{"id":675,"date":"2013-02-27T12:31:13","date_gmt":"2013-02-27T17:31:13","guid":{"rendered":"https:\/\/blogs.nature.com\/methagora\/?p=675"},"modified":"2013-04-09T10:36:34","modified_gmt":"2013-04-09T14:36:34","slug":"an-all-encompassing-term-to-describe-protein-complexity","status":"publish","type":"post","link":"https:\/\/blogs.nature.com\/methagora\/2013\/02\/an-all-encompassing-term-to-describe-protein-complexity.html","title":{"rendered":"An all-encompassing term to describe protein complexity"},"content":{"rendered":"

Neil Kelleher and Lloyd Smith propose that the scientific community adopt the term ‘proteoform’ to refer to all the different forms that a protein can take. Will the community adopt it? <\/strong><\/p>\n

The field of top-down proteomics, in which intact proteins are analyzed by a mass spectrometer, provides rich information about the genetic variations, alternative splicing and post-translational modifications that can be lost in a bottom-up proteomics approach (where proteins are digested into peptides prior to analysis). An unsolved problem in the top-down field, however, has been what exactly to call these various protein forms. Besides \u2018protein forms\u2019, a handful of other terms have been batted around in the literature, including \u2018protein variants\u2019, \u2018protein isoforms\u2019 and \u2018protein species.\u2019<\/p>\n

In a Correspondence<\/a> in the March issue of Nature Methods<\/em>, Neil Kelleher and Lloyd Smith lay out the reasons why none of these terms are satisfactory. What is needed, they argue, is a novel, unique, intuitive, single-word term with a precise definition that is all-encompassing in describing protein complexity, and is also compatible with a gene-centric approach to protein naming. They believe that they have the perfect term: proteoform<\/a>.<\/p>\n

\u201cIt\u2019s not just a term, it\u2019s a movement,\u201d says Kelleher. Kelleher has been one of the key drivers of top down methodology development, and argues that using a controlled vocabulary to describe proteins will serve a catalytic role in moving the field forward. \u201cThe implicit thing about this term is that it puts a focal point on the fact\u00a0that [the proteoforms] are the functional players, insofar as protein\u00a0primary structure is concerned,\u201d he says. Especially in clinical research, he notes, different proteoforms are tied strongly to function and phenotype.<\/p>\n

Kelleher and Smith have been gathering support for their term over the last several months by introducing it at conferences and inviting researchers to comment on a LinkedIn forum<\/a>. The term also has the full support of the Consortium for Top Down Proteomics<\/a>. At their latest conference in Florida, about a month ago, Kelleher says that \u201ceveryone\u201d was using \u201cproteoform\u201d in their talks. \u201cIt just catches on\u2026it fills a void the rolls right off the tongue at conferences and sits well in the gut while digesting text,\u201d he says. The consortium website maintains a repository of proteoforms<\/a>, which they hope will grow. Kelleher also notes that the term is being embraced by key protein informatics players at UniProt <\/a>and the Protein Information Resource<\/a>, both of which have adopted a gene-centric approach to protein naming.<\/p>\n

What do you think about the term \u201cproteoform\u201d? Will you adopt it? We\u2019d love to hear from you!<\/p>\n","protected":false},"excerpt":{"rendered":"

Neil Kelleher and Lloyd Smith propose that the scientific community adopt the term \u2018proteoform\u2019 to refer to all the different forms that a protein can take. Will the community adopt it?  Read more<\/a> Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":100,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[15,3,13],"tags":[50,104],"class_list":["post-675","post","type-post","status-publish","format-standard","hentry","category-mass-spectrometry","category-nature-methods-papers","category-proteomics","tag-proteins","tag-proteomics-2"],"_links":{"self":[{"href":"https:\/\/blogs.nature.com\/methagora\/wp-json\/wp\/v2\/posts\/675","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.nature.com\/methagora\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.nature.com\/methagora\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.nature.com\/methagora\/wp-json\/wp\/v2\/users\/100"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.nature.com\/methagora\/wp-json\/wp\/v2\/comments?post=675"}],"version-history":[{"count":0,"href":"https:\/\/blogs.nature.com\/methagora\/wp-json\/wp\/v2\/posts\/675\/revisions"}],"wp:attachment":[{"href":"https:\/\/blogs.nature.com\/methagora\/wp-json\/wp\/v2\/media?parent=675"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.nature.com\/methagora\/wp-json\/wp\/v2\/categories?post=675"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.nature.com\/methagora\/wp-json\/wp\/v2\/tags?post=675"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}