Data aggregation

The aggregation of the data is complex. This article describes the process step by step for a better understanding of the data transformation.

Aggregation of the data - visualization

Let’s see how the data is transformed. We will use the example file “KD_180110_CD160_HVEM.csv” from the HaDeX package and focus on just one peptide - “LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL” in the state “CD160”. The measurement was made for timepoint 1 min.

Below is shown the original and unaggregated data for chosen peptide.

##      Protein Start End                             Sequence Modification
##  1: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
##  2: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
##  3: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
##  4: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
##  5: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
##  6: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
##  7: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
##  8: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
##  9: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
## 10: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
## 11: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
## 12: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
## 13: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
## 14: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
## 15: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
## 16: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
## 17: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
## 18: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
## 19: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
## 20: db_CD160    34  69 LCKDRSGDCSPETSLKQLRLKRDPGIDGVGEISSQL           NA
##     Fragment MaxUptake      MHP State Exposure                    File z
##  1:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_01 3
##  2:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_01 4
##  3:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_01 5
##  4:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_01 6
##  5:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_01 7
##  6:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_02 3
##  7:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_02 4
##  8:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_02 5
##  9:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_02 6
## 10:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_02 7
## 11:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_03 3
## 12:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_03 4
## 13:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_03 5
## 14:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_03 6
## 15:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_03 7
## 16:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_04 3
## 17:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_04 4
## 18:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_04 5
## 19:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_04 6
## 20:       NA        33 3900.991 CD160        1 KD_160530_CD160_1min_04 7
##           RT   Inten    Center
##  1: 4.524763  325032 1307.8329
##  2: 4.524404  753259  981.0960
##  3: 4.523707 1340447  785.0905
##  4: 4.524032 2076956  654.3858
##  5: 4.525778  759271  561.0548
##  6: 4.522330  239810 1307.7777
##  7: 4.521255  583325  981.0817
##  8: 4.521919 1011160  785.0811
##  9: 4.521726 1584254  654.4194
## 10: 4.522196  600218  561.0268
## 11: 4.523605  176788 1307.8942
## 12: 4.524804  402630  981.1597
## 13: 4.521938  746309  785.0906
## 14: 4.522238 1117344  654.4344
## 15: 4.524647  397718  561.0833
## 16: 4.531138  189258 1307.8739
## 17: 4.530608  441817  981.1656
## 18: 4.528928  796722  785.1220
## 19: 4.530066 1186263  654.4411
## 20: 4.531333  451071  561.0588

As we can see from the File column, there are four replicates of the experiment. Each measurement of a replicate provide values for different possible charge values for each peptide. The result of a measurement is in column Center - this is a geometrical centroid of an isotopic envelope - the product of the measurement from a mass spectrometer.

Let’s take a look for values for each replicate.

The centroid values for different charge values are not useful. We have to transform it to the mass values, according to an equation:

\[ aggMass = z*(Center - protonMass)\] The results are shown below.

This results are just for one repetition. We have four of them:

Values from each replicate are aggregated into one value, using weighted mean (with intencity value as weight):

The results from replicates are aggregated into the final result (mean), and the uncertainty (standard deviation of the mean) is calculated.

Now we have the mass value for chosen peptide in the chosen state, measured in the chosen time point. This calculation is done for every other peptide, and these values of mass and uncertainty are used in the calculation of deuterium uptake, as described in the Data processing article.