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The tutorial builds on the 2016 MaxQuant Summer School presentations and documents core concepts such as protein groups, razor peptides, label-free quantification, posterior error probability (PEP), match-between-runs, and normalization. It further covers dependent peptide search, output table structures, and a practical tutorial workflow including Andromeda configuration, raw files, viewer usage, and group-specific parameters.",{"@graph":63,"@context":118},[64,80,101],{"@type":65,"itemListElement":66},"BreadcrumbList",[67,71,74,77],{"item":68,"name":69,"@type":70,"position":9},"https://docshare.wps.com","Home","ListItem",{"item":72,"name":10,"@type":70,"position":73},"https://docshare.wps.com/template/",2,{"item":75,"name":11,"@type":70,"position":76},"https://docshare.wps.com/template/presentations/",3,{"item":78,"name":59,"@type":70,"position":79},"https://docshare.wps.com/template/maxquant-information-and-tutorial/572166/",4,{"url":78,"name":59,"@type":81,"image":82,"author":87,"headline":59,"publisher":90,"fileFormat":93,"inLanguage":57,"description":61,"dateModified":94,"datePublished":95,"encodingFormat":93,"isAccessibleForFree":96,"interactionStatistic":97},"DigitalDocument",{"url":83,"@type":84,"width":85,"height":86},"https://docshare.wps.com/thumbnails/maxquant-information-and-tutorial/572166.png","ImageObject",442,249,{"name":88,"@type":89},"Noah","Person",{"url":68,"name":91,"@type":92},"DocShare","Organization","application/pdf","2026-10-19","2026-10-13",true,{"@type":98,"interactionType":99,"userInteractionCount":76},"InteractionCounter",{"@type":100},"ViewAction",{"@type":102,"mainEntity":103},"FAQPage",[104,110,114],{"name":105,"@type":106,"acceptedAnswer":107},"What is the purpose of this MaxQuant tutorial paper?","Question",{"text":108,"@type":109},"It provides documentation and a structured tutorial for the MaxQuant computational platform used in mass-spectrometry-based shotgun proteomics.","Answer",{"name":111,"@type":106,"acceptedAnswer":112},"Which label-free quantification concepts are covered?",{"text":113,"@type":109},"The tutorial explains quantification options and key methods including Posterior Error Probability (PEP), match between runs, and normalization.",{"name":115,"@type":106,"acceptedAnswer":116},"What practical topics are included in the MaxQuant tutorial workflow?",{"text":117,"@type":109},"It covers Andromeda search engine configuration, handling raw files, using the MaxQuant Viewer, and setting group-specific parameters such as digestion, modifications, and instrument details.","https://schema.org",{"og:url":78,"og:type":120,"og:title":59,"og:site_name":91,"og:description":61},"article",{"robots":122,"canonical":78},"index,follow",{"doc_id":124,"site_id":56},572166,1792436726,{"code":4,"msg":5,"data":127},{"doc_id":124,"user_id":128,"nickname":88,"user_avatar":129,"doc_module":9,"category_id":8,"category_name":11,"doc_title":59,"doc_description":61,"doc_content":130,"file_id":131,"file_url":132,"file_type":133,"file_size":134,"view_count":76,"is_deleted":4,"is_public":9,"is_downloadable":9,"audit_status":9,"page_count":135,"language":136,"language_code":57,"site_id":56,"html_lang":57,"table_of_contents":137,"faqs":138,"seo_title":139,"seo_description":61,"update_tm":140,"read_time":141},8796095462418,"https://ap-avatar.wpscdn.com/avatar/80000253c1241d02b47?x-image-process=image/resize,m_fixed,w_180,h_180&k=1778826106357471780","MaxQuant – Information and Tutorial  \nby Tjorven Hinzke  \nThe tutorial is based on the 2016 MaxQuant Summer School presentations (MaxQuant version [1.5.5.1](1.5.5.1))–the credit goes to the developers of MaxQuant and Perseus and the speakers of the 2016 MaxQuant Summer School.  \nThis is the documentation paper: Tyanova et al. 2016, The MaxQuant computational platform for massspectrometry-based shotgun proteomics, Nature Protocols 11, 2301-2319;  \n[http://www.nature.com/nprot/journal/v11/n12/pdf/nprot.2016.136.pdf](http://www.nature.com/nprot/journal/v11/n12/pdf/nprot.2016.136.pdf).  \nAdditionally, the “Max Quant” youtube channel provides videos of MaxQuant Summer School talks, which are a great source for further information.  \nTable of contents  \n1. MaxQuant background...........................................................................................................................................2  \n1.1 General...........................................................................................................................................................2  \n1.2 Download and Installation............................................................................................................................2  \n1.3 How does it work? .........................................................................................................................................2  \n1.3.1 Protein groups and razor peptides ......................................................................................................3  \n1.4 Label-free quantification in MaxQuant ........................................................................................................3  \n1.4.1 Quantification possibilities in general.................................................................................................3  \n1.4.2 label-free quantification.......................................................................................................................3  \n1.4.3 Posterior Error Probability (PEP) .......................................................................................................4  \n1.4.4 Match between runs .............................................................................................................................5  \n1.4.5 Normalization.......................................................................................................................................5  \n1.5 Dependent peptide search ............................................................................................................................6  \n1.6 Output tables .................................................................................................................................................6  \n1.6.1 General .................................................................................................................................................6  \n1.6.2 Scans ..................................................................................................................................................... 7  \n1.6.3 Identification ........................................................................................................................................ 7  \n1.6.4 Features ................................................................................................................................................8  \n1.6.5 Metadata ...............................................................................................................................................8  \n2. MaxQuant Tutorial .................................................................................................................................................9  \n2.1 generally.........................................................................................................................................................9  \n2.2 Configuration of the Andromeda search engine ...","cbCaijKFOeVD852u","https://ap.wps.com/l/cbCaijKFOeVD852u","pdf",872698,19,"English","# MaxQuant background\n## General\n## Download and Installation\n## How does it work?\n### Protein groups and razor peptides\n## Label-free quantification in MaxQuant\n## Dependent peptide search\n## Output tables\n# MaxQuant Tutorial\n## Configuration of the Andromeda search engine\n## Raw files\n## MaxQuant Viewer\n## Group-specific parameters","[{\"question\":\"What is the purpose of this MaxQuant tutorial paper?\",\"answer\":\"It provides documentation and a structured tutorial for the MaxQuant computational platform used in mass-spectrometry-based shotgun proteomics.\"},{\"question\":\"Which label-free quantification concepts are covered?\",\"answer\":\"The tutorial explains quantification options and key methods including Posterior Error Probability (PEP), match between runs, and normalization.\"},{\"question\":\"What practical topics are included in the MaxQuant tutorial workflow?\",\"answer\":\"It covers Andromeda search engine configuration, handling raw files, using the MaxQuant Viewer, and setting group-specific parameters such as digestion, modifications, and instrument details.\"}]","MaxQuant - Information and Tutorial | PDF",1791925891,7]