14  Read MS datasets into R

Pre-processed MS datasets refers to data exported from MS rawdata processing software, such as Agilent MassHunter, Sciex Multiquant, and open-source tools as MRMkit and Skyline. These datasets usually contain peak/signal intensities and associated data such as retention time, FWHM, as well as information about the sample.

The R package SLINGtools provided helper functions to import data files obtained from different tools.

14.1 Import peak areas from Agilent MassHunter CSV file

library(SLINGtools)
data_file_path <- here::here("data/Testdata_Lipidomics_MHQuant_Detailed_V2.csv")
d_wide <- SLINGtools::read_MassHunterCSV_wide(data_file_path, field = "Area")

Reading 'Testdata_Lipidomics_MHQuant_Detailed_V2.csv' ... 

indexing Testdata_Lipidomics_MHQuant_Detailed_V2.csv [======] 2.15GB/s, eta:  0s
                                                                                
Imported  215 samples with 428 transitions 

print(d_wide)

# A tibble: 215 × 432
   DataFileName  AcqTimeStamp        SampleType VialPosition `CE 14:0` `CE 15:0`
   <chr>         <dttm>              <chr>      <chr>            <dbl>     <dbl>
 1 001_EQC_TQC … 2018-04-12 18:28:00 EQC        Vial 2            1532       515
 2 002_EQC_TQC … 2018-04-12 18:39:00 EQC        Vial 2            1029       911
 3 003_EQC_TQC … 2018-04-12 18:51:00 EQC        Vial 2             685       649
 4 004_EQC_TQC … 2018-04-12 19:02:00 EQC        Vial 2            1283       576
 5 005_EQC_TQC … 2018-04-12 19:13:00 EQC        Vial 2             946       732
 6 006_EBLK_Ext… 2018-04-12 19:25:00 PBLK       P1-A1              132        75
 7 007_SOLV_Bla… 2018-04-12 19:36:00 SBLK       Vial 1             241        56
 8 008_LTR_LTR0… 2018-04-12 19:48:00 LTR        P1-A2             1118       905
 9 009_NIST_NIS… 2018-04-12 19:59:00 NIST       P1-A3             1499       482
10 010_TQCd-0_T… 2018-04-12 20:11:00 RQC        Vial 4              77        96
# … with 205 more rows, and 426 more variables: `CE 16:0` <dbl>,
#   `CE 16:1` <dbl>, `CE 16:2` <dbl>, `CE 17:0` <dbl>, `CE 17:1` <dbl>,
#   `CE 18:0` <dbl>, `CE 18:1` <dbl>, `CE 18:1 d7 (ISTD)` <dbl>,
#   `CE 18:2` <dbl>, `CE 18:3` <dbl>, `CE 20:1` <dbl>, `CE 20:2` <dbl>,
#   `CE 20:3` <dbl>, `CE 20:4` <dbl>, `CE 20:5` <dbl>, `CE 22:0` <dbl>,
#   `CE 22:1` <dbl>, `CE 22:4` <dbl>, `CE 22:5` <dbl>, `CE 22:6` <dbl>,
#   `CE 24:4` <dbl>, `Cer d18:0/16:0` <dbl>, `Cer d18:0/18:0` <dbl>, …

14.2 Import all data from an Agilent MassHunter CSV file

Detail MassHunter Quant.

data_file_path <- here::here("data/Testdata_Lipidomics_MHQuant_Detailed_V2.csv")
d_all_long <- SLINGtools::read_MassHunterCSV(data_file_path)

Reading 'Testdata_Lipidomics_MHQuant_Detailed_V2.csv' ... 

indexing Testdata_Lipidomics_MHQuant_Detailed_V2.csv [======] 2.15GB/s, eta:  0s
                                                                                
Imported  215 samples with 428 transitions 

print(d_all_long)

# A tibble: 92,020 × 14
   DataFileName     DataName SampleType AcqTimeStamp        VialPosition Feature
   <chr>            <chr>    <chr>      <dttm>              <chr>        <chr>  
 1 001_EQC_TQC pre… 001_EQC… EQC        2018-04-12 18:28:00 Vial 2       CE 14:0
 2 001_EQC_TQC pre… 001_EQC… EQC        2018-04-12 18:28:00 Vial 2       CE 15:0
 3 001_EQC_TQC pre… 001_EQC… EQC        2018-04-12 18:28:00 Vial 2       CE 16:0
 4 001_EQC_TQC pre… 001_EQC… EQC        2018-04-12 18:28:00 Vial 2       CE 16:1
 5 001_EQC_TQC pre… 001_EQC… EQC        2018-04-12 18:28:00 Vial 2       CE 16:2
 6 001_EQC_TQC pre… 001_EQC… EQC        2018-04-12 18:28:00 Vial 2       CE 17:0
 7 001_EQC_TQC pre… 001_EQC… EQC        2018-04-12 18:28:00 Vial 2       CE 17:1
 8 001_EQC_TQC pre… 001_EQC… EQC        2018-04-12 18:28:00 Vial 2       CE 18:0
 9 001_EQC_TQC pre… 001_EQC… EQC        2018-04-12 18:28:00 Vial 2       CE 18:1
10 001_EQC_TQC pre… 001_EQC… EQC        2018-04-12 18:28:00 Vial 2       CE 18:…
# … with 92,010 more rows, and 8 more variables: IonPolarity <fct>,
#   PrecursorMZ <dbl>, ProductMZ <dbl>, CollisionEnergy <dbl>, RT <dbl>,
#   Area <dbl>, FWHM <dbl>, MI <lgl>