Example of annotation file for raw.pd, which is the PSM output of Proteome Discoverer

Annotation of example data, raw.pd, in this package. It should be prepared by users. The variables are as follows:

annotation.pd

Format

A data frame with 150 rows and 7 variables.

Details

  • Run : MS run ID. It should be the same as Spectrum.File info in raw.pd.

  • Channel : Labeling information (126, ... 131). It should be consistent with the channel columns in raw.pd.

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

  • Mixture : Mixture of samples labeled with different TMT reagents, which can be analyzed in a single mass spectrometry experiment. If the channal doesn't have sample, please add `Empty' under Condition.

  • TechRepMixture : Technical replicate of one mixture. One mixture may have multiple technical replicates. For example, if `TechRepMixture' = 1, 2 are the two technical replicates of one mixture, then they should match with same `Mixture' value.

  • Fraction : Fraction ID. One technical replicate of one mixture may be fractionated into multiple fractions to increase the analytical depth. Then one technical replicate of one mixture should correspond to multuple fractions. For example, if `Fraction' = 1, 2, 3 are three fractions of the first technical replicate of one TMT mixture of biological subjects, then they should have same `TechRepMixture' and `Mixture' value.

  • BioReplicate : Unique ID for biological subject. If the channal doesn't have sample, please add `Empty' under BioReplicate.

Examples

head(annotation.pd)

#>                                            Run Fraction TechRepMixture Channel
#> 1 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw        1              1     126
#> 2 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw        1              1    127N
#> 3 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw        1              1    127C
#> 4 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw        1              1    128N
#> 5 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw        1              1    128C
#> 6 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw        1              1    129N
#>   Condition  Mixture   BioReplicate
#> 1      Norm Mixture1  Mixture1_Norm
#> 2     0.667 Mixture1 Mixture1_0.667
#> 3     0.125 Mixture1 Mixture1_0.125
#> 4       0.5 Mixture1   Mixture1_0.5
#> 5         1 Mixture1     Mixture1_1
#> 6     0.125 Mixture1 Mixture1_0.125