Maxquant

https://www.jianshu.com/p/e6559c6dc026

MaxQuant_Infos_and_Tutorial_07.pdf

nprot-2016-maxquant.pdf

官网：http://coxdocs.org/doku.php?id=maxquant:manual:beginner

https://www.youtube.com/watch?v=DRlJJLMWNbA&list=PL6yHRLjecpwBN36HskkbjazNss8_iUbQt&index=17

43:18观看多个database的问题

label-free, fraction, experiment: PXD002395

Input

1. fasta
   1. MaxQuant序列名字>name中不能含有分号”;” 可以用”, |_-“
2. raw
   1. “Load”: 将.raw文件直接导入软件，根据样本选择”No fractions”或者”Set fractions”。
3. expreiment
   1. sample
4. fraction
   1. fractions: e.g. slices of a gel lane (fraction numbering is important for matching between runs, see above)

1. LFQ

Parameters

1. Label
2. Modification 1. “Modifications”: 选择样本相关的修饰，点击”<”添加或删除。
3. Instrument: 1. Instrument”：MaxQuant会自动选择机器类型，也可以手动修改，参数选择软件默认的即可。

Result

filses: https://blog.csdn.net/qq_42712141/article/details/112209501

differential expression analysis: https://www.bioinfo-scrounger.com/archives/541/

1. proteinGroups.txt http://www.coxdocs.org/doku.php?id=maxquant:table:proteingrouptable#:~:text=Majority%20protein%20IDs.%20These%20are%20the%20IDs%20of,protein%20IDs%20occur%20in%20the%20%27Protein%20IDs%27%20column.
   1. ProteinGroups.txt: identified protein groups, including quantification, protein properties, sequence coverage, peptide counts (all, razor, unique), who was protein identified (MS/MS or only match between runs), Q values and Andromeda scores (e.g. for filtering)
      1. • “+” in “Only identified by side” column: proteins which where only identified by PTMs, should not be counted when reporting the number of identified protein groups
      2. • “Majority protein IDs”: contains proteins which have been filtered, so that they contain at least half of the peptides belonging to the respective protein group (whereas “Protein IDs” contains all proteins that have passed the identification criteria -> for subsequent analyses (e.g. functional analysis), the “Majority protein IDs” should be used)