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