{"id":2335,"date":"2025-02-11T16:46:41","date_gmt":"2025-02-11T15:46:41","guid":{"rendered":"https:\/\/wp.unil.ch\/paf\/?page_id=2335"},"modified":"2026-03-27T10:39:34","modified_gmt":"2026-03-27T09:39:34","slug":"ressources","status":"publish","type":"page","link":"https:\/\/wp.unil.ch\/paf\/ressources\/","title":{"rendered":"Ressources"},"content":{"rendered":"\n

Discover essentials tools, softwares and guides to analyse your data. Click the link to download.<\/p>\n\n\n\n

Tutorials & Guides<\/h2>\n\n\n\n
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This guide<\/a> covers (almost) everything for interpreting MS data from proteome quantitation. A commented version is available here.<\/p>\n<\/div>\n<\/div>\n\n\n\n

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This document helps you with Mascot & Scaffold<\/mark><\/a>.<\/mark><\/p>\n<\/div>\n<\/div>\n\n\n\n

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For specific analyses, see the phosphoproteomic<\/a> or affinity purification<\/a> document.<\/p>\n<\/div>\n<\/div>\n\n\n\n

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Most journals require data sharing via public repositories. We will upload your data but need all required information firs<\/a>t<\/a><\/mark>. Please complete this document and send it to us.<\/p>\n<\/div>\n<\/div>\n\n\n\n

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This manual <\/a>provides insights into why the Jess Simple Western offers significant advantages over traditional Western blot methods. A summary is available here<\/a>.
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Some protocols<\/h2>\n\n\n\n
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SILAC labeling<\/a>
Secretome preparation<\/a>
Gingras lab<\/a> protocols for affinity purification.
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Useful databases<\/h2>\n\n\n\n
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THE reference protein database: Uniprot<\/a>
Proteomics data repository: ProteomeXchange<\/a><\/p>\n<\/div>\n<\/div>\n\n\n\n

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A comprehensive database of multiple organisms: ProteomicsDB<\/a>
The most extensive PTM database: PhosphositePlus<\/a>
A database of non-specific proteins in interactomics: REPRINT<\/a>
A database of known & predicted protein-protein interactions: STRING<\/a>

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A list of more than 6’000 antibodies validated for the Jess<\/a> Simple Western.
Our gel migration database for evaluating your western blot results: PUMBA<\/a>
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Software<\/h2>\n\n\n\n
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Peptides & proteins identification & quantification
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MaxQuant<\/a> (DDA)
Spectronaut<\/a> (DIA)
Proteome Discoverer<\/a> (DDA)<\/p>\n<\/div>\n<\/div>\n\n\n\n

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Post-processing of proteomics data
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Perseus<\/a>
Scaffold<\/a><\/p>\n<\/div>\n<\/div>\n\n\n\n

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Simple Western analysis
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Compass<\/a><\/p>\n<\/div>\n<\/div>\n<\/div><\/div>\n\n\n\n

<\/p>\n","protected":false},"excerpt":{"rendered":"

Discover essentials tools, softwares and guides to analyse your data. Click the link to download. Tutorials & Guides This guide covers (almost) everything for interpreting MS data from…<\/p>\n","protected":false},"author":1002530,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_seopress_robots_primary_cat":"","_seopress_titles_title":"","_seopress_titles_desc":"","_seopress_robots_index":"","footnotes":""},"class_list":["post-2335","page","type-page","status-publish","has-post-thumbnail"],"_links":{"self":[{"href":"https:\/\/wp.unil.ch\/paf\/wp-json\/wp\/v2\/pages\/2335","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wp.unil.ch\/paf\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wp.unil.ch\/paf\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wp.unil.ch\/paf\/wp-json\/wp\/v2\/users\/1002530"}],"replies":[{"embeddable":true,"href":"https:\/\/wp.unil.ch\/paf\/wp-json\/wp\/v2\/comments?post=2335"}],"version-history":[{"count":5,"href":"https:\/\/wp.unil.ch\/paf\/wp-json\/wp\/v2\/pages\/2335\/revisions"}],"predecessor-version":[{"id":2698,"href":"https:\/\/wp.unil.ch\/paf\/wp-json\/wp\/v2\/pages\/2335\/revisions\/2698"}],"wp:attachment":[{"href":"https:\/\/wp.unil.ch\/paf\/wp-json\/wp\/v2\/media?parent=2335"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}