Introduction

The validation of xcms package at the first stage was reported. The Mass Spectrometry Facility at the Simon Fraser University (MSF-SFU) used to upload mass spectrometry data to xcms for the research work. The online service has not always been consistent, therefore, I joined in their efforts to validate the xcms offline package.

A ginger solution was split into two portions, one was served as blank, another was fortified with four pesticides, as control. Four replicates of blanks and controls were analyzed on an UPLC coupling with Bruker Daltonics Quadrupole TOF. There were eight mass spectrometry data, one was associated with one replicate.

We were able to find these four pesticide residues using xcms package at this stage.

These four compounds generated m/z [M+H]+ and [M+Na]+ adduct ions shown as follows.

Table 1: Exact Molecular Weights and Associated Adducts

Compounds

Adduct [M+H]+

Adduct [M+Na]+

Compound A

143.0354

165.0191

Compound B

153.0564

175.0395

Compound C

167.0728

189.0554

Compound D

213.085

235.0607

Figure 1: The chromatogram of each [M+H]+ adduct

Chromatograms of Total Ion Currents

All Blanks and Fortified Blanks

Chromatogram Overlay of One Blank and One Fortified Blank

The Workflow Mass-Spectrometry Based Metabolomics

The workflow is as follows:

The optimization of arguments taken in xcmsSet() made difference in outcome.

Here I omitted details through steps and presented the final difference report.

Adducts RT(min.) rank name fold tstat pvalue mzmed mzmin mzmax rtmed rtmin rtmax npeaks Blanks Fortified blank.1 blank.2 blank.3 blank.4 fortified.1 fortified.2 fortified.3 fortified.4
D+Na 4.95 2 M235T297 12.722494 -47.0539368 0.0000000 235.0606 235.0606 235.0607 297.23944 297.23903 297.23985 2 0 2 16362.9336 8979.456 9265.746 9604.9163 138769.479 144748.233 135605.893 143376.701
C+Na 4.54 15 M189T272 19.150255 -17.9843852 0.0000019 189.0550 189.0549 189.0554 272.22737 272.22465 272.23506 4 0 4 1742.4620 0.000 0.000 508.2202 11748.698 10650.130 10860.342 9841.968
A+H 0.54 72 M143T32 105.842576 -19.0442708 0.0002090 143.0358 143.0355 143.0362 32.15331 32.06478 32.27640 4 0 4 535.4052 0.000 0.000 0.0000 12925.168 16263.252 13742.748 13737.493
B+H 4.69 75 M153T281 75.770376 -19.2788121 0.0002180 153.0568 153.0565 153.0572 281.23717 281.22606 300.26668 7 0 4 1000.8656 0.000 0.000 516.1211 25272.421 31282.424 27409.481 30978.323
B+Na 4.69 88 M175T281 Inf -18.7630252 0.0003305 175.0392 175.0391 175.0394 281.23265 281.22606 281.23717 4 0 4 0.0000 0.000 0.000 0.0000 42026.004 53107.169 49164.383 53270.524
NA 485 M175T320 1.229206 -2.5615067 0.0460445 175.0779 175.0773 175.0782 320.13724 319.23609 321.26567 6 3 3 8670.1670 11635.785 8698.676 10014.8606 12484.538 13107.494 11663.739 10707.211
NA 1170 M235T32 1.244690 1.4033054 0.2366223 235.0513 235.0023 235.0524 32.15650 29.25142 39.93599 10 4 4 18092.8235 9539.668 14684.893 17665.4339 11336.121 10778.155 11967.988 14108.701
NA 2309 M235T265 1.151564 0.6721756 0.5375485 235.0946 235.0940 235.0947 265.22253 264.23452 266.22547 3 1 2 15397.0510 7788.147 8370.202 8517.4144 10330.775 8130.438 9538.667 6798.718
NA 2833 M167T429 1.283488 -0.3871870 0.7120827 167.0577 167.0362 167.0581 429.36393 425.22325 430.28211 5 3 2 2259.9489 3513.171 11798.359 25236.4093 4659.266 3878.867 18587.717 27817.562
NA 2995 M235T318 1.153729 -0.3121869 0.7742490 235.0977 235.0608 235.1336 318.00649 297.23913 364.62328 17 4 4 55875.9600 56500.846 63128.467 41392.1706 34286.824 35802.226 38723.386 141428.397
NA 3408 M213T260 1.007439 0.0483463 0.9633647 213.0782 213.0778 213.0787 260.49008 259.23163 262.71309 4 3 1 12763.5444 7784.446 13343.693 8734.6196 11934.763 10740.487 8210.931 11425.358

Summary And The Future Work

Four spiked pesticide residues were identified at the first stage. The MSF-SFU would like to optimize the performance so that the ranks of them would be within 10.

Created Date: 2022-08-09

Last Modified Date: 2022-09-12