Example of output from proteinSummarizaiton function

It is made from input.pd. It is the output of proteinSummarization function. It should include the required columns as below. The variables are as follows:

quant.pd.msstats

Format

A data frame with 100 rows and 8 variables.

Details

  • Run : MS run ID

  • Protein : Protein ID

  • Abundance: Protein-level summarized abundance

  • Channel : Labeling information (126, ... 131)

  • Condition : Condition (ex. Healthy, Cancer, Time0)

  • BioReplicate : Unique ID for biological subject.

  • TechRepMixture : Unique ID for technical replicate of one TMT mixture.

  • Mixture : Unique ID for TMT mixture.

Examples

head(quant.pd.msstats)

#>                                            Run Protein Abundance Channel
#> 1 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw  P04406  16.59812    127C
#> 2 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw  P04406  16.55729    129N
#> 3 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw  P04406  16.71783    128N
#> 4 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw  P04406  16.67190    129C
#> 5 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw  P04406  16.51106    127N
#> 6 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw  P04406  16.49448    130C
#>     BioReplicate Condition TechRepMixture  Mixture
#> 1 Mixture1_0.125     0.125              1 Mixture1
#> 2 Mixture1_0.125     0.125              1 Mixture1
#> 3   Mixture1_0.5       0.5              1 Mixture1
#> 4   Mixture1_0.5       0.5              1 Mixture1
#> 5 Mixture1_0.667     0.667              1 Mixture1
#> 6 Mixture1_0.667     0.667              1 Mixture1