{"id":384,"date":"2016-09-23T13:22:26","date_gmt":"2016-09-23T16:22:26","guid":{"rendered":"http:\/\/pages.cnpem.br\/proteomicsworkshop\/?page_id=384"},"modified":"2016-09-23T13:22:26","modified_gmt":"2016-09-23T16:22:26","slug":"quantification-strategies-for-proteins-containing-posttranslational-modifications","status":"publish","type":"page","link":"https:\/\/pages.cnpem.br\/proteomicsworkshop\/quantification-strategies-for-proteins-containing-posttranslational-modifications\/","title":{"rendered":"Quantification Strategies for Proteins containing Posttranslational Modifications"},"content":{"rendered":"<p>Birgit Schilling<br \/>\n<em>San Francisco State University, Novato, CA, USA<\/em><\/p>\n<p style=\"text-align: justify;\"><strong>Quantification Strategies for Proteins containing Posttranslational Modifications \u2013 different workflow strategies using Skyline, including data-dependent and data-independent acquisitions. <\/strong><\/p>\n<p style=\"text-align: justify;\">Proteins containing posttranslational modifications play an important role in many diseases or metabolic disorders.\u00a0 We are particularly interested in mass spectrometric workflows to quantitatively assess changes in posttranslational modifications.\u00a0 More specifically, we investigated changes in phosphorylation or glycosylation in relation to breast cancer as part of a \u2018Clinical Proteomics Technology Assessment for Cancer\u2019 study (CPTAC).\u00a0 Separate projects assessed changes in lysine acylation, such as acetylation and succinylation studying the effects of the mitochondrial sirtuins (SIRT3 and SIRT5) in metabolic dysregulation and diabetes.\u00a0 Dynamic reorganization of the acetylome in bacterial <em>E. coli<\/em> strains has also been investigated.\u00a0 We use Skyline, an open-source software algorithm for targeted proteomics from the University of Washington, Seattle for our post-acquisition processing.\u00a0 Skyline provides advanced and accurate tools and visualization techniques for our relative quantification approaches.\u00a0 Data will be presented from large multi-laboratory SRM verification studies taking advantage of Skyline\u2019s platform independent features. \u00a0Focusing on posttranslational modification projects label-free protein quantitation approaches have been chosen investigating data-dependent mass spectrometric data sets (DDA and Skyline MS1 Filtering), as well as newer quantitative workflows, such as high resolution data-independent acquisitions (SWATH-DIA and parallel reaction monitoring PRM). \u00a0We have co-developed some algorithms for the Skyline Tool Store and also extensively used the interactive data sharing and spectral &amp; chromatographic library features of the Panorama webserver.<\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Birgit Schilling San Francisco State University, Novato, CA, USA Quantification Strategies for Proteins containing Posttranslational Modifications \u2013 different workflow strategies using Skyline, including data-dependent and data-independent acquisitions. Proteins containing posttranslational modifications play an important role in many diseases or metabolic disorders.\u00a0 We are particularly interested in mass spectrometric workflows to quantitatively assess changes in posttranslational&hellip;<\/p>\n","protected":false},"author":8,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-384","page","type-page","status-publish","hentry","description-off"],"_links":{"self":[{"href":"https:\/\/pages.cnpem.br\/proteomicsworkshop\/wp-json\/wp\/v2\/pages\/384","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/pages.cnpem.br\/proteomicsworkshop\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/pages.cnpem.br\/proteomicsworkshop\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/pages.cnpem.br\/proteomicsworkshop\/wp-json\/wp\/v2\/users\/8"}],"replies":[{"embeddable":true,"href":"https:\/\/pages.cnpem.br\/proteomicsworkshop\/wp-json\/wp\/v2\/comments?post=384"}],"version-history":[{"count":0,"href":"https:\/\/pages.cnpem.br\/proteomicsworkshop\/wp-json\/wp\/v2\/pages\/384\/revisions"}],"wp:attachment":[{"href":"https:\/\/pages.cnpem.br\/proteomicsworkshop\/wp-json\/wp\/v2\/media?parent=384"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}