Raw MS data processing using massprocesser

Xiaotao Shen (https://www.shenxt.info/)

Created on 2020-04-01 and updated on 2022-09-19

Source: vignettes/raw_data_processing.Rmd

Download demo data

Raw data can be downloaded from the Google drive. Link is here

Data preparation

massprocesser can used to processed the raw MS data for peak detection and alignment, and generate a peak table for next analysis.

The MS raw data from Mass Spectrometry should be converted to mzXML or mzMLformat and then placed in different folders according to their class, for example Subject, QC, and Blank samples.

You can convert raw MS data to mzXML or mzML format using ProteoWizard software. And the parameter setting is shown the below figure:

Data organization

All the mzXML format files should be placed in different folder according to sample type, such as QC, Subject, Control, Case, and Blank.

Run process_data() function

This function is used to peak picking and peak alignment.

Data processing

Next, we use the process_data() function for peak detection and alignment.

We first do the positive mode.

massprocesser::process_data(
  path = "massprocesser_demo_data/POS/",
  polarity = "positive",
  ppm = 15,
  peakwidth = c(10, 60),
  snthresh = 5,
  noise = 500,
  threads = 6,
  output_tic = TRUE,
  output_bpc = TRUE,
  output_rt_correction_plot = TRUE,
  min_fraction = 0.5,
  fill_peaks = FALSE,
  group_for_figure = "QC"
)
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Some important arguments:

  • ppm: Peak detection ppm. See the xcms package.

  • peakwidth: Peak width. It is dependent on your column and LC system. See the xcms package.

  • snthresh: Signal to noise threshold. See the xcms package.

  • noise: Noise cutoff. See the xcms package.

  • threads: The core number for performing.

  • output_tic, output_bpc, and group_for_figure: Do you want to output the TIC or BPC of samples? Some times there are a lot of samples, so you can set the group_for_figure as the group name, for example, you can set it as QC.

  • min_fraction: If one peak appears more than min.fraction sample in at least one group samples it will be kept.

  • fill_peaks: Do you want to fill the missing values (NA)?

Other parameters you can find here: process_data().

Output results

After all done, all the results are placed in a new folder named as Result.

object

object is a mass_dataset class object which can be used for next analysis. See more about mass_dataset class here.

load("massprocesser_demo_data/POS/Result/object")
library(massdataset)
object
#> -------------------- 
#> massdataset version: 0.99.1 
#> -------------------- 
#> 1.expression_data:[ 15597 x 9 data.frame]
#> 2.sample_info:[ 9 x 4 data.frame]
#> 3.variable_info:[ 15597 x 3 data.frame]
#> 4.sample_info_note:[ 4 x 2 data.frame]
#> 5.variable_info_note:[ 3 x 2 data.frame]
#> 6.ms2_data:[ 0 variables x 0 MS2 spectra]
#> -------------------- 
#> Processing information (extract_process_info())
#> create_mass_dataset ---------- 
#>       Package         Function.used                Time
#> 1 massdataset create_mass_dataset() 2022-01-15 00:34:49
#> process_data ---------- 
#>         Package Function.used                Time
#> 1 massprocesser  process_data 2022-01-15 00:05:38

Peak_table.csv

The peak table for next analysis.

peak.name mzmed mzmin mzmax rtmed rtmin rtmax npeaks Case Control QC sample_11 sample_30 sample_64 sample_16 sample_52 sample_78 sample_QC_06.mzxml sample_QC_14.mzxml sample_QC_21.mzxml
M70T73_POS 70.04073 70.02958 70.04074 73.02776 72.97240 85.27800 3 0 1 2 NA NA NA NA 656237.0 NA NA 808121.4 1140375.3
M70T39_POS 70.03772 70.03771 70.03772 38.96619 37.37341 40.55898 2 2 0 0 2630939.3 2971757.5 NA NA NA NA NA NA NA
M70T53_POS 70.06595 70.06582 70.06619 53.29675 38.91578 57.12863 9 3 3 3 12457637.4 22073807.0 99560991.1 8612390.1 62430304.3 39586341.8 71036674.2 62833527.0 23876315.3
M70T785_POS 70.06597 70.06594 70.06598 785.47821 784.48400 788.71820 4 1 1 2 4322094.9 NA NA NA 6247303.4 NA 3811413.1 4338755.5 NA
M70T184_POS 70.19946 70.19934 70.19948 184.40106 182.55200 188.36940 5 1 1 3 2653462.1 NA NA NA NA 1618438.4 1972338.8 1874043.0 2005881.4
M70T527_POS 70.36072 70.36069 70.36088 527.33194 527.02509 527.33978 6 2 1 3 2394719.9 1302905.6 NA 2298883.3 NA NA 1777337.6 1612577.3 2613431.8
M71T696_POS 70.56915 70.56911 70.56921 696.15692 695.54272 709.37866 5 1 1 3 NA NA 3797467.3 1849405.9 NA NA 2641658.4 3990473.4 3291488.2
M71T184_POS 70.75003 70.74999 70.75011 184.40106 182.55200 188.67758 5 1 1 3 1143559.9 NA NA NA NA 739133.4 1046777.0 1086292.6 1804452.6
M71T427_POS 70.81580 70.81570 70.81602 427.47917 427.16959 428.16153 6 1 2 3 NA NA 662289.0 NA 914575.0 689459.8 759124.3 883688.3 650932.6
M71T787_POS 70.95856 70.95847 70.95860 786.92017 783.37543 796.31909 9 3 3 3 7461698.5 12374875.9 7646545.3 7071576.8 8338619.7 6738974.8 6590363.3 4953852.7 5748891.5
M71T776_POS 70.98126 70.98110 70.98140 776.25800 775.63837 777.17078 9 3 3 3 215352341.1 191541937.9 128238885.3 213702835.4 172940306.8 168506301.2 168866921.5 134879566.7 185902264.7
M71T292_POS 70.98129 70.98125 70.98132 291.72879 288.78699 295.31616 8 3 2 3 46854406.2 33839615.7 38612293.0 35386570.0 NA 39659893.8 47799349.2 39587801.2 21312500.7
M71T714_POS 70.98125 70.98110 70.98141 713.89049 705.62378 720.91925 12 3 3 3 67258958.2 123657303.7 63775173.5 69757281.7 94002509.6 86831284.0 64311452.5 44769039.2 120267183.0
M71T629_POS 70.98125 70.98123 70.98131 628.95834 624.64300 632.58752 6 1 2 3 NA NA 56685538.4 NA 70627778.5 66929259.5 39336726.7 49183844.8 90877147.8
M71T670_POS 70.98125 70.98114 70.98132 670.48145 668.03375 670.78700 5 2 2 1 124017954.8 163443722.6 NA 99888336.6 136948466.7 NA NA 48663019.8 NA
M71T683_POS 70.98128 70.98123 70.98134 683.32501 682.58215 683.63098 5 1 1 3 NA NA 61964053.3 NA NA 66334653.6 64763963.1 64277218.8 123919875.6
M71T582_POS 70.98128 70.98121 70.98130 581.96024 576.93604 587.32025 6 2 2 2 158576610.8 47745587.2 NA NA 51185750.0 122941310.4 91940340.9 85874085.9 NA
M71T327_POS 70.98132 70.98126 70.98135 326.90817 317.22964 341.67477 8 3 2 3 38053257.4 80487177.9 80602065.9 NA 43507378.9 166523405.2 30538914.9 39736948.4 79877298.8
M71T458_POS 70.98132 70.98128 70.98139 458.11707 444.32919 460.68613 7 2 1 3 38066913.2 61807242.4 NA NA NA 44333119.3 58175879.7 66382640.3 69864572.3
M71T389_POS 70.98132 70.98125 70.98140 389.47409 376.51562 410.62405 9 3 2 3 180449677.3 68388863.3 137622644.3 79391875.5 NA 47824746.5 72017385.8 145368772.9 93522432.1
M71T654_POS 70.98126 70.98122 70.98130 653.62750 652.13080 660.07922 5 1 1 3 NA NA 69495830.3 NA NA 65673720.9 67372585.8 60648752.8 107817042.1
M71T611_POS 70.98127 70.98121 70.98128 610.57562 606.90894 617.92316 5 1 2 2 NA 89880723.4 NA 166726672.0 NA 42005282.8 NA 65173733.9 93661941.7
M71T745_POS 70.98125 70.98112 70.98128 744.76843 742.01400 753.02362 5 1 2 2 NA 63960772.0 NA NA 64109726.1 61164446.3 NA 51252231.3 94403781.3
M71T539_POS 70.98128 70.98121 70.98131 538.50201 531.30823 541.41162 4 1 2 1 NA 73869299.0 NA NA 197149089.2 64625585.1 NA 96228000.5 NA
M71T563_POS 70.98130 70.98129 70.98133 562.53217 558.86298 565.89624 3 2 0 1 NA 57635659.7 209848445.9 NA NA NA NA NA 243762766.9
M71T503_POS 70.98128 70.98124 70.98136 502.83505 498.85141 506.20380 3 1 0 2 NA 90781235.9 NA NA NA NA 79392797.2 98735949.3 NA
M71T428_POS 70.98134 70.98130 70.98137 427.62129 420.43423 436.97806 4 1 0 2 NA NA 39197385.7 NA NA NA 50136132.0 NA 167432612.4
M71T73_1_POS 71.02480 71.01363 71.02483 73.33136 66.01401 74.50822 3 0 0 3 NA NA NA NA NA NA 4284521.6 461269.0 879616.1
M71T53_POS 71.02481 71.02481 71.02481 53.21515 52.02824 54.40205 2 2 0 0 707982.6 834335.1 NA NA NA NA NA NA NA
M71T467_POS 71.04991 71.04978 71.04996 467.01095 466.65588 467.52686 6 1 2 3 NA 3156855.1 NA NA 4466698.0 4157289.3 3856971.8 3112838.1 4620338.4
M71T584_POS 71.04981 71.04972 71.04994 584.10574 583.04034 584.87177 6 3 2 1 5590769.4 4019258.4 4622361.3 5713748.7 NA 4103293.4 3282786.9 NA NA
M71T171_POS 71.05000 71.04997 71.05003 171.38001 170.57735 172.43188 6 3 0 3 8586093.0 7873459.6 6107291.4 NA NA NA 5297588.4 4229598.6 3717396.9
M71T55_POS 71.05000 71.04998 71.05001 54.82500 52.02824 56.33631 6 3 0 3 28372950.8 13215100.9 22123402.7 NA NA NA 16693898.0 10660606.8 9318486.1
M71T73_2_POS 71.05000 71.05000 71.05001 73.45341 72.66583 74.24100 2 0 0 2 NA NA NA NA NA NA NA 9900135.8 8432662.7
M71T695_POS 71.08581 71.08575 71.08618 695.24347 694.76959 695.84766 9 3 3 3 25403639.4 32821640.3 20149178.5 43752476.2 24791237.3 14759406.0 16755069.3 17831509.4 20968354.2
M71T637_POS 71.08584 71.08578 71.08607 636.85745 622.85626 637.66937 10 3 3 3 55106613.1 47002568.1 32840879.9 43793472.2 27024917.9 25225960.6 27225778.7 13263135.5 17025690.8
M71T755_POS 71.08594 71.08589 71.08603 755.47156 752.22339 758.83685 9 3 3 3 14277178.7 12373604.9 11265554.1 12074002.4 11551141.8 9757914.4 17063939.4 11192673.3 12069978.8
M71T669_POS 71.08594 71.08589 71.08626 669.10716 666.50452 673.58350 8 3 2 3 10521626.7 12270045.0 7878224.7 NA 9955723.1 10398366.5 10012626.6 7765748.1 8829148.3
M71T554_POS 71.08610 71.08597 71.08618 554.27277 553.96643 555.06268 7 3 1 3 3792743.1 6573058.5 6349709.7 7255160.3 NA NA 6657487.0 5741862.6 2134070.5
M71T315_POS 71.45836 71.45831 71.45836 315.36478 315.02332 316.19144 4 1 0 3 NA 48483607.0 NA NA NA NA 36867104.0 34527667.6 36952272.8
M72T315_POS 71.57037 71.57034 71.57039 315.21765 314.75125 316.19144 4 1 0 3 NA 9210592.3 NA NA NA NA 6593722.0 6221264.5 7482215.2
M72T787_POS 71.93003 71.92997 71.93005 786.61383 784.00940 790.23810 7 3 3 1 4762186.5 5436506.0 2789644.1 4822881.8 3558428.8 3266833.4 NA NA 2079643.2
M72T776_POS 71.98897 71.98885 71.98900 776.25800 775.33508 777.17200 9 3 3 3 57965519.4 54785336.9 44567373.7 57159306.4 43385663.0 34345976.6 41023563.2 27055571.5 31573360.9
M72T680_POS 71.98898 71.98887 71.98903 680.09485 671.72858 685.46700 5 2 2 1 51628058.7 22021498.4 NA 31607556.5 14331125.9 NA NA NA 22928579.0
M72T705_POS 71.98897 71.98889 71.98903 705.32000 703.79822 706.39355 3 0 2 1 NA NA NA 17309147.2 13883247.2 NA NA NA 14834399.2
M72T631_POS 71.98897 71.98889 71.98899 631.12970 630.69489 631.36823 3 0 1 2 NA NA NA 15475246.6 NA NA NA 9896270.8 11962139.5
M72T478_POS 72.04502 72.04497 72.04502 477.72300 477.37442 480.16827 3 1 2 0 NA 4044959.0 NA NA 3042764.1 2364623.9 NA NA NA
M72T556_POS 72.06270 72.06265 72.06271 555.80219 555.49554 555.80341 6 3 2 1 1284253.7 1283771.6 1182522.8 1268102.1 NA 1258898.3 1246450.4 NA NA
M72T778_POS 72.08160 72.08157 72.08162 777.78129 777.18182 779.00043 8 3 3 2 14258903.9 12039619.8 13958118.8 14202518.5 17336638.4 10149111.4 18391088.8 11493049.8 NA
M72T54_POS 72.08165 72.08143 72.08167 54.01814 53.59370 54.37598 6 1 2 3 NA NA 235808285.0 NA 184873856.9 163393748.5 260140017.8 284240078.8 284017236.2
M72T38_POS 72.08160 72.08160 72.08160 38.48114 37.27135 42.70284 3 2 1 0 27107020.2 50633224.0 NA 47430209.5 NA NA NA NA NA
M73T800_POS 72.93786 72.93769 72.93796 800.03516 791.59460 802.07965 9 3 3 3 100052315.0 110078383.4 109471137.1 76887012.4 107185305.7 99307794.8 118635551.4 75806954.5 141157817.9
M73T863_POS 72.93795 72.93768 72.93807 862.63208 855.96399 868.26666 9 2 3 3 36119088.8 29809818.8 NA 23220638.3 23303239.9 16435272.4 15487146.8 14917962.0 32070062.6
M73T845_POS 72.93797 72.93777 72.93809 845.46481 840.80713 850.26758 8 3 3 2 35056825.8 23507184.5 26415857.8 32962097.8 28507377.5 22159427.1 18083829.4 NA 60796016.5
M73T883_POS 72.93795 72.93775 72.93800 883.05106 876.56262 888.38458 8 3 3 2 21603346.1 24778942.6 20763186.6 51145215.3 17397188.5 12344336.8 NA 27596963.3 23429379.1
M73T999_POS 72.93796 72.93774 72.93808 998.92114 994.62600 1008.73340 9 3 3 3 27032977.2 23893383.9 24366122.7 44774696.1 23568707.5 10235570.9 32280246.1 15491168.1 19146455.7
M73T38_POS 72.93796 72.93783 72.93805 37.55469 36.86950 38.21457 6 1 2 3 NA NA 9833664.6 NA 11310823.2 8651613.7 9038253.5 9176532.1 19613092.6
M73T943_POS 72.93801 72.93780 72.93808 942.65442 932.96881 954.13200 11 2 3 3 NA 33410955.7 13753271.3 25350529.6 17166258.7 24588087.3 34865743.8 24015199.7 29653200.4
M73T918_POS 72.93796 72.93778 72.93799 917.79291 915.80042 923.44391 6 2 2 2 32087443.8 NA 31597797.5 NA 20933040.8 11321805.9 NA 28481241.7 24518651.7
M73T898_POS 72.93798 72.93779 72.93800 897.86237 894.03784 906.60223 6 2 2 2 24542996.8 27024065.0 NA NA 14553205.2 15857089.5 26700947.7 NA 33011850.1
M73T972_POS 72.93794 72.93774 72.93808 972.38480 958.73468 987.26135 12 3 2 3 21837794.0 19317552.3 14786429.0 NA 11117288.9 13799829.7 11913972.8 13962721.1 29306136.2
M73T829_POS 72.93795 72.93772 72.93801 828.77765 823.32397 833.35687 5 2 1 1 27739882.4 23419144.4 NA 36450652.8 NA NA NA 28859682.7 NA
M73T1020_POS 72.93791 72.93774 72.93793 1020.08980 1018.86078 1020.70002 4 2 1 1 15995185.5 19318660.3 NA NA 7928168.1 NA NA 4631712.4 NA
M73T86_POS 73.01148 73.01146 73.01150 85.87304 75.26891 86.21927 7 1 3 3 777867.5 NA NA 1254477.1 2025850.8 885017.7 1049892.7 843856.8 1391950.9
M73T59_POS 73.02923 73.02921 73.02925 59.03071 54.68877 68.54877 6 1 2 3 NA NA 23749298.3 NA 5219138.1 6827992.8 30262399.9 15428009.9 13889926.4
M73T40_POS 73.02922 73.02920 73.02923 39.52006 38.48114 40.55898 2 2 0 0 30976281.8 18156130.7 NA NA NA NA NA NA NA
M73T808_POS 73.06563 73.06557 73.06568 808.37979 801.82947 830.00244 16 3 3 3 19096867.5 17959352.2 27539499.7 29113727.8 23769678.0 20153062.3 16936938.0 24123729.7 45034169.7
M73T907_POS 73.06564 73.06554 73.06569 906.90900 905.06757 923.77118 9 3 3 3 22604524.8 32455162.8 56894651.9 20150720.5 50023498.9 61462975.6 41568432.6 43486051.0 43480692.3
M73T608_POS 73.06567 73.06560 73.06572 608.13004 598.64136 615.77692 10 3 3 3 269099276.5 271790997.3 129081238.1 131501643.0 286359678.1 126716004.5 119784352.2 242978415.1 135325362.6
M73T631_POS 73.06565 73.06561 73.06573 631.14526 629.47986 634.72968 7 2 2 3 146874044.0 NA 174939790.4 147710130.6 NA 179891166.6 150042522.2 112006716.9 158563645.8
M73T945_POS 73.06564 73.06559 73.06575 945.47235 936.95892 956.58588 10 2 3 3 15817368.8 NA 38758540.6 15064347.7 42555643.7 40248241.2 40540321.8 22038965.2 31488901.7
M73T1005_POS 73.06563 73.06561 73.06569 1004.73068 997.38623 1014.26172 10 3 2 3 16142878.2 8222526.7 10716169.8 NA 10672477.9 12415894.7 15275404.1 9907087.5 11688203.7
M73T979_POS 73.06565 73.06563 73.06567 978.97937 964.56116 989.71698 11 3 3 3 9342270.7 11465626.5 16295316.0 11698026.8 15384899.8 17836505.7 14704170.1 12626061.5 14537278.7
M73T762_POS 73.06566 73.06560 73.06570 762.20166 752.38306 776.85065 11 3 3 3 229550512.1 484760436.8 488337864.4 444606856.8 427909951.2 323051817.6 117352361.4 532961832.9 150789773.6
M73T694_POS 73.06565 73.06560 73.06575 694.32440 686.37610 705.40131 10 2 3 3 NA 129489130.0 546000363.3 106225328.2 158282889.2 249849876.1 155555098.5 147960968.3 267205771.7
M73T671_POS 73.06567 73.06562 73.06571 671.24771 668.34000 677.92175 6 2 2 2 423778041.2 397875423.2 NA NA 121330057.3 230382462.7 155568996.4 362693826.5 NA
M73T877_POS 73.06563 73.06561 73.06566 877.15350 857.56470 888.21210 11 3 2 3 65038051.7 42093116.9 24879003.0 112858937.8 23325795.0 NA 16943158.2 15645056.2 18944616.9
M73T540_POS 73.06568 73.06557 73.06575 539.88104 529.77930 544.47443 7 2 3 2 NA 114335972.4 286704224.5 151827955.6 195282507.2 295818942.0 234820987.7 NA 131042926.2
M73T575_POS 73.06567 73.06560 73.06577 575.08429 555.18872 588.24371 11 3 3 2 320458360.3 153880594.2 245896342.0 154528387.7 145551905.6 273572516.4 194399613.2 NA 379961356.0
M73T651_POS 73.06565 73.06560 73.06567 651.06373 649.44025 652.50439 4 0 2 2 NA NA NA 150631001.5 183170161.8 NA 206478155.5 NA 191404688.6
M73T719_POS 73.06565 73.06564 73.06574 719.38431 716.33200 723.36523 4 1 2 1 NA 119358475.6 NA 142251910.7 168524884.5 NA NA NA 125360212.0
M73T734_POS 73.06565 73.06564 73.06568 733.91388 730.39917 737.36249 4 1 2 1 125080784.7 NA NA NA 132433380.0 151893721.1 232412360.0 NA NA
M73T847_POS 73.06564 73.06562 73.06570 846.92508 844.61133 854.38391 4 2 1 1 16115415.0 14801639.7 NA 24674274.8 NA NA NA NA 14962590.9
M73T511_POS 73.06562 73.06554 73.06569 510.95536 506.20400 515.70673 2 0 2 0 NA NA NA 70740193.2 156098251.0 NA NA NA NA
M73T54_POS 73.08496 73.08494 73.08499 53.99380 42.70284 54.37598 7 1 3 3 NA NA 9789232.1 1021179.5 8024848.6 6504216.0 10160104.1 10536874.4 11868484.6
M73T67_POS 73.27377 73.27373 73.27379 67.22857 65.77097 67.79080 5 0 2 3 NA NA NA NA 8321814.0 12012537.2 6841144.4 5930713.8 6958837.1
M74T498_POS 73.79693 73.79688 73.79696 498.24194 497.93298 498.54712 8 3 3 2 969222.1 1060255.3 1066934.0 1080524.7 1130919.0 1029821.6 1085730.6 941152.6 NA
M74T56_1_POS 73.88962 73.88961 73.88970 55.55984 55.28285 55.86568 4 1 0 3 NA NA 2028972.9 NA NA NA 2045930.6 1804252.1 2646462.0
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M81T51_POS 80.94861 80.94842 80.94867 50.81723 50.33201 51.30504 6 1 2 3 NA NA 707198202.0 NA 1152498500.5 953760858.7 638050104.6 565532289.9 560366505.7
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M81T255_POS 81.03424 81.03424 81.03428 254.62273 254.32448 254.96713 4 2 2 0 5916740.1 6824248.5 NA NA 3186986.8 6574048.7 NA NA NA
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M81T696_POS 81.07060 81.07055 81.07064 695.54272 694.82837 695.66284 9 3 3 3 53260815.5 62085007.0 40314132.2 56487852.8 34027185.7 28192590.9 33462600.6 27817278.2 36636125.0
M81T481_POS 81.07066 81.07064 81.07069 480.78391 478.62616 482.00800 9 3 3 3 58092159.1 63992083.4 38377582.7 69631533.7 45846132.1 36788678.2 38039176.1 27279243.3 24608826.0
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M81T448_POS 81.07066 81.07066 81.07070 447.50952 440.96121 450.06961 4 2 1 1 20908125.6 NA 16179625.2 NA 17708923.4 NA NA 18862315.3 NA
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M82T192_POS 82.05321 82.05318 82.05329 191.69513 191.51662 192.37276 3 0 0 3 NA NA NA NA NA NA 5961519.9 5661259.7 8051458.2
M82T86_POS 82.06591 82.06588 82.06593 85.60232 75.26891 85.91332 8 2 3 3 2485226.7 NA 4343681.9 3951058.5 5200238.9 3382757.8 5403008.4 5028988.9 6293513.2
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M82T640_POS 82.17723 82.17717 82.17729 640.06430 639.30157 640.82703 2 2 0 0 NA 5379610.1 6623844.2 NA NA NA NA NA NA
M83T695_1_POS 82.82017 82.82013 82.82028 695.23828 694.93744 695.66284 9 3 3 3 8254652.6 10427930.6 6048825.2 10842911.5 4760196.5 3686267.8 4311771.7 4451825.7 4555488.6
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M83T35_POS 82.94564 82.94563 82.94564 34.59420 34.52635 36.18497 3 2 1 0 10678019.8 22047180.0 NA 17798524.1 NA NA NA NA NA
M83T666_POS 82.98999 82.98996 82.99003 665.89282 664.90881 666.50690 7 3 1 3 1630169.8 1732542.4 1910885.0 NA NA 1821632.3 1939317.0 1536902.7 1182636.2
M83T777_POS 82.99835 82.99831 82.99840 777.18182 776.24493 777.78162 9 3 3 3 12003999.3 20684152.5 7366762.7 8805365.6 7757807.5 7039409.3 9027737.7 6577175.0 13375034.4
M83T45_POS 83.00470 82.99798 83.01350 45.09744 36.81782 49.76104 12 3 2 3 10737489.4 8342133.0 14567716.4 NA 45890760.9 38460440.1 42085497.8 42989411.8 51344112.6
M83T780_POS 83.02229 83.02228 83.02231 779.69977 779.30804 782.32568 4 2 1 1 16335315.8 13606900.5 NA 13438102.6 NA NA NA NA 4381967.3
M83T114_POS 83.02235 83.02233 83.02239 113.89506 110.30820 116.27110 4 2 2 0 48583542.4 NA 24439702.4 NA 52356700.8 30622641.0 NA NA NA
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M83T554_POS 83.04990 83.04986 83.04994 553.66028 553.20203 553.66100 9 3 3 3 12810024.2 11926637.3 12504303.1 12377556.4 15633888.1 13524957.0 11558653.9 14009830.1 7505791.3
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M83T116_POS 83.04989 83.04987 83.04995 115.90024 102.00214 117.61654 7 3 2 0 30661317.9 48925561.2 18296397.1 13896072.5 NA 19183436.8 NA NA NA
M83T697_POS 83.04984 83.04979 83.04985 696.76685 694.02100 700.71985 4 1 3 0 15019194.8 NA NA 9106619.0 11790038.4 9918505.1 NA NA NA
M83T37_POS 83.04987 83.04984 83.04990 37.04078 36.26247 37.81910 2 2 0 0 52395966.6 53764773.2 NA NA NA NA NA NA NA
M83T774_POS 83.06110 83.06107 83.06114 774.42464 773.51465 774.73676 8 3 3 2 10086576.9 7879662.8 6757334.9 7689521.9 8966071.6 9146173.5 6204771.7 5710886.6 NA
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M83T55_POS 83.06111 83.06108 83.06113 54.65065 53.38120 55.28285 5 1 1 3 NA NA 6286183.2 NA 6594993.8 NA 6757560.3 8242751.5 11472719.6
M83T483_POS 83.08625 83.08622 83.08630 482.92500 481.34488 496.70929 11 3 3 3 14468510.4 15352052.7 15134352.4 13885916.7 14563945.9 12839170.8 16545290.1 11396872.1 10559964.4
M83T636_POS 83.08609 83.08602 83.08615 635.64587 635.33600 636.50891 7 3 1 3 28055529.0 23413770.8 28280240.5 NA 20595735.2 NA 21481102.7 12664651.5 11600408.7
M83T340_POS 83.08630 83.08627 83.08635 340.25543 332.65231 343.51428 9 3 3 3 16894774.2 12919309.1 38330814.4 11912606.5 46098730.5 12395629.9 28793758.5 13651195.2 19882023.4
M83T311_POS 83.08629 83.08623 83.08631 310.77721 309.49500 312.25266 6 1 2 3 9062533.5 NA NA 6833200.4 NA 6090670.7 5332951.1 6719950.3 3977173.2
M83T583_POS 83.08613 83.08611 83.08616 583.34467 582.12225 584.57062 3 2 0 1 NA 9333079.6 7393609.8 NA NA NA 11161575.8 NA NA
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M84T440_POS 84.04515 84.04514 84.04519 439.97085 434.52457 442.49197 6 3 2 1 48758831.1 30206132.5 21566074.8 NA 112306697.6 24190678.1 NA 25374611.5 NA
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M84T58_POS 84.04512 84.04500 84.04525 58.14347 56.47311 69.31870 7 1 2 3 NA NA 130066563.2 NA 314691318.8 167067525.9 148549621.3 133553081.3 124163513.6
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M84T412_POS 84.04516 84.04511 84.04517 411.54401 394.68475 414.46521 7 3 2 1 34186081.7 38049081.6 35259169.1 NA 30367152.4 34100770.4 NA 50878173.7 NA
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M84T284_POS 84.04515 84.04514 84.04516 284.28426 281.06375 287.46213 4 2 1 1 54329216.1 50618130.0 NA NA NA 39288898.7 NA 83446031.0 NA
M84T484_POS 84.04516 84.04510 84.04517 484.30173 476.11542 493.33978 6 3 2 1 22834221.8 18218817.5 40900606.7 NA 19928270.5 22492629.8 NA 45382935.7 NA
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M84T361_POS 84.04513 84.04508 84.04515 361.03387 356.76468 363.95203 4 2 1 1 21671049.1 23768899.8 NA NA NA 23564663.7 NA 48351490.7 NA
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M84T382_POS 84.04517 84.04509 84.04518 381.96255 374.42447 385.18300 4 3 1 0 35237968.0 28528664.0 64090420.1 NA 44579692.9 NA NA NA NA
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M84T305_POS 84.04516 84.04512 84.04517 305.20828 298.19208 307.34708 3 2 1 0 NA 29953449.9 43015536.7 NA NA 33785139.8 NA NA NA
M84T213_POS 84.04515 84.04515 84.04516 213.38905 212.31647 214.46164 2 2 0 0 47848053.0 43002839.2 NA NA NA NA NA NA NA
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M84T232_POS 84.08153 84.08151 84.08155 232.24380 231.94162 232.85956 5 1 2 2 NA 7688609.5 NA 5693542.5 NA 26067155.0 9974590.1 NA 7840655.1
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M84T38_POS 84.08155 84.08152 84.08162 37.65864 37.27135 38.48114 3 2 1 0 31189306.6 18917787.0 NA 14273783.7 NA NA NA NA NA
M84T670_POS 84.28402 84.28400 84.28405 670.47028 667.42773 670.79230 5 1 2 2 NA NA 66214847.7 NA 55136345.1 33059469.9 64805291.0 NA 30404943.6
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M84T687_POS 84.39553 84.39550 84.39591 686.99500 680.87866 686.99573 3 0 2 1 NA NA NA NA 12089545.7 11580487.3 NA 8796997.4 NA
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M85T707_POS 84.61971 84.61969 84.61976 707.15674 702.27008 707.76440 3 0 0 3 NA NA NA NA NA NA 9749444.5 10461555.1 6717750.8
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M88T511_POS 88.11322 88.11284 88.11325 510.64876 504.67596 514.17212 4 2 2 0 NA 349387938.2 116963304.6 222668089.2 111914528.4 NA NA NA NA
M88T605_POS 88.11306 88.11280 88.11331 604.91299 590.68982 612.71800 6 2 3 1 NA 732972972.0 202485462.4 420715629.6 227427193.4 399751985.2 206461970.4 NA NA
M88T682_POS 88.11304 88.11281 88.11306 682.40700 680.89490 688.78986 3 1 2 0 NA 756437026.2 NA 470072490.9 595032611.3 NA NA NA NA
M88T668_POS 88.11299 88.11298 88.11311 667.72870 665.89801 672.93323 3 2 0 1 534020245.1 NA 332054356.8 NA NA NA 166282983.8 NA NA
M88T578_POS 88.11315 88.11305 88.11331 578.13440 572.93823 581.19800 3 0 2 1 NA NA NA NA 204944944.7 158771547.4 315699279.7 NA NA
M88T532_POS 88.11308 88.11293 88.11314 532.07425 524.57690 541.71900 4 1 2 1 NA NA 247888491.2 220503574.9 222386965.6 NA 466440840.8 NA NA
M88T492_POS 88.11318 88.11311 88.11326 492.11405 489.05011 495.17800 2 0 2 0 NA NA NA 121604714.5 97998692.7 NA NA NA NA
M88T362_POS 88.27180 88.27169 88.27192 362.10657 361.88138 362.75079 4 1 0 3 NA 4577156.2 NA NA NA NA 2194831.0 1795635.0 2234081.6
M88T695_POS 88.31543 88.31540 88.31553 694.93744 694.82837 695.24176 9 3 3 3 19051271.0 27043320.5 17922491.6 25581659.1 13751725.0 10739011.5 12598239.1 12198731.6 18171778.7
M89T695_POS 88.56638 88.56634 88.56642 695.24176 694.85675 695.66284 9 3 3 3 3952984.4 4997240.1 3451910.7 5094873.6 2557762.3 1864284.3 2258980.8 2275545.9 3440180.3
M89T522_POS 88.55592 88.55586 88.55597 522.12897 521.82123 522.43750 9 3 3 3 1660358.2 1503631.6 1485024.6 1673992.7 1615260.8 1369494.3 1625637.0 1182757.7 859873.0
M89T802_POS 88.95288 88.95280 88.95304 801.87860 799.09637 803.29163 9 3 3 3 66528745.9 80172625.1 78036867.0 75353881.9 104389701.4 94078625.5 95713144.0 79412141.5 99301751.4
M89T38_1_POS 88.95301 88.95300 88.95303 37.55469 37.07954 38.33126 6 1 2 3 NA NA 17716762.1 NA 17624396.6 12823819.3 17950562.7 15825933.7 19757303.1
M89T975_POS 88.95299 88.95280 88.95307 975.19031 965.48132 984.19348 6 1 1 2 NA NA 24931953.0 44689235.3 NA NA NA 18230236.3 19881762.5
M89T1016_POS 88.95298 88.95293 88.95301 1016.10318 1008.73633 1020.10004 4 1 1 2 NA NA 13708741.1 60843084.6 NA NA 17788323.5 24313205.0 NA
M89T777_1_POS 88.95377 88.95377 88.95381 777.49042 776.25360 778.69611 3 0 2 1 NA NA NA 4707949.1 NA 4195129.6 5528081.1 NA NA
M89T1001_POS 88.95303 88.95290 88.95308 1001.37390 992.78571 1001.98755 3 1 0 2 NA NA 23446819.2 NA NA NA NA 14001420.9 24067536.3
M89T944_POS 88.95303 88.95293 88.95306 944.02875 941.25195 950.14648 3 1 0 2 NA NA 39244868.6 NA NA NA NA 20434145.9 44807911.1
M89T831_POS 88.95294 88.95220 88.95307 830.73590 829.02734 837.35248 3 2 1 0 38450023.6 NA 30567496.6 60139836.5 NA NA NA NA NA
M89T786_POS 88.96881 88.96856 88.96895 786.49042 784.81598 787.80432 9 3 3 3 129943745.0 166894997.2 115338504.0 123386985.5 133853663.7 118675097.3 121211522.7 88077800.6 105637782.0
M89T38_2_POS 88.96913 88.96911 88.96916 37.66284 36.91802 38.01700 5 1 1 3 NA NA 2536663.7 NA 2290836.2 NA 2488783.3 1910927.6 2655762.1
M89T816_POS 88.96908 88.96903 88.96911 815.92902 815.03906 818.00134 5 1 1 3 NA NA 10628166.0 9735719.4 NA NA 7525961.8 7811765.5 14170751.5
M89T923_POS 88.96913 88.96912 88.96915 923.01666 917.02545 926.84000 4 1 2 1 NA NA 3658686.8 NA 4204674.5 4101426.4 3924815.7 NA NA
M89T866_POS 88.96910 88.96908 88.96916 866.14442 859.09674 872.57843 4 1 2 1 NA NA 5105760.2 NA 8833587.4 4090626.8 NA 4541493.1 NA
M89T711_POS 88.99165 88.99151 88.99195 711.44867 705.79523 720.92212 10 3 3 3 296274066.0 221777073.6 199244966.7 122796288.6 282835654.6 284630253.9 195684741.9 268023564.5 417810004.8
M89T748_POS 88.99170 88.99162 88.99191 748.40228 738.04260 751.49457 9 2 3 3 NA 136952348.0 134428870.8 112701939.2 140728059.1 134791450.5 121881937.1 137906413.1 139358279.6
M89T996_POS 88.99167 88.96910 88.99172 995.54600 985.42084 1001.67432 9 3 2 2 5700835.8 8881501.3 3492785.1 NA 4823715.2 9525351.2 8426811.6 NA 5958201.0
M89T947_POS 88.99168 88.96911 88.99173 946.97964 940.04053 952.90625 8 3 3 1 7183972.6 8279787.3 14071317.2 31885407.5 10675201.7 3460582.1 NA NA 3692377.5
M89T962_POS 88.99166 88.96914 88.99173 962.41461 957.16821 965.78857 7 2 1 3 NA 8251594.4 3623787.7 NA 2527959.9 NA 7979137.9 22874993.0 4121227.3
M89T618_POS 88.99174 88.99150 88.99187 617.92169 612.41058 632.04095 10 2 3 3 NA 264006975.7 291858691.6 269553366.0 218480745.5 166713549.9 130376559.3 259564526.3 165053866.6
M89T538_POS 88.99174 88.99143 88.99187 538.34854 534.36871 550.90405 8 3 3 2 120950647.1 140818614.5 170067973.9 133539513.6 683487364.4 140561973.3 712094945.3 705086267.0 NA
M89T668_POS 88.99165 88.99152 88.99194 668.18967 664.66895 670.78760 6 3 3 0 175647749.3 418295261.0 103755674.0 376131876.6 378605344.5 369628148.2 NA NA NA
M89T493_POS 88.99170 88.99168 88.99180 492.87884 486.27069 494.56552 6 2 3 1 441290911.1 152111650.0 NA 518545306.8 191164256.7 206841619.3 NA 165157913.6 NA
M89T477_POS 88.99172 88.99168 88.99176 476.80600 472.53735 480.78406 5 2 1 2 NA 115331075.8 181072966.7 NA 173905641.4 NA 251324687.3 144803670.0 NA
M89T413_POS 88.99182 88.99168 88.99202 413.29752 404.79901 424.46637 7 3 2 2 144995604.3 149356054.2 783418074.4 214293530.8 NA 707719289.8 697470378.2 178963928.6 NA
M89T654_POS 88.99182 88.99152 88.99205 653.51047 652.12799 654.83374 4 1 0 3 NA NA 133857167.4 NA NA NA 180133783.5 194439954.7 241297238.3
M89T567_POS 88.99193 88.99168 88.99202 567.42798 557.94489 570.79498 5 2 2 1 NA 368130566.8 481377071.3 131691564.8 NA 204767539.4 NA NA 472612731.8
M89T977_POS 88.99170 88.99168 88.99172 977.44623 976.21979 978.71069 3 2 0 1 7625373.6 NA 10593687.1 NA NA NA 7293694.1 NA NA
M89T585_POS 88.99174 88.99163 88.99199 584.86768 579.38043 586.70800 4 1 2 1 342894020.7 NA NA NA 147688383.2 238198635.5 NA 265666650.0 NA
M89T443_POS 88.99176 88.99171 88.99197 442.52658 432.99191 449.47479 5 2 2 1 103325451.4 155281792.1 NA 300498395.9 289861591.0 NA NA 233491418.7 NA
M89T460_POS 88.99178 88.99174 88.99183 459.94339 457.51227 459.96756 3 2 0 1 NA 149702660.2 176169621.3 NA NA NA 246486299.7 NA NA
M89T328_POS 88.99183 88.96909 88.99200 327.77234 315.00369 333.99460 5 2 1 1 NA 154285620.2 224085873.7 NA NA 467373663.7 NA 451860082.3 NA
M89T384_POS 88.99174 88.99158 88.99193 384.26657 372.31479 388.38800 5 2 2 1 186380359.7 247418322.1 NA 134077092.1 NA 122969510.7 NA 596781820.7 NA
M89T511_POS 88.99176 88.99168 88.99198 511.41418 508.96530 514.17230 3 2 1 0 NA 151833774.1 274922597.0 NA NA 336808769.0 NA NA NA
M89T777_2_POS 88.99157 88.99146 88.99196 777.17078 775.94165 777.78200 9 3 3 3 516772616.0 552089068.7 484897982.2 534286488.0 490075321.3 475317042.7 495961367.8 434709627.9 430213814.3
M89T817_POS 88.99166 88.99159 88.99169 816.84500 813.71893 818.37585 9 3 3 3 17497092.4 17186703.7 21312132.0 12605739.8 14253556.7 12765657.3 15298286.1 12638315.0 7954112.9
M89T893_POS 88.99169 88.99166 88.99171 893.42111 881.65509 901.67450 10 3 3 3 23566212.2 11743174.5 10863474.8 7973186.3 13100864.6 12946273.5 15568257.2 5136039.4 3712653.3
M89T1018_POS 88.99167 88.99163 88.99172 1017.63623 1009.65411 1019.78943 7 3 2 2 6483193.2 5873116.3 16831828.3 16604829.4 NA 4300668.0 7597028.4 7931109.3 NA
M89T850_POS 88.99169 88.99164 88.99169 849.84161 834.81934 860.93793 9 2 3 2 8632452.7 14829984.1 NA 11295372.6 9913011.9 14163995.5 7642366.3 NA 3431700.3
M89T684_POS 88.99178 88.99153 88.99213 683.82397 681.02771 685.45758 5 2 0 3 123253651.8 NA 166847227.0 NA NA NA 160165605.9 249905118.9 227463162.5
M89T921_POS 88.99169 88.99162 88.99176 921.01141 909.36230 933.57141 9 3 2 3 7479409.5 8637574.7 8395563.6 NA 10967585.3 5834146.7 8697724.6 7462314.7 4780979.1
M89T869_POS 88.99167 88.99166 88.99172 868.97345 863.07989 871.27948 4 2 0 2 NA 10214561.8 8478256.0 NA NA NA NA 6688436.7 4046711.6
M89T350_POS 88.99186 88.99159 88.99198 350.26019 339.63837 360.05597 6 3 2 1 236852679.2 174464985.1 250958823.2 329227312.4 NA 177435800.0 635484433.9 NA NA
M89T291_POS 88.99186 88.99167 88.99216 291.41919 278.54974 303.33997 5 2 1 2 NA 182115206.2 326491941.6 NA NA 154962494.7 121067720.2 138517648.2 NA
M89T160_POS 89.03905 89.03901 89.03918 159.86534 159.56264 160.17497 9 3 3 3 4100944.3 3431940.6 3205848.9 2031973.1 3057463.8 2574606.0 3152260.6 2480767.9 3610526.8
M89T634_POS 89.06033 89.06026 89.06036 634.42395 633.20166 634.72800 9 3 3 3 20373346.8 44602690.5 17979507.3 19403261.3 35333934.2 37864081.2 27913929.1 20662364.4 29447295.1
M89T200_POS 89.06039 89.06038 89.06042 199.83501 199.12430 200.35477 6 2 3 1 19584676.0 52235346.9 NA 58694708.8 16713757.5 15378956.4 NA NA 12102400.5
M89T332_POS 89.06033 89.06012 89.06049 331.93970 331.21780 332.56247 6 3 3 0 61309511.6 40594705.1 16648500.8 25325659.3 25449725.4 27394825.3 NA NA NA
M89T73_POS 89.06042 89.06039 89.06043 72.83548 72.71791 72.97240 3 1 0 2 NA NA 16329788.8 NA NA NA 16749968.2 10303242.4 NA
M89T53_POS 89.06037 89.06036 89.06038 53.21552 52.57287 53.85816 2 2 0 0 18371416.4 13635811.2 NA NA NA NA NA NA NA
M89T751_POS 89.11610 89.11607 89.11613 750.88480 745.64758 763.72559 8 3 3 2 43159113.1 43350532.6 14349246.4 32822185.7 38593562.1 27009923.3 30218455.6 26092550.8 NA
M90T763_POS 89.61728 89.61723 89.61736 762.96521 747.82361 766.78800 6 1 2 3 NA NA 16846245.1 NA 12889096.5 14883159.6 13125719.5 13572064.1 37227295.3
M90T670_POS 89.61739 89.61726 89.61767 670.33035 661.00281 683.63098 8 1 2 3 NA NA 28494202.7 NA 20995397.5 17465825.4 6558229.5 4245875.7 12419392.5
M90T603_POS 89.61746 89.61733 89.61759 603.38306 598.33600 610.88007 6 1 2 3 NA NA 7556265.6 NA 8729314.0 6744584.7 13274089.7 11255307.7 10361959.7
M90T725_POS 89.61728 89.61719 89.61745 725.35229 722.44900 735.59576 4 0 2 2 NA NA NA NA 22866153.2 8047848.4 12835555.6 9823494.6 NA
M90T711_POS 89.61733 89.61727 89.61756 711.15518 708.37915 716.94299 4 1 1 2 NA NA 13950859.5 NA NA 11866627.7 7720920.4 5803565.4 NA
M90T623_POS 89.61735 89.61735 89.61744 622.81097 622.50400 625.55908 3 1 2 0 NA NA 8364594.1 NA 10040536.9 6762993.5 NA NA NA
M90T641_POS 89.61745 89.61744 89.61746 640.83136 638.39062 643.27209 2 0 0 2 NA NA NA NA NA NA 7758988.0 5983918.4 NA
M90T522_POS 89.79477 89.79469 89.79479 522.12800 521.82294 522.13684 5 1 2 2 NA NA 677372.8 NA 726203.0 690947.3 711094.4 NA 880556.3
M90T640_POS 89.82791 89.82786 89.82794 639.61353 638.08240 644.01965 9 3 3 3 11150636.5 8202838.0 8017938.1 8651874.8 3597333.3 3580739.1 3680067.0 1608277.2 2261067.0

Only top 500 features show.

Peak_table_for_cleaning.csv

Some usefulness columns are deleted from the Peak_table.csv, this can be directory used for next data cleaning.

variable_id mz rt sample_11 sample_30 sample_64 sample_16 sample_52 sample_78 sample_QC_06.mzxml sample_QC_14.mzxml sample_QC_21.mzxml
M70T73_POS 70.04073 73.02776 NA NA NA NA 656237.0 NA NA 808121.4 1140375.3
M70T39_POS 70.03772 38.96619 2630939.3 2971757.5 NA NA NA NA NA NA NA
M70T53_POS 70.06595 53.29675 12457637.4 22073807.0 99560991.1 8612390.1 62430304.3 39586341.8 71036674.2 62833527.0 23876315.3
M70T785_POS 70.06597 785.47821 4322094.9 NA NA NA 6247303.4 NA 3811413.1 4338755.5 NA
M70T184_POS 70.19946 184.40106 2653462.1 NA NA NA NA 1618438.4 1972338.8 1874043.0 2005881.4
M70T527_POS 70.36072 527.33194 2394719.9 1302905.6 NA 2298883.3 NA NA 1777337.6 1612577.3 2613431.8
M71T696_POS 70.56915 696.15692 NA NA 3797467.3 1849405.9 NA NA 2641658.4 3990473.4 3291488.2
M71T184_POS 70.75003 184.40106 1143559.9 NA NA NA NA 739133.4 1046777.0 1086292.6 1804452.6
M71T427_POS 70.81580 427.47917 NA NA 662289.0 NA 914575.0 689459.8 759124.3 883688.3 650932.6
M71T787_POS 70.95856 786.92017 7461698.5 12374875.9 7646545.3 7071576.8 8338619.7 6738974.8 6590363.3 4953852.7 5748891.5
M71T776_POS 70.98126 776.25800 215352341.1 191541937.9 128238885.3 213702835.4 172940306.8 168506301.2 168866921.5 134879566.7 185902264.7
M71T292_POS 70.98129 291.72879 46854406.2 33839615.7 38612293.0 35386570.0 NA 39659893.8 47799349.2 39587801.2 21312500.7
M71T714_POS 70.98125 713.89049 67258958.2 123657303.7 63775173.5 69757281.7 94002509.6 86831284.0 64311452.5 44769039.2 120267183.0
M71T629_POS 70.98125 628.95834 NA NA 56685538.4 NA 70627778.5 66929259.5 39336726.7 49183844.8 90877147.8
M71T670_POS 70.98125 670.48145 124017954.8 163443722.6 NA 99888336.6 136948466.7 NA NA 48663019.8 NA
M71T683_POS 70.98128 683.32501 NA NA 61964053.3 NA NA 66334653.6 64763963.1 64277218.8 123919875.6
M71T582_POS 70.98128 581.96024 158576610.8 47745587.2 NA NA 51185750.0 122941310.4 91940340.9 85874085.9 NA
M71T327_POS 70.98132 326.90817 38053257.4 80487177.9 80602065.9 NA 43507378.9 166523405.2 30538914.9 39736948.4 79877298.8
M71T458_POS 70.98132 458.11707 38066913.2 61807242.4 NA NA NA 44333119.3 58175879.7 66382640.3 69864572.3
M71T389_POS 70.98132 389.47409 180449677.3 68388863.3 137622644.3 79391875.5 NA 47824746.5 72017385.8 145368772.9 93522432.1
M71T654_POS 70.98126 653.62750 NA NA 69495830.3 NA NA 65673720.9 67372585.8 60648752.8 107817042.1
M71T611_POS 70.98127 610.57562 NA 89880723.4 NA 166726672.0 NA 42005282.8 NA 65173733.9 93661941.7
M71T745_POS 70.98125 744.76843 NA 63960772.0 NA NA 64109726.1 61164446.3 NA 51252231.3 94403781.3
M71T539_POS 70.98128 538.50201 NA 73869299.0 NA NA 197149089.2 64625585.1 NA 96228000.5 NA
M71T563_POS 70.98130 562.53217 NA 57635659.7 209848445.9 NA NA NA NA NA 243762766.9
M71T503_POS 70.98128 502.83505 NA 90781235.9 NA NA NA NA 79392797.2 98735949.3 NA
M71T428_POS 70.98134 427.62129 NA NA 39197385.7 NA NA NA 50136132.0 NA 167432612.4
M71T73_1_POS 71.02480 73.33136 NA NA NA NA NA NA 4284521.6 461269.0 879616.1
M71T53_POS 71.02481 53.21515 707982.6 834335.1 NA NA NA NA NA NA NA
M71T467_POS 71.04991 467.01095 NA 3156855.1 NA NA 4466698.0 4157289.3 3856971.8 3112838.1 4620338.4
M71T584_POS 71.04981 584.10574 5590769.4 4019258.4 4622361.3 5713748.7 NA 4103293.4 3282786.9 NA NA
M71T171_POS 71.05000 171.38001 8586093.0 7873459.6 6107291.4 NA NA NA 5297588.4 4229598.6 3717396.9
M71T55_POS 71.05000 54.82500 28372950.8 13215100.9 22123402.7 NA NA NA 16693898.0 10660606.8 9318486.1
M71T73_2_POS 71.05000 73.45341 NA NA NA NA NA NA NA 9900135.8 8432662.7
M71T695_POS 71.08581 695.24347 25403639.4 32821640.3 20149178.5 43752476.2 24791237.3 14759406.0 16755069.3 17831509.4 20968354.2
M71T637_POS 71.08584 636.85745 55106613.1 47002568.1 32840879.9 43793472.2 27024917.9 25225960.6 27225778.7 13263135.5 17025690.8
M71T755_POS 71.08594 755.47156 14277178.7 12373604.9 11265554.1 12074002.4 11551141.8 9757914.4 17063939.4 11192673.3 12069978.8
M71T669_POS 71.08594 669.10716 10521626.7 12270045.0 7878224.7 NA 9955723.1 10398366.5 10012626.6 7765748.1 8829148.3
M71T554_POS 71.08610 554.27277 3792743.1 6573058.5 6349709.7 7255160.3 NA NA 6657487.0 5741862.6 2134070.5
M71T315_POS 71.45836 315.36478 NA 48483607.0 NA NA NA NA 36867104.0 34527667.6 36952272.8
M72T315_POS 71.57037 315.21765 NA 9210592.3 NA NA NA NA 6593722.0 6221264.5 7482215.2
M72T787_POS 71.93003 786.61383 4762186.5 5436506.0 2789644.1 4822881.8 3558428.8 3266833.4 NA NA 2079643.2
M72T776_POS 71.98897 776.25800 57965519.4 54785336.9 44567373.7 57159306.4 43385663.0 34345976.6 41023563.2 27055571.5 31573360.9
M72T680_POS 71.98898 680.09485 51628058.7 22021498.4 NA 31607556.5 14331125.9 NA NA NA 22928579.0
M72T705_POS 71.98897 705.32000 NA NA NA 17309147.2 13883247.2 NA NA NA 14834399.2
M72T631_POS 71.98897 631.12970 NA NA NA 15475246.6 NA NA NA 9896270.8 11962139.5
M72T478_POS 72.04502 477.72300 NA 4044959.0 NA NA 3042764.1 2364623.9 NA NA NA
M72T556_POS 72.06270 555.80219 1284253.7 1283771.6 1182522.8 1268102.1 NA 1258898.3 1246450.4 NA NA
M72T778_POS 72.08160 777.78129 14258903.9 12039619.8 13958118.8 14202518.5 17336638.4 10149111.4 18391088.8 11493049.8 NA
M72T54_POS 72.08165 54.01814 NA NA 235808285.0 NA 184873856.9 163393748.5 260140017.8 284240078.8 284017236.2
M72T38_POS 72.08160 38.48114 27107020.2 50633224.0 NA 47430209.5 NA NA NA NA NA
M73T800_POS 72.93786 800.03516 100052315.0 110078383.4 109471137.1 76887012.4 107185305.7 99307794.8 118635551.4 75806954.5 141157817.9
M73T863_POS 72.93795 862.63208 36119088.8 29809818.8 NA 23220638.3 23303239.9 16435272.4 15487146.8 14917962.0 32070062.6
M73T845_POS 72.93797 845.46481 35056825.8 23507184.5 26415857.8 32962097.8 28507377.5 22159427.1 18083829.4 NA 60796016.5
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Only top 500 features show.

BPC.pdf

Base peak chromatogram.

Default it only shows the samples which are in the group you set in group_for_figure. If you want to show other samples, you can try to do use the below script.

###load data
load("massprocesser_demo_data/POS/Result/intermediate_data/xdata2")
##set threads
if(tinytools::get_os() == "windows") {
  bpparam <-
    BiocParallel::SnowParam(workers = 4,
                            progressbar = TRUE)
} else{
  bpparam <- BiocParallel::MulticoreParam(workers = 4,
                                          progressbar = TRUE)
}
###extract bpc plot object
bpc.plot <- xcms::chromatogram(object = xdata2,
                               aggregationFun = "max",
                               BPPARAM = bpparam)
#> 
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####plot_chromatogram to show the plot
##set the group_for_figure if you want to show specific groups. And set it as "all" if you want to show all samples.
plot <- plot_chromatogram(object = bpc.plot,
                          title = "BPC",
                          group_for_figure = c("Case", "QC"))
plot

plot <- plot_chromatogram(object = bpc.plot,
                          title = "BPC",
                          group_for_figure = c("all"))
plot

##if you want to show specific samples, set the `sample_for_figure` parameter
plot <- plot_chromatogram(object = bpc.plot,
                          title = "BPC",
                          sample_for_figure = c("sample_11", "sample_78"))
plot

##set `interactive` as TRUE to get interactive plot
plot <- plot_chromatogram(object = bpc.plot,
                          title = "BPC",
                          sample_for_figure = c("sample_11", "sample_78"),
                          interactive = TRUE
                          )
plot

TIC.pdf

Total ion peak chromatogram

Default it only shows the samples which are in the group you set in group_for_figure. If you want to show other samples, you can try to do use the below script.

###load data
load("massprocesser_demo_data/POS/Result/intermediate_data/xdata2")
##set threads
if(tinytools::get_os() == "windows") {
  bpparam <-
    BiocParallel::SnowParam(workers = 4,
                            progressbar = TRUE)
} else{
  bpparam <- BiocParallel::MulticoreParam(workers = 4,
                                          progressbar = TRUE)
}
###extract tic plot object
tic.plot <- xcms::chromatogram(object = xdata2,
                               aggregationFun = "sum",
                               BPPARAM = bpparam)
#> 
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####plot_chromatogram to show the plot
##set the group_for_figure if you want to show specific groups. And set it as "all" if you want to show all samples.
plot <- plot_chromatogram(object = tic.plot,
                          title = "TIC",
                          group_for_figure = c("Case", "QC"))
plot

plot <- plot_chromatogram(object = tic.plot,
                          title = "TIC",
                          group_for_figure = c("all"))
plot

##if you want to show specific samples, set the `sample_for_figure` parameter
plot <- plot_chromatogram(object = tic.plot,
                          title = "TIC",
                          sample_for_figure = c("sample_11", "sample_78"))
plot

##set `interactive` as TRUE to get interactive plot
plot <- plot_chromatogram(object = tic.plot,
                          title = "TIC",
                          sample_for_figure = c("sample_11", "sample_78"),
                          interactive = TRUE
                          )
plot

RT correction plot.pdf

RT correction.

Default it only shows the samples which are in the group you set in group_for_figure. If you want to show other samples, you can try to do use the below script.

###load data
load("massprocesser_demo_data/POS/Result/intermediate_data/xdata2")
##set the group_for_figure if you want to show specific groups. And set it as "all" if you want to show all samples.
plot = 
plot_adjusted_rt(object = xdata2, 
                 group_for_figure = c("Case", "QC"))
plot

plot = 
plot_adjusted_rt(object = xdata2, 
                 group_for_figure = "all")
plot

plot = 
plot_adjusted_rt(object = xdata2, 
                sample_for_figure = c("sample_11", "sample_78"))
plot

plot = 
plot_adjusted_rt(object = xdata2, 
                sample_for_figure = "all", 
                interactive = TRUE)
plot

intermediate_data

This is a folder which contains some intermediate data. If you want to re-run the data processing, please delete this folder first.

Session information 

sessionInfo()
#> R Under development (unstable) (2022-01-11 r81473)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur/Monterey 10.16
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats4    stats     graphics  grDevices utils     datasets  methods  
#> [8] base     
#> 
#> other attached packages:
#>  [1] tinytools_0.9.1      massdataset_0.99.1   magrittr_2.0.1      
#>  [4] kableExtra_1.3.4     forcats_0.5.1        stringr_1.4.0       
#>  [7] dplyr_1.0.7          purrr_0.3.4          readr_2.1.1         
#> [10] tidyr_1.1.4          tibble_3.1.6         ggplot2_3.3.5       
#> [13] tidyverse_1.3.1      xcms_3.17.1          MSnbase_2.21.3      
#> [16] ProtGenerics_1.27.2  S4Vectors_0.33.10    mzR_2.29.1          
#> [19] Rcpp_1.0.7           Biobase_2.55.0       BiocGenerics_0.41.2 
#> [22] BiocParallel_1.29.10 massprocesser_0.9.2 
#> 
#> loaded via a namespace (and not attached):
#>   [1] circlize_0.4.14             readxl_1.3.1               
#>   [3] backports_1.4.1             systemfonts_1.0.3          
#>   [5] plyr_1.8.6                  lazyeval_0.2.2             
#>   [7] crosstalk_1.2.0             leaflet_2.0.4.1            
#>   [9] GenomeInfoDb_1.31.1         digest_0.6.29              
#>  [11] yulab.utils_0.0.4           foreach_1.5.1              
#>  [13] htmltools_0.5.2             fansi_1.0.0                
#>  [15] memoise_2.0.1               cluster_2.1.2              
#>  [17] doParallel_1.0.16           openxlsx_4.2.5             
#>  [19] tzdb_0.2.0                  limma_3.51.2               
#>  [21] ComplexHeatmap_2.11.0       modelr_0.1.8               
#>  [23] matrixStats_0.61.0          svglite_2.0.0              
#>  [25] MsFeatures_1.3.0            pkgdown_2.0.1              
#>  [27] colorspace_2.0-2            rvest_1.0.2                
#>  [29] textshaping_0.3.6           haven_2.4.3                
#>  [31] xfun_0.29                   crayon_1.4.2               
#>  [33] RCurl_1.98-1.5              jsonlite_1.7.2             
#>  [35] impute_1.69.0               iterators_1.0.13           
#>  [37] glue_1.6.0                  gtable_0.3.0               
#>  [39] zlibbioc_1.41.0             XVector_0.35.0             
#>  [41] webshot_0.5.2               GetoptLong_1.0.5           
#>  [43] DelayedArray_0.21.2         shape_1.4.6                
#>  [45] DEoptimR_1.0-10             scales_1.1.1               
#>  [47] vsn_3.63.0                  DBI_1.1.2                  
#>  [49] viridisLite_0.4.0           clue_0.3-60                
#>  [51] gridGraphics_0.5-1          preprocessCore_1.57.0      
#>  [53] clisymbols_1.2.0            MsCoreUtils_1.7.1          
#>  [55] htmlwidgets_1.5.4           httr_1.4.2                 
#>  [57] RColorBrewer_1.1-2          ellipsis_0.3.2             
#>  [59] pkgconfig_2.0.3             XML_3.99-0.8               
#>  [61] sass_0.4.0                  dbplyr_2.1.1               
#>  [63] utf8_1.2.2                  ggplotify_0.1.0            
#>  [65] tidyselect_1.1.1            rlang_0.4.12               
#>  [67] munsell_0.5.0               cellranger_1.1.0           
#>  [69] tools_4.2.0                 cachem_1.0.6               
#>  [71] cli_3.1.0                   generics_0.1.1             
#>  [73] broom_0.7.11                evaluate_0.14              
#>  [75] fastmap_1.1.0               mzID_1.33.0                
#>  [77] yaml_2.2.1                  ragg_1.2.1                 
#>  [79] knitr_1.37                  fs_1.5.2                   
#>  [81] zip_2.2.0                   robustbase_0.93-8          
#>  [83] RANN_2.6.1                  ncdf4_1.17                 
#>  [85] pbapply_1.5-0               xml2_1.3.3                 
#>  [87] compiler_4.2.0              rstudioapi_0.13            
#>  [89] plotly_4.10.0               png_0.1-7                  
#>  [91] affyio_1.65.0               reprex_2.0.1               
#>  [93] MassSpecWavelet_1.61.0      bslib_0.3.1                
#>  [95] stringi_1.7.6               desc_1.4.0                 
#>  [97] lattice_0.20-45             Matrix_1.4-0               
#>  [99] ggsci_2.9                   vctrs_0.3.8                
#> [101] pillar_1.6.4                lifecycle_1.0.1            
#> [103] BiocManager_1.30.16         GlobalOptions_0.1.2        
#> [105] jquerylib_0.1.4             MALDIquant_1.21            
#> [107] data.table_1.14.2           bitops_1.0-7               
#> [109] GenomicRanges_1.47.6        R6_2.5.1                   
#> [111] pcaMethods_1.87.0           affy_1.73.0                
#> [113] IRanges_2.29.1              codetools_0.2-18           
#> [115] MASS_7.3-55                 assertthat_0.2.1           
#> [117] SummarizedExperiment_1.25.3 rjson_0.2.21               
#> [119] rprojroot_2.0.2             withr_2.4.3                
#> [121] GenomeInfoDbData_1.2.7      parallel_4.2.0             
#> [123] hms_1.1.1                   grid_4.2.0                 
#> [125] rmarkdown_2.11              MatrixGenerics_1.7.0       
#> [127] lubridate_1.8.0