{"id":2966,"date":"2024-08-02T11:29:16","date_gmt":"2024-08-02T15:29:16","guid":{"rendered":"https:\/\/www.med.unc.edu\/proteomics-metabolomics\/?page_id=2966"},"modified":"2024-09-17T16:27:42","modified_gmt":"2024-09-17T20:27:42","slug":"rigor-and-reproducibility","status":"publish","type":"page","link":"https:\/\/www.med.unc.edu\/proteomics-metabolomics\/resources\/rigor-and-reproducibility\/","title":{"rendered":"Rigor &#038; Reproducibility"},"content":{"rendered":"<p>The Metabolomics and Proteomics (MAP) Core at ºÚÁÏÍø is committed to ensuring rigorous and reproducible mass spectrometry-based proteomics and metabolomics analyses to accomplish research needs. The following are examples of procedures employed by the core to ensure rigor and reproducibility:<\/p>\n<ul>\n<li>MAP Core instrumentation is subjected to weekly calibration and performance checks to ensure continued quality of results. Our liquid chromatography (LC) and mass spectrometry (MS) instruments are covered by comprehensive service contracts, and yearly preventive maintenance is carried out on these instruments to ensure reproducible performance.<\/li>\n<li>System reproducibility is routinely monitored using quality control (QC) standards. For example, for proteomics complex lysate digest standard (HELA; Pierce) is analyzed weekly to determine reproducible protein identification-based parameters. Analysis of a single protein digest standard (BSA; Waters) is analyzed daily to ensure the reproducibility of identification-free parameters. QC data is monitored using the software QuiC (Biognosys), which generates identification-based and identification-free plots that allow the core staff to assess instrument performance.<\/li>\n<li>MAP Core follows SOPs for routine sample preparation and documents all steps (sample preparation, mass spectrometry analysis, and data analysis) that are carried out at the core.<\/li>\n<li>All reports and datasets produced by a member of the MAP Core are reviewed by another member of the Core prior to being shared with collaborators.<\/li>\n<li>MAP Core stores raw and processed data on a local Network Shared Drive provided by the University that is HIPPA secure. Snapshot backups are done daily. MAP Core retains data for up to 5 years.<\/li>\n<li>At the time of publication, data is uploaded to a public repository, such as the ProteomeXchange consortium via PRIDE.<\/li>\n<\/ul>\n<p>While the MAP Core guarantees the quality of work performed directly by its staff, it is the responsibility of individual scientists to ensure that our recommendations are followed. Suggested steps to this end include:<\/p>\n<ul>\n<li>Consult with MAP Core staff during the planning stages of your proteomics experiments prior to sample preparation. The MAP Core staff will help you design your experiments with sufficient controls and replicates.<\/li>\n<li>Follow MAP Core-provided guidelines for sample preparation, provided during consultation and specific to project type.<\/li>\n<li>Have a clear and detailed protocol (SOP). Ensure that the protocol is strictly followed or that any deviation is well documented.<\/li>\n<li>Ensure that the staff or students performing the experiment are well-trained and understand each step and the importance of performing them precisely.<\/li>\n<li>Ensure that all reagents (e.g., purified proteins, antibodies, cell lines) are fully validated. If applicable, retain any certificates of analysis.<\/li>\n<li>Document all steps, reagents, equipment and data analysis methods used in the experiment. Ensure that both the documentation and the data itself are properly stored in a safe data management repository.<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>The Metabolomics and Proteomics (MAP) Core at ºÚÁÏÍø is committed to ensuring rigorous and reproducible mass spectrometry-based proteomics and metabolomics analyses to accomplish research needs. The following are examples of procedures employed by the core to ensure rigor and reproducibility: MAP Core instrumentation is subjected to weekly calibration and performance checks to ensure continued quality &hellip; <a href=\"https:\/\/www.med.unc.edu\/proteomics-metabolomics\/resources\/rigor-and-reproducibility\/\" aria-label=\"Read more about Rigor &#038; Reproducibility\">Read more<\/a><\/p>\n","protected":false},"author":112631,"featured_media":0,"parent":2273,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"layout":"","cellInformation":"","apiCallInformation":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2966","page","type-page","status-publish","hentry","odd"],"acf":[],"_links_to":[],"_links_to_target":[],"_links":{"self":[{"href":"https:\/\/www.med.unc.edu\/proteomics-metabolomics\/wp-json\/wp\/v2\/pages\/2966","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.med.unc.edu\/proteomics-metabolomics\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.med.unc.edu\/proteomics-metabolomics\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/proteomics-metabolomics\/wp-json\/wp\/v2\/users\/112631"}],"replies":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/proteomics-metabolomics\/wp-json\/wp\/v2\/comments?post=2966"}],"version-history":[{"count":4,"href":"https:\/\/www.med.unc.edu\/proteomics-metabolomics\/wp-json\/wp\/v2\/pages\/2966\/revisions"}],"predecessor-version":[{"id":3163,"href":"https:\/\/www.med.unc.edu\/proteomics-metabolomics\/wp-json\/wp\/v2\/pages\/2966\/revisions\/3163"}],"up":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/proteomics-metabolomics\/wp-json\/wp\/v2\/pages\/2273"}],"wp:attachment":[{"href":"https:\/\/www.med.unc.edu\/proteomics-metabolomics\/wp-json\/wp\/v2\/media?parent=2966"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}