| MSstatsTMT-package | MSstatsTMT: A package for protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling |
| 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 |
| designSampleSizeTMT | Planning future experimental designs of Tandem Mass Tag (TMT) experiments acquired with Data-Dependent Acquisition (DDA or shotgun) |
| 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 |