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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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Input data #78

Closed Giu-F closed 4 months ago

Giu-F commented 7 months ago

Hi, I have acquired proteome and phospho-enriched runs from the same original samples. To get the right input for MS stat PTM, shall I do only one search for all the files? In other words, shall I add pSTY as variable modification for the proteome runs as well? Thanks in advance

tonywu1999 commented 4 months ago

Hi,

Apologies for the delay in response. You can do separate searches for the proteome and phospho-enriched runs.

For future questions, please post them on the MSstats google groups forum https://groups.google.com/g/msstats. We will answer more promptly to questions posted there.

Tony