{"id":7401,"date":"2024-02-14T09:37:39","date_gmt":"2024-02-14T09:37:39","guid":{"rendered":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=7401"},"modified":"2025-11-26T13:53:25","modified_gmt":"2025-11-26T13:53:25","slug":"maxquant","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/maxquant\/","title":{"rendered":"MaxQuant"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labelling techniques as well as label-free quantification are supported. The Command Line version has been enabled on the CSF<\/p>\n<h2>Restrictions on use<\/h2>\n<p>MaxQuant is freely available under the Freeware licence. For details see the license file with <code>cat $MAXQUANT_LICENSE<\/code><\/p>\n<h2>Set up procedure<\/h2>\n<p>We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run.<br \/>\nLoad one of the following modulefiles:<\/p>\n<pre>\r\nmodule load apps\/binapps\/maxquant\/2.7.5.0\r\nmodule load apps\/binapps\/maxquant\/2.4.3.0\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>MaxQuant is built for the .NET framework and is executed on the CSF3 using dotnet You can invoke the command line program in a job script. Note that there are minor differences between versions.<\/p>\n<p>Once the module is loaded, you can get command line help information with:<\/p>\n<pre>\r\nmaxquant --help\r\n<\/pre>\n<h3>Serial batch job submission 2.7.5.0<\/h3>\n<p>Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n<pre>\r\n#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n                    # NO -V line - we load modulefiles in the jobscript\r\n\r\n\r\nmodule load apps\/binapps\/maxquant\/2.7.5.0\r\n\r\nmaxquant [OPTIONS]\r\n\r\n# or\r\n\r\n# dotnet $MAXQUANTDIR\/bin\/MaxQuantCmd.dll [OPTIONS]\r\n<\/pre>\n<h3>Serial batch job submission 2.4.3.0<\/h3>\n<p>Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n<pre>\r\n#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n                    # NO -V line - we load modulefiles in the jobscript\r\n\r\n\r\nmodule load apps\/binapps\/maxquant\/2.4.3.0\r\n\r\nmaxquant [OPTIONS]\r\n\r\n# or\r\n\r\n# dotnet $MAXQUANTDIR\/bin\/MaxQuantCmd.exe  [OPTIONS]\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h2>Further information<\/h2>\n<p><a href=\"https:\/\/maxquant.org\/\">MaxQuant website<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labelling techniques as well as label-free quantification are supported. The Command Line version has been enabled on the CSF Restrictions on use MaxQuant is freely available under the Freeware licence. For details see the license file with cat $MAXQUANT_LICENSE Set up procedure We now recommend loading modulefiles within your jobscript so.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/maxquant\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":12,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-7401","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/7401","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/12"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=7401"}],"version-history":[{"count":6,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/7401\/revisions"}],"predecessor-version":[{"id":11437,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/7401\/revisions\/11437"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=7401"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}