MSstatsTMT

[Thi Xuan Nguyen]

Hi MSstatsTMT team,

I am a new user of MSstatsTMT. Thank you very much for developing this package. I find it's very useful but have some doubts and I think it would be great if you can explain these questions to me. 

1. Annotation file: BioReplicate: I have 4 groups, each group has 5 animals which is equivalent to 5 replicates. Should I state in the BioReplicate as animal 1, animal 2, etc., or animal ID (such as 3, 5; each animal has a unique ID).

2. I don't know why MSstatsTMT chooses a very limited number of proteins (24 or 30) to normalize while I have around 1000 proteins in total. Does it means that MSstatsTMT can't normalize other proteins or you set up some criteria for proteins to be normalized? 

For many comparisons, I got no significant proteins so I think the limited input proteins may cause this problem. 

I am looking forward to hearing from you,

Thank you very much beforehand,

Best regards,

Xuan 

[thuan...@gmail.com]

Hi Xuan,

For the BioReplicate column in the annotation file, each animal should have a unique ID. So either animal 1 or animal ID works as long as they are different for different animals. 

For the normalization method, MSstatsTMT does not select a subset of proteins to normalize. Global median normalization (global_norm) performs normalization on peptide level data using all the proteins. Reference channel-based normalization (reference_norm) performs normalization on protein level data for each protein separately. More information can be found in manuscript: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8015007/pdf/main.pdf

Best,

Ting

[Thi Xuan Nguyen]

Hello MSstats team,

I am now looking at the groupComparisonPlots. You set up these using the adj-p value. Can I make the same plots using p-value (such as for volcano plot)? 

Moreover, for the heatmap, you set up at least two comparisons that are needed for heatmaps. But is it possible if I want the heatmap for each sample in all groups so I can see the changes of abundance (of sig proteins) in each sample for all groups? 

Hope you can help,

Thank you very much beforehand,

Best wishes,

Xuan