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Detect Pharmaceutical Quality Deviations with MS, Raman and Statistics

Fusion of Mass Spectrometry and Raman Spectroscopy Data

Ricardo Cunha

29 November, 2024

Source: vignettes/articles/demo_paracetamol_fusion.Rmd
demo_paracetamol_fusion.Rmd



This article demonstrates how StreamFind, using mass spectrometry (MS) combined with Raman spectroscopy data, can be used to assess quality variation in the pharmaceutical Fizamol, which contains paracetamol as the active ingredient (API). Each product sample was measured by both MS and Raman spectroscopy. The data are pre-processed and fused to be used in unsupervised and supervised statistical analysis for quality assessment.

Pre-processing

Data is pre-processed using StreamFind’s built-in data-specific engines for MS and Raman data. Pre-processing workflows for each data type are performed prior to data fusion to improve statistical analysis.

MS

Overview of MS analyses and respective analysis replicate groups and blanks.
analysis replicate blank description
01_20240415_Paracetamol_4152024_Paracetamol-Coffein-Aspirin_Blank_100 blank_01 blank_01 Reference background 1
01_20240415_Paracetamol_4152024_Paracetamol-Coffein-Aspirin_Blank_101 blank_01 blank_01 Reference background 1
01_20240415_Paracetamol_4152024_Paracetamol-Coffein-Aspirin_Blank_111 blank_01 blank_01 Reference background 1
01_20240415_Paracetamol_4152024_Paracetamol-Coffein-Aspirin_Blank_112 blank_01 blank_01 Reference background 1
02_20240415-33-1_025 fiz_01 blank_01 Paracetamol product
02_20240415-33-1_026 fiz_01 blank_01 Paracetamol product
02_20240415-33-1_027 fiz_01 blank_01 Paracetamol product
02_20240415-33-2_028 fiz_02 blank_01 Paracetamol product
02_20240415-33-2_029 fiz_02 blank_01 Paracetamol product
02_20240415-33-2_030 fiz_02 blank_01 Paracetamol product
02_20240415-33-3_031 fiz_03 blank_01 Paracetamol product
02_20240415-33-3_032 fiz_03 blank_01 Paracetamol product
02_20240415-33-3_033 fiz_03 blank_01 Paracetamol product
03_20240415-36-1_058 fiz_04 blank_01 Paracetamol product
03_20240415-36-1_059 fiz_04 blank_01 Paracetamol product
03_20240415-36-1_060 fiz_04 blank_01 Paracetamol product
03_20240415-36-2_061 fiz_05 blank_01 Paracetamol product
03_20240415-36-2_062 fiz_05 blank_01 Paracetamol product
03_20240415-36-2_063 fiz_05 blank_01 Paracetamol product
03_20240415-36-3_064 fiz_06 blank_01 Paracetamol product
03_20240415-36-3_065 fiz_06 blank_01 Paracetamol product
03_20240415-36-3_066 fiz_06 blank_01 Paracetamol product
04_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_Blank_009 blank_02 blank_02 Reference background 2
04_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_Blank_010 blank_02 blank_02 Reference background 2
04_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_Blank_020 blank_02 blank_02 Reference background 2
04_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_Blank_021 blank_02 blank_02 Reference background 2
04_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_Blank_031 blank_02 blank_02 Reference background 2
04_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_Blank_032 blank_02 blank_02 Reference background 2
04_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_Blank_042 blank_02 blank_02 Reference background 2
04_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_Blank_043 blank_02 blank_02 Reference background 2
05_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-2-1-1_022 fiz_07 blank_02 Paracetamol product
05_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-2-1-2_023 fiz_07 blank_02 Paracetamol product
05_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-2-1-3_024 fiz_07 blank_02 Paracetamol product
05_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-2-2-1_025 fiz_08 blank_02 Paracetamol product
05_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-2-2-2_026 fiz_08 blank_02 Paracetamol product
05_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-2-2-3_027 fiz_08 blank_02 Paracetamol product
05_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-2-3-1_028 fiz_09 blank_02 Paracetamol product
05_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-2-3-2_029 fiz_09 blank_02 Paracetamol product
05_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-2-3-3_030 fiz_09 blank_02 Paracetamol product
06_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-3-1-1_033 fiz_10 blank_02 Paracetamol product
06_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-3-1-2_034 fiz_10 blank_02 Paracetamol product
06_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-3-1-3_035 fiz_10 blank_02 Paracetamol product
06_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-3-2-1_036 fiz_11 blank_02 Paracetamol product
06_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-3-2-2_037 fiz_11 blank_02 Paracetamol product
06_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-3-2-3_038 fiz_11 blank_02 Paracetamol product
06_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-3-3-1_039 fiz_12 blank_02 Paracetamol product
06_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-3-3-2_040 fiz_12 blank_02 Paracetamol product
06_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-3-3-3_041 fiz_12 blank_02 Paracetamol product
07_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-4-1-1_044 fiz_13 blank_02 Paracetamol product
07_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-4-1-2_045 fiz_13 blank_02 Paracetamol product
07_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-4-1-3_046 fiz_13 blank_02 Paracetamol product
07_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-4-2-1_047 fiz_14 blank_02 Paracetamol product
07_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-4-2-2_048 fiz_14 blank_02 Paracetamol product
07_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-4-2-3_049 fiz_14 blank_02 Paracetamol product
07_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-4-3-1_050 fiz_15 blank_02 Paracetamol product
07_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-4-3-2_051 fiz_15 blank_02 Paracetamol product
07_20240516_Paracetamol_5162024_Paracetamol-Coffein-Aspirin_12-4-3-3_052 fiz_15 blank_02 Paracetamol product
08_acid_20240415-37-1_069 fiz_acid_1 blank_01 Paracetamol with acetic acid
08_acid_20240415-37-1_070 fiz_acid_1 blank_01 Paracetamol with acetic acid
08_acid_20240415-37-1_071 fiz_acid_1 blank_01 Paracetamol with acetic acid
08_acid_20240415-37-2_072 fiz_acid_2 blank_01 Paracetamol with acetic acid
08_acid_20240415-37-2_073 fiz_acid_2 blank_01 Paracetamol with acetic acid
08_acid_20240415-37-2_074 fiz_acid_2 blank_01 Paracetamol with acetic acid
08_acid_20240415-37-3_075 fiz_acid_3 blank_01 Paracetamol with acetic acid
08_acid_20240415-37-3_076 fiz_acid_3 blank_01 Paracetamol with acetic acid
08_acid_20240415-37-3_077 fiz_acid_3 blank_01 Paracetamol with acetic acid
09_ass_20240415-35-1_047 fiz_ass_1 blank_01 Paracetamol with aspirin
09_ass_20240415-35-1_048 fiz_ass_1 blank_01 Paracetamol with aspirin
09_ass_20240415-35-1_049 fiz_ass_1 blank_01 Paracetamol with aspirin
09_ass_20240415-35-2_050 fiz_ass_2 blank_01 Paracetamol with aspirin
09_ass_20240415-35-2_051 fiz_ass_2 blank_01 Paracetamol with aspirin
09_ass_20240415-35-2_052 fiz_ass_2 blank_01 Paracetamol with aspirin
09_ass_20240415-35-3_053 fiz_ass_3 blank_01 Paracetamol with aspirin
09_ass_20240415-35-3_054 fiz_ass_3 blank_01 Paracetamol with aspirin
09_ass_20240415-35-3_055 fiz_ass_3 blank_01 Paracetamol with aspirin
10_caff_20240415-34-1_036 fiz_caff_1 blank_01 Paracetamol with caffeine
10_caff_20240415-34-1_037 fiz_caff_1 blank_01 Paracetamol with caffeine
10_caff_20240415-34-1_038 fiz_caff_1 blank_01 Paracetamol with caffeine
10_caff_20240415-34-2_039 fiz_caff_2 blank_01 Paracetamol with caffeine
10_caff_20240415-34-2_040 fiz_caff_2 blank_01 Paracetamol with caffeine
10_caff_20240415-34-2_041 fiz_caff_2 blank_01 Paracetamol with caffeine
10_caff_20240415-34-3_042 fiz_caff_3 blank_01 Paracetamol with caffeine
10_caff_20240415-34-3_043 fiz_caff_3 blank_01 Paracetamol with caffeine
10_caff_20240415-34-3_044 fiz_caff_3 blank_01 Paracetamol with caffeine
11_old_20240415-31-1_003 fiz_old_1 blank_01 Paracetamol stored
11_old_20240415-31-1_004 fiz_old_1 blank_01 Paracetamol stored
11_old_20240415-31-1_005 fiz_old_1 blank_01 Paracetamol stored
11_old_20240415-31-2_006 fiz_old_2 blank_01 Paracetamol stored
11_old_20240415-31-2_007 fiz_old_2 blank_01 Paracetamol stored
11_old_20240415-31-2_008 fiz_old_2 blank_01 Paracetamol stored
11_old_20240415-31-3_009 fiz_old_3 blank_01 Paracetamol stored
11_old_20240415-31-3_010 fiz_old_3 blank_01 Paracetamol stored
11_old_20240415-31-3_011 fiz_old_3 blank_01 Paracetamol stored 


ms_workflow <- list(
  MassSpecSettings_LoadSpectra_StreamFind(levels = 1, mzmax = 300, rtmax = 120),
  MassSpecSettings_BinSpectra_StreamFind(binNames = c("rt", "mz"), binValues = c(5, 2), refBinAnalysis = 1),
  MassSpecSettings_NormalizeSpectra_minmax(),
  MassSpecSettings_AverageSpectra_StreamFind(),
  MassSpecSettings_SubtractBlankSpectra_StreamFind(negativeToZero = TRUE),
  MassSpecSettings_NormalizeSpectra_blockweight()
)

ms$workflow <- ms_workflow

ms$print_workflow()
1: LoadSpectra (StreamFind)
2: BinSpectra (StreamFind)
3: NormalizeSpectra (minmax)
4: AverageSpectra (StreamFind)
5: SubtractBlankSpectra (StreamFind)
6: NormalizeSpectra (blockweight)
ms$run_workflow()
ms$plot_spectra()

Pre-processed spectra for each analysis. Retention time dimension in he created bins is collapsed for each mass-to-charge ratio

Raman

Overview of MS analyses and respective analysis replicate groups and blanks.
analysis replicate blank description
01_240411_blank_200mW_OD3_2s_36n_pos1_r1 blank_01 blank_01 Reference background 1
01_240411_blank_200mW_OD3_2s_36n_pos1_r2 blank_01 blank_01 Reference background 1
01_240411_blank_200mW_OD3_2s_36n_pos1_r3 blank_01 blank_01 Reference background 1
01_240411_blank_200mW_OD3_2s_36n_pos2_r1 blank_01 blank_01 Reference background 1
01_240411_blank_200mW_OD3_2s_36n_pos2_r2 blank_01 blank_01 Reference background 1
01_240411_blank_200mW_OD3_2s_36n_pos2_r3 blank_01 blank_01 Reference background 1
01_240411_blank_200mW_OD3_2s_36n_pos3_r1 blank_01 blank_01 Reference background 1
01_240411_blank_200mW_OD3_2s_36n_pos3_r2 blank_01 blank_01 Reference background 1
01_240411_blank_200mW_OD3_2s_36n_pos3_r3 blank_01 blank_01 Reference background 1
02_240411_Fizamol-11_200mW_OD3_2s_36n_pos1_r1 fiz_01 blank_01 Paracetamol product
02_240411_Fizamol-11_200mW_OD3_2s_36n_pos1_r2 fiz_01 blank_01 Paracetamol product
02_240411_Fizamol-11_200mW_OD3_2s_36n_pos1_r3 fiz_01 blank_01 Paracetamol product
02_240411_Fizamol-11_200mW_OD3_2s_36n_pos2_r1 fiz_02 blank_01 Paracetamol product
02_240411_Fizamol-11_200mW_OD3_2s_36n_pos2_r2 fiz_02 blank_01 Paracetamol product
02_240411_Fizamol-11_200mW_OD3_2s_36n_pos2_r3 fiz_02 blank_01 Paracetamol product
02_240411_Fizamol-11_200mW_OD3_2s_36n_pos3_r1 fiz_03 blank_01 Paracetamol product
02_240411_Fizamol-11_200mW_OD3_2s_36n_pos3_r2 fiz_03 blank_01 Paracetamol product
02_240411_Fizamol-11_200mW_OD3_2s_36n_pos3_r3 fiz_03 blank_01 Paracetamol product
03_240411_Fizamol-12_200mW_OD3_2s_36n_pos1_r1 fiz_04 blank_01 Paracetamol product
03_240411_Fizamol-12_200mW_OD3_2s_36n_pos1_r2 fiz_04 blank_01 Paracetamol product
03_240411_Fizamol-12_200mW_OD3_2s_36n_pos1_r3 fiz_04 blank_01 Paracetamol product
03_240411_Fizamol-12_200mW_OD3_2s_36n_pos2_r1 fiz_05 blank_01 Paracetamol product
03_240411_Fizamol-12_200mW_OD3_2s_36n_pos2_r2 fiz_05 blank_01 Paracetamol product
03_240411_Fizamol-12_200mW_OD3_2s_36n_pos2_r3 fiz_05 blank_01 Paracetamol product
03_240411_Fizamol-12_200mW_OD3_2s_36n_pos3_r1 fiz_06 blank_01 Paracetamol product
03_240411_Fizamol-12_200mW_OD3_2s_36n_pos3_r2 fiz_06 blank_01 Paracetamol product
03_240411_Fizamol-12_200mW_OD3_2s_36n_pos3_r3 fiz_06 blank_01 Paracetamol product
04_240412_BlankH2O_200mW_OD3_2s_36n_pos1_r1 blank_02 blank_02 Reference background 2
04_240412_BlankH2O_200mW_OD3_2s_36n_pos1_r2 blank_02 blank_02 Reference background 2
04_240412_BlankH2O_200mW_OD3_2s_36n_pos1_r3 blank_02 blank_02 Reference background 2
04_240412_BlankH2O_200mW_OD3_2s_36n_pos2_r1 blank_02 blank_02 Reference background 2
04_240412_BlankH2O_200mW_OD3_2s_36n_pos2_r2 blank_02 blank_02 Reference background 2
04_240412_BlankH2O_200mW_OD3_2s_36n_pos2_r3 blank_02 blank_02 Reference background 2
04_240412_BlankH2O_200mW_OD3_2s_36n_pos3_r1 blank_02 blank_02 Reference background 2
04_240412_BlankH2O_200mW_OD3_2s_36n_pos3_r2 blank_02 blank_02 Reference background 2
04_240412_BlankH2O_200mW_OD3_2s_36n_pos3_r3 blank_02 blank_02 Reference background 2
05_240412_Fizamol12-2_200mW_OD3_2s_36n_pos1_r1 fiz_07 blank_02 Paracetamol product
05_240412_Fizamol12-2_200mW_OD3_2s_36n_pos1_r2 fiz_07 blank_02 Paracetamol product
05_240412_Fizamol12-2_200mW_OD3_2s_36n_pos1_r3 fiz_07 blank_02 Paracetamol product
05_240412_Fizamol12-2_200mW_OD3_2s_36n_pos2_r1 fiz_08 blank_02 Paracetamol product
05_240412_Fizamol12-2_200mW_OD3_2s_36n_pos2_r2 fiz_08 blank_02 Paracetamol product
05_240412_Fizamol12-2_200mW_OD3_2s_36n_pos2_r3 fiz_08 blank_02 Paracetamol product
05_240412_Fizamol12-2_200mW_OD3_2s_36n_pos3_r1 fiz_09 blank_02 Paracetamol product
05_240412_Fizamol12-2_200mW_OD3_2s_36n_pos3_r2 fiz_09 blank_02 Paracetamol product
05_240412_Fizamol12-2_200mW_OD3_2s_36n_pos3_r3 fiz_09 blank_02 Paracetamol product
06_240412_Fizamol12-3_200mW_OD3_2s_36n_pos1_r1 fiz_10 blank_02 Paracetamol product
06_240412_Fizamol12-3_200mW_OD3_2s_36n_pos1_r2 fiz_10 blank_02 Paracetamol product
06_240412_Fizamol12-3_200mW_OD3_2s_36n_pos1_r3 fiz_10 blank_02 Paracetamol product
06_240412_Fizamol12-3_200mW_OD3_2s_36n_pos2_r1 fiz_11 blank_02 Paracetamol product
06_240412_Fizamol12-3_200mW_OD3_2s_36n_pos2_r2 fiz_11 blank_02 Paracetamol product
06_240412_Fizamol12-3_200mW_OD3_2s_36n_pos2_r3 fiz_11 blank_02 Paracetamol product
06_240412_Fizamol12-3_200mW_OD3_2s_36n_pos3_r1 fiz_12 blank_02 Paracetamol product
06_240412_Fizamol12-3_200mW_OD3_2s_36n_pos3_r2 fiz_12 blank_02 Paracetamol product
06_240412_Fizamol12-3_200mW_OD3_2s_36n_pos3_r3 fiz_12 blank_02 Paracetamol product
07_240412_Fizamol12-4_200mW_OD3_2s_36n_pos1_r1 fiz_13 blank_02 Paracetamol product
07_240412_Fizamol12-4_200mW_OD3_2s_36n_pos1_r2 fiz_13 blank_02 Paracetamol product
07_240412_Fizamol12-4_200mW_OD3_2s_36n_pos1_r3 fiz_13 blank_02 Paracetamol product
07_240412_Fizamol12-4_200mW_OD3_2s_36n_pos2_r1 fiz_14 blank_02 Paracetamol product
07_240412_Fizamol12-4_200mW_OD3_2s_36n_pos2_r2 fiz_14 blank_02 Paracetamol product
07_240412_Fizamol12-4_200mW_OD3_2s_36n_pos2_r3 fiz_14 blank_02 Paracetamol product
07_240412_Fizamol12-4_200mW_OD3_2s_36n_pos3_r1 fiz_15 blank_02 Paracetamol product
07_240412_Fizamol12-4_200mW_OD3_2s_36n_pos3_r2 fiz_15 blank_02 Paracetamol product
07_240412_Fizamol12-4_200mW_OD3_2s_36n_pos3_r3 fiz_15 blank_02 Paracetamol product
08_240412_Fizamol-11+2prozentEssig_200mW_OD3_2s_36n_pos1_r1 fiz_acid_1 blank_01 Paracetamol with acetic acid
08_240412_Fizamol-11+2prozentEssig_200mW_OD3_2s_36n_pos1_r2 fiz_acid_1 blank_01 Paracetamol with acetic acid
08_240412_Fizamol-11+2prozentEssig_200mW_OD3_2s_36n_pos1_r3 fiz_acid_1 blank_01 Paracetamol with acetic acid
08_240412_Fizamol-11+2prozentEssig_200mW_OD3_2s_36n_pos2_r1 fiz_acid_2 blank_01 Paracetamol with acetic acid
08_240412_Fizamol-11+2prozentEssig_200mW_OD3_2s_36n_pos2_r2 fiz_acid_2 blank_01 Paracetamol with acetic acid
08_240412_Fizamol-11+2prozentEssig_200mW_OD3_2s_36n_pos2_r3 fiz_acid_2 blank_01 Paracetamol with acetic acid
08_240412_Fizamol-11+2prozentEssig_200mW_OD3_2s_36n_pos3_r1 fiz_acid_3 blank_01 Paracetamol with acetic acid
08_240412_Fizamol-11+2prozentEssig_200mW_OD3_2s_36n_pos3_r2 fiz_acid_3 blank_01 Paracetamol with acetic acid
08_240412_Fizamol-11+2prozentEssig_200mW_OD3_2s_36n_pos3_r3 fiz_acid_3 blank_01 Paracetamol with acetic acid
09_240411_Fizamol-11+1mgmLASS2_200mW_OD3_2s_36n_pos1_r1 fiz_ass_1 blank_01 Paracetamol with aspirin
09_240411_Fizamol-11+1mgmLASS2_200mW_OD3_2s_36n_pos1_r2 fiz_ass_1 blank_01 Paracetamol with aspirin
09_240411_Fizamol-11+1mgmLASS2_200mW_OD3_2s_36n_pos1_r3 fiz_ass_1 blank_01 Paracetamol with aspirin
09_240411_Fizamol-11+1mgmLASS2_200mW_OD3_2s_36n_pos2_r1 fiz_ass_2 blank_01 Paracetamol with aspirin
09_240411_Fizamol-11+1mgmLASS2_200mW_OD3_2s_36n_pos2_r2 fiz_ass_2 blank_01 Paracetamol with aspirin
09_240411_Fizamol-11+1mgmLASS2_200mW_OD3_2s_36n_pos2_r3 fiz_ass_2 blank_01 Paracetamol with aspirin
09_240411_Fizamol-11+1mgmLASS2_200mW_OD3_2s_36n_pos3_r1 fiz_ass_3 blank_01 Paracetamol with aspirin
09_240411_Fizamol-11+1mgmLASS2_200mW_OD3_2s_36n_pos3_r2 fiz_ass_3 blank_01 Paracetamol with aspirin
09_240411_Fizamol-11+1mgmLASS2_200mW_OD3_2s_36n_pos3_r3 fiz_ass_3 blank_01 Paracetamol with aspirin
10_240411_Fizamol-11+1mgmLcoffein_200mW_OD3_2s_36n_pos1_r1 fiz_caff_1 blank_01 Paracetamol with caffeine
10_240411_Fizamol-11+1mgmLcoffein_200mW_OD3_2s_36n_pos1_r2 fiz_caff_1 blank_01 Paracetamol with caffeine
10_240411_Fizamol-11+1mgmLcoffein_200mW_OD3_2s_36n_pos1_r3 fiz_caff_1 blank_01 Paracetamol with caffeine
10_240411_Fizamol-11+1mgmLcoffein_200mW_OD3_2s_36n_pos2_r1 fiz_caff_2 blank_01 Paracetamol with caffeine
10_240411_Fizamol-11+1mgmLcoffein_200mW_OD3_2s_36n_pos2_r2 fiz_caff_2 blank_01 Paracetamol with caffeine
10_240411_Fizamol-11+1mgmLcoffein_200mW_OD3_2s_36n_pos2_r3 fiz_caff_2 blank_01 Paracetamol with caffeine
10_240411_Fizamol-11+1mgmLcoffein_200mW_OD3_2s_36n_pos3_r1 fiz_caff_3 blank_01 Paracetamol with caffeine
10_240411_Fizamol-11+1mgmLcoffein_200mW_OD3_2s_36n_pos3_r2 fiz_caff_3 blank_01 Paracetamol with caffeine
10_240411_Fizamol-11+1mgmLcoffein_200mW_OD3_2s_36n_pos3_r3 fiz_caff_3 blank_01 Paracetamol with caffeine
11_240411_Fizamol-11gealtert_200mW_OD3_2s_36n_pos1_r1 fiz_old_1 blank_01 Paracetamol stored
11_240411_Fizamol-11gealtert_200mW_OD3_2s_36n_pos1_r2 fiz_old_1 blank_01 Paracetamol stored
11_240411_Fizamol-11gealtert_200mW_OD3_2s_36n_pos1_r3 fiz_old_1 blank_01 Paracetamol stored
11_240411_Fizamol-11gealtert_200mW_OD3_2s_36n_pos2_r1 fiz_old_2 blank_01 Paracetamol stored
11_240411_Fizamol-11gealtert_200mW_OD3_2s_36n_pos2_r2 fiz_old_2 blank_01 Paracetamol stored
11_240411_Fizamol-11gealtert_200mW_OD3_2s_36n_pos2_r3 fiz_old_2 blank_01 Paracetamol stored
11_240411_Fizamol-11gealtert_200mW_OD3_2s_36n_pos3_r1 fiz_old_3 blank_01 Paracetamol stored
11_240411_Fizamol-11gealtert_200mW_OD3_2s_36n_pos3_r2 fiz_old_3 blank_01 Paracetamol stored
11_240411_Fizamol-11gealtert_200mW_OD3_2s_36n_pos3_r3 fiz_old_3 blank_01 Paracetamol stored 
raman_workflow <- list(
  RamanSettings_AverageSpectra_StreamFind(),
  RamanSettings_SubtractBlankSpectra_StreamFind(),
  RamanSettings_SmoothSpectra_savgol(fl = 21, forder = 4, dorder = 0),
  RamanSettings_DeleteSpectraSection_StreamFind(shiftmin = -100, shiftmax = 350),
  RamanSettings_DeleteSpectraSection_StreamFind(shiftmin = 1800, shiftmax = 2500),
  RamanSettings_CorrectSpectraBaseline_airpls(lambda = 45, differences = 1, itermax = 30),
  RamanSettings_NormalizeSpectra_minmax(),
  RamanSettings_NormalizeSpectra_blockweight()
)

raman$workflow <- raman_workflow

raman$print_workflow()
1: AverageSpectra (StreamFind)
2: SubtractBlankSpectra (StreamFind)
3: SmoothSpectra (savgol)
4: DeleteSpectraSection (StreamFind)
5: DeleteSpectraSection (StreamFind)
6: CorrectSpectraBaseline (airpls)
7: NormalizeSpectra (minmax)
8: NormalizeSpectra (blockweight)
raman$run_workflow()
raman$plot_spectra()

Pre-processed Raman spectra for analysis replicate.

Fusion

Statistical analysis is performed on the merged data for combination of orthogonal information in MS and Raman data.

ms_spec_mat <- ms$get_spectra_matrix()
raman_spec_mat <- raman$get_spectra_matrix()
fused_mat <- cbind(ms_spec_mat, raman_spec_mat)
# The fused matrix is mean centered using the mdatools R package
fused_mat <- mdatools::prep.autoscale(fused_mat, center = TRUE, scale = FALSE)
str(fused_mat)
 num [1:27, 1:3599] 9.07e-04 6.18e-04 9.10e-05 9.96e-05 -6.17e-04 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:27] "fiz_01" "fiz_02" "fiz_03" "fiz_04" ...
  ..$ : chr [1:3599] "0-101" "0-103" "0-105" "0-107" ...
 - attr(*, "prep:center")= Named num [1:3599] 0.000617 0.000175 0.00112 0 0.00044 ...
  ..- attr(*, "names")= chr [1:3599] "0-101" "0-103" "0-105" "0-107" ...
 - attr(*, "prep:scale")= logi FALSE

Statistic analysis

Unsupervised

Principle Components Analysis (PCA) can be used for unsupervised evaluation, that is, we assume that the main (or training) set of analyses is of good quality and we test new analyses to evaluate their closeness to the main set. You could say it is a supervised approach, but in the sense that we assume the quality of the main set. However, we do not classify the possible deviation of the new analyses, which would be a clearly supervised approach, as we show in the next subchapter.

main_set_idx <- c(1:10)

main_set <- fused_mat[main_set_idx, ]
rownames(main_set)
 [1] "fiz_01" "fiz_02" "fiz_03" "fiz_04" "fiz_05" "fiz_06" "fiz_07" "fiz_08"
 [9] "fiz_09" "fiz_10"
test_set <- fused_mat[-main_set_idx, ]
rownames(test_set)
 [1] "fiz_11"     "fiz_12"     "fiz_13"     "fiz_14"     "fiz_15"    
 [6] "fiz_acid_1" "fiz_acid_2" "fiz_acid_3" "fiz_ass_1"  "fiz_ass_2" 
[11] "fiz_ass_3"  "fiz_caff_1" "fiz_caff_2" "fiz_caff_3" "fiz_old_1" 
[16] "fiz_old_2"  "fiz_old_3" 
stat <- StatisticEngine$new(analyses = main_set)
# The alpha and gamma parameters are used to evaluate the model limits
stat$run(StatisticSettings_MakeModel_pca_mdatools(ncomp = 3, alpha = 0.01, gamma = 0.001))
plot(stat$model, showText = TRUE)

PCA model (native plot from mdatools R package). 

stat$predict(test_set)
plot(stat$model, showText = TRUE)

PCA model prediction distances. For more information about the distances plese consult the mdatools guide in https://mdatools.com/docs/pca--distances-and-limits.html.

Supervised (classification)

K-Nearest Neighbors (KNN) can be used to classify analyses based on pre-classified training analyses.

train_idx <- unique(c(grep("1", rownames(fused_mat)), grep("2", rownames(fused_mat))))

train_set <- fused_mat[train_idx, ]
train_set <- train_set[order(rownames(train_set)), ]
rownames(train_set)
 [1] "fiz_01"     "fiz_02"     "fiz_10"     "fiz_11"     "fiz_12"    
 [6] "fiz_13"     "fiz_14"     "fiz_15"     "fiz_acid_1" "fiz_acid_2"
[11] "fiz_ass_1"  "fiz_ass_2"  "fiz_caff_1" "fiz_caff_2" "fiz_old_1" 
[16] "fiz_old_2" 
test_set <- fused_mat[-train_idx, ]
rownames(test_set)
 [1] "fiz_03"     "fiz_04"     "fiz_05"     "fiz_06"     "fiz_07"    
 [6] "fiz_08"     "fiz_09"     "fiz_acid_3" "fiz_ass_3"  "fiz_caff_3"
[11] "fiz_old_3" 
labels <- c(
  rep("fiz", 8),
  rep("fiz_acid", 2),
  rep("fiz_ass", 2),
  rep("fiz_caff", 2),
  rep("fiz_old", 2)
)
stat2 <- StatisticEngine$new(analyses = train_set)
stat2$add_classes(labels)
stat2$run(StatisticSettings_MakeModel_knn(k = 3))
stat2$predict(test_set)
stat2$model$prediction$results
        result   analysis    class probability
        <char>     <char>   <fctr>       <num>
 1: prediction     fiz_03      fiz         0.7
 2: prediction     fiz_04  fiz_ass         0.7
 3: prediction     fiz_05  fiz_ass         0.7
 4: prediction     fiz_06  fiz_ass         0.7
 5: prediction     fiz_07      fiz         1.0
 6: prediction     fiz_08      fiz         1.0
 7: prediction     fiz_09      fiz         1.0
 8: prediction fiz_acid_3 fiz_acid         0.7
 9: prediction  fiz_ass_3  fiz_ass         0.7
10: prediction fiz_caff_3 fiz_caff         0.7
11: prediction  fiz_old_3  fiz_old         0.7