura Menchén,

    1. Translational Oncology Unit, Instituto de Investigaciones Biomédicas “Alberto Sols”, Spanish National Research Council (CSIC), Madrid, Spain
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  • Claudia Diema,

    1. Mass Spectrometry Core Facility, Institut de Recerca Biomèdica (IRB Barcelona), Barcelona, Spain
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  • Susana Sellés-Marchart,

    1. Proteomics and Functional Genomics Group, Departamento de Agroquímica y Bioquímica, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
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  • María José Martínez-Esteso,

    1. Proteomics and Functional Genomics Group, Departamento de Agroquímica y Bioquímica, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
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  • Noemí Yubero,

    1. Translational Oncology Unit, Instituto de Investigaciones Biomédicas “Alberto Sols”, Spanish National Research Council (CSIC), Madrid, Spain
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  • Roque Bru-Martínez,

    1. Proteomics and Functional Genomics Group, Departamento de Agroquímica y Bioquímica, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
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  • Juan Caelos Lacal

    1. Translational Oncology Unit, Instituto de Investigaciones Biomédicas “Alberto Sols”, Spanish National Research Council (CSIC), Madrid, Spain
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Errata

This article is corrected by:

  1. Errata: Erratum: Lights and shadows of proteomic technologies for the study of protein species including isoforms, splicing variants and protein post-translational modifications Volume 11, Issue 7, 1370, Article first published online: 24 March 2011

Abstract

Recent reviews pinpointed the enormous diversity of proteins found in living organisms, especially in higher eukaryotes. Protein diversity is driven through three main processes: first, at deoxyribonucleic acid (DNA) level (i.e. gene polymorphisms), second, at precursor messenger ribonucleic acid (pre-mRNA) or messenger ribonucleic acid (mRNA) level (i.e. alternative splicing, also termed as differential splicing) and, finally, at the protein level (i.e. PTM). Current proteomic technologies allow the identification, characterization and quantitation of up to several thousands of proteins in a single experiment. Nevertheless, the identification and characterization of protein species using these technologies are still hampered. Here, we review the use of the terms “protein species” and “protein isoform.” We evidence that the appropriate selection of the database used for searches can impede or facilitate the identification of protein species. We also describe examples where protein identification search engines systematically fail in the attribution of protein species. We briefly review the characterization of protein species using proteomic technologies including gel-based, gel-free, bottom-up and top-down analysis and discuss their limitations. As an example, we discuss the theoretical characterization of the two human choline kinase species, α-1 and α-2, sharing the same catalytic activity but generated by alternative splicing on CHKA gene.

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