annotation.mine |
Example of annotation file for raw.mine, which is the output of SpectroMine. |
annotation.mq |
Example of annotation file for evidence, which is the output of MaxQuant. |
annotation.pd |
Example of annotation file for raw.pd, which is the PSM output of Proteome Discoverer |
dataProcessPlotsTMT |
Visualization for explanatory data analysis - TMT experiment |
evidence |
Example of output from MaxQuant for TMT-10plex experiments. |
groupComparisonTMT |
Finding differentially abundant proteins across conditions in TMT experiment |
input.pd |
Example of output from PDtoMSstatsTMTFormat function |
MaxQtoMSstatsTMTFormat |
Generate MSstatsTMT required input format from MaxQuant output |
MSstatsTMT |
MSstatsTMT: A package for protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling |
OpenMStoMSstatsTMTFormat |
Generate MSstatsTMT required input format for OpenMS output |
PDtoMSstatsTMTFormat |
Convert Proteome Discoverer output to MSstatsTMT format. |
PhilosophertoMSstatsTMTFormat |
Convert Philosopher (Fragpipe) output to MSstatsTMT format. |
proteinGroups |
Example of proteinGroups file from MaxQuant for TMT-10plex experiments. |
proteinSummarization |
Summarizing peptide level quantification to protein level quantification |
raw.mine |
Example of output from SpectroMine for TMT-6plex experiments. |
raw.om |
Example of MSstatsTMT report from OpenMS for TMT-10plex experiments. |
raw.pd |
Example of output from Proteome Discoverer 2.2 for TMT-10plex experiments. |
SpectroMinetoMSstatsTMTFormat |
Import data from SpectroMine |