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maxquant:start [2015/12/15 14:33]
art ↷ Links adapted because of a move operation
maxquant:start [2019/02/26 12:04] (current)
yeroslaviz [Documentation outline]
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 ====== MaxQuant ====== ====== MaxQuant ======
  
-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 labeling techniques as well as label-free quantification are supported. MaxQuant is freely available and can be downloaded from this site. The download includes the search engine [[maxquant:​andromeda:​start]],​ which is integrated into MaxQuant as well as the [[maxquant:​viewer:​start]] application for inspection of raw data and identification and quantification results. For statistical analysis of MaxQuant output, we offer the [[Perseus:​start]] framework.+MaxQuant is a proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported. MaxQuant is freely available and can be downloaded from this site. The download includes the search engine [[maxquant:​andromeda:​start]],​ which is integrated into MaxQuant as well as the [[maxquant:​viewer:​start]] application for inspection of raw data and identification and quantification results. For statistical analysis of MaxQuant output, we offer the [[Perseus:​start]] framework. 
  
-To run MaxQuant, you will need [[:​maxquant:​common:​download_and_installation#​.NET framework 4.5]] as well as the [[:​maxquant:​common:​download_and_installation#​MSFileReader]] for Thermo data and/or SQLite for Bruker data (you can find a [[http://​www.bruker.com/​fileadmin/​user_upload/​8-PDF-Docs/​Separations_MassSpectrometry/​Literature/​literature/​TechNotes/​Quick_Start_Guide_-_Processing_Bruker_proteomics_data_using_MaxQuant.pdf|manual]] here). If you use Windows you should have Vista or newer. Like most Windows software, MaxQuant can also be run on a Mac. There is currently no support for linux, but it is [[http://​www.drdobbs.com/​windows/​c-and-nets-sudden-ubiquity/​240169282|on the horizon]]. 
  
  
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 ==== Documentation outline ==== ==== Documentation outline ====
-This documentation is organized as a wiki, so if you find anything that is wrong or hard to understand, in most cases you can fix it yourself. The wiki can be browsed by using the links below or by searching with the box in the upper right. Anyone is allowed to read the wiki, but to make changes you will have to register and login using the button in the upper right. (The registration mechanism is currently not working properly and probably cannot be fixed before the beginning of November (2015). If you do not need to edit the wiki right nowplease try to register again in a few weeks.)+This documentation is organized as a wiki, so if you find anything that is wrong or hard to understand, in most cases you can fix it yourself. The wiki can be browsed by using the links below or by searching with the box in the upper right. Anyone is allowed to read the wiki, but to make changes you will have to register and login using the button in the upper right. If you are an **internal user at the MPI of Biochemistry**you can get access ​to some restricted pages; contact the Cox group after you have registered.
  
   * [[:​maxquant:​common:​Download and installation]]   * [[:​maxquant:​common:​Download and installation]]
-  * [[maxquant:​manual:​Beginner|First steps in MaxQuant]] +  * [[:maxquant:​manual:​Beginner|First steps in MaxQuant]] 
-  * [[Background]] (how it works under the hood) +  * [[:maxquant:viewer:​start]] 
-  * [[.viewer:​start]] +  * [[:maxquant:andromeda:​start]]
-  * [[.andromeda:​start]]+
   * [[:​maxquant:​common:​Google groups]]   * [[:​maxquant:​common:​Google groups]]
   * [[:​maxquant:​common:​Bug reporting]]   * [[:​maxquant:​common:​Bug reporting]]
-<ifauth @internal> ​ * [[maxquant:​common:​Glossary]] +<ifauth @internal>​ 
-  * [[FAQ]]+These pages are only visible to internal users: 
 +  * [[:maxquant:​common:internal:​Glossary]] 
 +  * [[:​maxquant:​internal:​FAQ]] 
 +  * [[:​maxquant:​internal:​background]] (how it works under the hood)
 </​ifauth>​ </​ifauth>​
  
-For additional training, consider attending the annual [[http://​mqsummerschool.biochem.mpg.de/​summerschool2016/​welcome.html|MaxQuant Summer School]]. Also watching some [[http://​www.youtube.com/​channel/​UCKYzYTm1cnmc0CFAMhxDO8w|MaxQuant videos]] provides more insight.+For additional training, consider attending the annual [[http://​mqsummerschool.biochem.mpg.de/​summerschool2017/​welcome.html|MaxQuant Summer School]]. Also watching some [[http://​www.youtube.com/​channel/​UCKYzYTm1cnmc0CFAMhxDO8w|MaxQuant videos]] provides more insight.
  
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 Cox, J. and Mann, M. [[http://​www.nature.com/​nbt/​journal/​v26/​n12/​full/​nbt.1511.html|MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.]] //Nat Biotechnol//,​ 2008, 26, pp 1367-72. Cox, J. and Mann, M. [[http://​www.nature.com/​nbt/​journal/​v26/​n12/​full/​nbt.1511.html|MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.]] //Nat Biotechnol//,​ 2008, 26, pp 1367-72.
 \\ **Note that the paper has a large supplement containing in-depth descriptions of algorithms.** \\ **Note that the paper has a large supplement containing in-depth descriptions of algorithms.**
- 
-Cox, J and Mann, M., [[http://​link.springer.com/​article/​10.1016%2Fj.jasms.2009.05.007|Computational principles of determining and improving mass precision and accuracy for proteome measurements in an Orbitrap.]] //J Am Soc Mass Spectrom.//,​ 2009, 20, pp 1477-85. 
  
 Cox, J., Michalski, A., and Mann, M., [[http://​link.springer.com/​article/​10.1007%2Fs13361-011-0142-8|Software Lock Mass by Two-Dimensional Minimization of Peptide Mass Errors.]] //J Am Soc Mass Spectrom.//,​ 2011, 22, pp 1373–1380. ​ Cox, J., Michalski, A., and Mann, M., [[http://​link.springer.com/​article/​10.1007%2Fs13361-011-0142-8|Software Lock Mass by Two-Dimensional Minimization of Peptide Mass Errors.]] //J Am Soc Mass Spectrom.//,​ 2011, 22, pp 1373–1380. ​
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 Tyanova, S., Temu, T., Carlson, A., Sinitcyn, P., Mann, M. and Cox, J., [[http://​onlinelibrary.wiley.com/​doi/​10.1002/​pmic.201400449/​abstract|Visualization of LC-MS/MS proteomics data in MaxQuant]], //​Proteomics//,​ 2015, 15, pp 1453–1456 Tyanova, S., Temu, T., Carlson, A., Sinitcyn, P., Mann, M. and Cox, J., [[http://​onlinelibrary.wiley.com/​doi/​10.1002/​pmic.201400449/​abstract|Visualization of LC-MS/MS proteomics data in MaxQuant]], //​Proteomics//,​ 2015, 15, pp 1453–1456
 +
 +Tyanova, S., Temu, T., and Cox, J., [[https://​www.nature.com/​articles/​nprot.2016.136|The MaxQuant computational platform for mass spectrometry-based shotgun proteomics]],​ //Nat Protocols//,​ 2016, 11, pp 2301–2319
 +\\ **Note that this paper explains how to run MaxQuant in detail.**
  
  
maxquant/start.1450186428.txt.gz · Last modified: 2015/12/15 14:33 by art