Comments (2)
huang704
commented on June 20, 2024
Hi Weixian,
MSstatsTMT hasn't had a converter for the output from Fragpipe yet. But we used MSstatsTMT to analyze the output from philosopher before. The reanalysis is available in massive.quant: https://massive.ucsd.edu/ProteoSAFe/reanalysis.jsp?task=2d0e2fea50bf4b46b77e9b5772e9d20e. The R script is in the ‘methods’ folder (FTP download -> methods).
Best,
Ting
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weixiandeng
commented on June 20, 2024
Hi Weixian,
MSstatsTMT hasn't had a converter for the output from Fragpipe yet. But we used MSstatsTMT to analyze the output from philosopher before. The reanalysis is available in massive.quant: https://massive.ucsd.edu/ProteoSAFe/reanalysis.jsp?task=2d0e2fea50bf4b46b77e9b5772e9d20e. The R script is in the ‘methods’ folder (FTP download -> methods).
Best,
Ting
Thank you for the quick response, it is very helpful.
Weixian
from msstatstmt.
Related Issues (20)
- onattach and onload HOT 1
- Run column changing to duplicate of Mixture after using PDtoMSstatsTMTFormat() HOT 3
- check if .getRunsMedian is OK
- annotation file issues for output of Proteom Discoverer
- difficulties in creating annotation.pd
- MaxQtoMSstatsTMTFormat failing to use which.proteinid = "Gene.names" HOT 5
- Error in proteinSummarization - possible annotation issue? HOT 14
- old version of MSstatsTMT HOT 1
- Fragpipe HOT 5
- MSstatsTMT within the shiny tool with MQ data crashes HOT 1
- What is the 'raw.mq' file supposed to be? HOT 1
- Problem with annotation file for proteome discoverer HOT 8
- Fractionated Data Not Handled With Data Frame Input to proteinSummarization()
- Norm channel doesn't handle capitalization correctly.
- .fitModelTMT calls wrong model if multiple subject and mixtures but one technical replicate
- input.mq does not extract Condition information from annotation file HOT 4
- Fraction variable in PD annotation HOT 2
- annotation.pd file not accepted HOT 9
- MaxQtoMSstatsTMTFormat fails HOT 1
- Exporting the protein-level data
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