MastatsTMT question with annotation

[Dezi Tse]

Hi MSstats team

I have seen a mail of how to get the channel of annotation. But I cant fine channel colume in evidence.txt. I dont know whether my evidence.txt is fault. Or the colume of channel has other name?

Thank you!

[thuan...@gmail.com]

Hi Dezi,

The evidence file of MaxQuant is the table with identified peptide features. It should have the channel columns, such as 

• Reporter intensity corrected X, where X is the index of the “tag”, starting with 0
  
• Reporter intensity X
  
• Reporter intensity count X

If your evidence file doesn't have those channel columns, then there maybe something wrong when you output the results. See this introduction to MaxQuant: https://www.labkey.org/Documentation/wiki-page.view?name=maxQuant. It shows how to get and view the evidence file.

Best,

Ting

[Kavee L]

Hi,

Just passing by and saw this post. The new MaxQuant version (1.6.3.3) has changed the way isobaric tags are numbered. Now they start with 1 instead of 0. 

See http://www.coxdocs.org/doku.php?id=maxquant:user:change_log

Best,

Kavee

[thuan...@gmail.com]

Hi Kevee,

Thank you for sharing this information. We will make corresponding update in the next release of MSstatsTMT. 

Best,

Ting