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annotSite()
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Annotate modification site |
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dataProcessPlotsPTM()
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Visualization for explanatory data analysis |
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dataSummarizationPTM()
|
Process MS PTM and global protein data |
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dataSummarizationPTM_TMT()
|
Process MS PTM and global protein data produced via tandem mass tag labeling |
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groupComparisonPlotsPTM()
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Visualization for model-based analysis and summarization |
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groupComparisonPTM()
|
Model PTM and/or protein data and make adjustments if needed |
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locateMod()
|
Locate modified sites with a peptide |
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locatePTM()
|
Annotate modified sites with associated peptides |
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MaxQtoMSstatsPTMFormat()
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Convert output of TMT labeled MaxQuant experiment into MSstatsPTM format |
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MSstatsPTM
|
MSstatsPTM: A package for detecting differencially abundant post
translational modifications (PTM) in shotgun mass spectrometry-bsed proteomic
experiments. |
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ProgenesistoMSstatsPTMFormat()
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Converts non-TMT Progenesis output into the format needed for MSstatsPTM |
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raw.input
|
Example of input PTM dataset for LabelFree/DDA/DIA experiments. |
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raw.input.tmt
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Example of input PTM dataset for TMT experiments. |
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SpectronauttoMSstatsPTMFormat()
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Converts raw PTM MS data from Spectronautt into the format needed for
MSstatsPTM. |
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summary.data
|
Example of output from dataSummarizationPTM function for non-TMT data |
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summary.data.tmt
|
Example of output from dataSummarizationPTM_TMT function for TMT data |
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tidyFasta()
|
Read and tidy a FASTA file |