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Vitek-Lab / MSstatsPTM

Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments
https://vitek-lab.github.io/MSstatsPTM/
Artistic License 2.0
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how to get maxq_tmt_annotation #89

Closed gaoxiangcao closed 4 months ago

gaoxiangcao commented 4 months ago

hi， i want to know how to get the maxq_tmt_annotation file？

tonywu1999 commented 4 months ago

Hi,

Did you load the MSstatsPTM package into your workspace? After loading the MSstatsPTM, you should be able to run the following command to view the first few rows:

library(MSstatsPTM)
head(maxq_tmt_annotation)
gaoxiangcao commented 4 months ago

Yes, I have downloaded it. But what I want to know is whether the maxq_tmt_annotation file was generated using the evidence file, or is there a specific function to process it? Is this a required step for format conversion?

tonywu1999 commented 4 months ago

Hi @gaoxiangcao

Below are my responses to your questions. Let me know if you have any additional questions.

But what I want to know is whether the maxq_tmt_annotation file was generated using the evidence file, or is there a specific function to process it?

The user of our package is responsible for creating the annotation file by hand. There's no specific function to auto-generate annotation files at the moment.

Is this a required step for format conversion?

This is a required step because in order to perform differential abundance analysis, each run needs to be annotated with BioReplicate & Condition information (additionally Mixture information in the case of TMT). Annotation information allows for the application of statistical tests to determine the significance of observed differences in abundance between conditions.