Author: Miao Yu
Date: 2025-01-15

# Paired Mass Distance(PMD) analysis for GC/LC-MS based non-targeted analysis

#### Miao Yu

#### 2025-01-15

## Introduction of Paired Mass Distance analysis

`pmd` package use Paired Mass Distance (PMD) relationship to analysis the GC/LC-MS based non-targeted data. PMD means the distance between two masses or mass to charge ratios. In mass spectrometry, PMD would keep the same value between two masses and two mass to charge ratios(m/z). There are two kinds of PMD involved in this package: PMD from the same compound and PMD from different compounds. In GC/LC-MS or XCMS based non-targeted data analysis, peaks could be separated by chronograph and same compound means ions from similar retention times or ions co-eluted by certain column.

### PMD from the same compound

For MS1 full scan data, we could build retention time(RT) bins to assign peaks into different RT groups by retention time hierarchical clustering analysis. For each RT group, the peaks should come from same compounds or co-elutes. If certain PMD appeared in multiple RT groups, it would be related to the relationship about adducts, neutral loss, isotopologues or common fragments ions.

### PMD from different compounds

The peaks from different retention time groups would like to be different compounds separated by chronograph. The PMD would reflect the relationship about homologous series or chemical reactions.

GlobalStd algorithm use the PMD within same RT group to find independent peaks among certain data set. Then, structure/reaction directed analysis use PMD from different RT groups to screen important compounds or reactions.

## Data format

The input data should be a `list` object with at least two elements from a peaks list:

- mass to charge ratio with name of `mz`, high resolution mass spectrometry is required
- retention time with name of `rt`

However, I suggested to add intensity and group information to the list for validation of PMD analysis.

In this package, a data set from in vivo solid phase micro-extraction(SPME) was attached. This data set contain 9 samples from 3 fish with triplicates samples for each fish. Here is the data structure:

    library(pmd)
    data("spmeinvivo")
    str(spmeinvivo)
    #> List of 4
    #>  $ data : num [1:1459, 1:9] 1095 10439 10154 2797 90211 ...
    #>   ..- attr(*, "dimnames")=List of 2
    #>   .. ..$ : chr [1:1459] "100.1/170" "100.5/86" "101/85" "103.1/348" ...
    #>   .. ..$ : chr [1:9] "1405_Fish1_F1" "1405_Fish1_F2" "1405_Fish1_F3" "1405_Fish2_F1" ...
    #>  $ group:'data.frame':   9 obs. of  2 variables:
    #>   ..$ sample_name : chr [1:9] "1405_Fish1_F1" "1405_Fish1_F2" "1405_Fish1_F3" "1405_Fish2_F1" ...
    #>   ..$ sample_group: chr [1:9] "fish1" "fish1" "fish1" "fish2" ...
    #>  $ mz   : num [1:1459] 100 101 101 103 104 ...
    #>  $ rt   : num [1:1459] 170.2 86.3 84.9 348.1 48.8 ...

You could build this `list` or `mzrt` object from the `xcms` objects via `enviGCMS` package. When you have a `xcmsSet` object or `XCMSnExp` object named `xset`, you could use `enviGCMS::getmzrt(xset)` to get such list. Of course you could build such list by yourself.

## GlobalStd algorithm

GlobalStd algorithm try to find independent peaks among certain peaks list. The first step is retention time hierarchical clustering analysis. The second step is to find the relationship among adducts, neutral loss, isotopologues and common fragments ions. The third step is to screen the independent peaks.

Here is a workflow for this algorithm:

    knitr::include_graphics('https://yufree.github.io/presentation/figure/GlobalStd.png')

### STEP1: Retention time hierarchical clustering

    pmd <- getpaired(spmeinvivo)
    #> 75 retention time cluster found.
    #> 369 paired masses found
    #> 5 unique within RT clusters high frequency PMD(s) used for further investigation.
    #> The unique within RT clusters high frequency PMD(s) is(are)  28.03 21.98 44.03 17.03 18.01.
    #> 719 isotopologue(s) related paired mass found.
    #> 492 multi-charger(s) related paired mass found.
    plotrtg(pmd)

This plot would show the distribution of RT groups. The `rtcutoff` in function `getpaired` could be used to set the cutoff of the distances in retention time hierarchical clustering analysis. Retention time cluster cutoff should fit the peak picking algorithm. For HPLC, 10 is suggested and 5 could be used for UPLC.

Global PMD’s retention time group numbers should be around 20 percent of the retention time cluster numbers. For example, if you find 100 retention time clusters, I suggested you use 20 as the cutoff of empirical global PMD’s retention time group numbers. If you don’t specifically assign a value to `ng`, the algorithm will select such recommendation by default setting.

Take care of the retention time cluster with lots of peaks. In this case, such cluster could be co-eluted compounds on certain column. It would be wise to trim the retention time window for high quality peaks. Another important hint is that pre-filter your peak list by black samples or other quality control samples. Otherwise the running time would be long and lots of pmd relationship would be just from noise.

### STEP2: Relationship among adducts, neutral loss, isotopologues and common fragments ions

The `ng` in function `getpaired` could be used to set cutoff of global PMD’s retention time group numbers. If `ng` is 10, at least 10 of the retention time groups should contain the shown PMD relationship. You could use `plotpaired` to show the distribution.

    plotpaired(pmd)

You could also show the distribution of PMD relationship by index:

    # show the unique PMD found by getpaired function
    for(i in 1:length(unique(pmd$paired$diff2))){
            diff <- unique(pmd$paired$diff2)[i]
            index <- pmd$paired$diff2 == diff
            plotpaired(pmd,index)
    }

This is an easy way to find potential adducts of the data by high frequency PMD from the same compound. For example, 21.98 Da could be the mass distances between \([M+H]^+\) and \([M+Na]^+\). In this case, user could find the potential adducts or neutral loss even when they have no preferred adducts list. If one adduct exist in certain analytical system, the high frequency PMD will reveal such relationship. The high frequency PMD list could also be used to check the fragmental pattern of in-source reactions as long as such patterns are popular among all collected ions.

### STEP3: Screen the independent peaks

You could use `getstd` function to get the independent peaks. Independent peaks mean the peaks list removing the redundant peaks such as adducts, neutral loss, isotopologues and comment fragments ions found by PMD analysis in STEP2. Ideally, those peaks could be molecular ions while they might still contain redundant peaks.

    std <- getstd(pmd)
    #> 8 retention group(s) have single peaks. 14 23 32 33 54 55 56 75
    #> 11 group(s) with multiple peaks while no isotope/paired relationship 4 5 7 8 11 41 42 49 68 72 73
    #> 9 group(s) with multiple peaks with isotope without paired relationship 2 9 22 26 52 62 64 66 70
    #> 4 group(s) with paired relationship without isotope 1 10 15 18
    #> 43 group(s) with paired relationship and isotope 3 6 12 13 16 17 19 20 21 24 25 27 28 29 30 31 34 35 36 37 38 39 40 43 44 45 46 47 48 50 51 53 57 58 59 60 61 63 65 67 69 71 74
    #> 291 std mass found.

Here you could plot the peaks by `plotstd` function to show the distribution of independent peaks:

    plotstd(std)

You could also plot the peaks distribution by assign a retention time group via `plotstdrt`:

    par(mfrow = c(2,3))
    plotstdrt(std,rtcluster = 23,main = 'Retention time group 23')
    plotstdrt(std,rtcluster = 9,main = 'Retention time group 9')
    plotstdrt(std,rtcluster = 18,main = 'Retention time group 18')
    plotstdrt(std,rtcluster = 67,main = 'Retention time group 67')
    plotstdrt(std,rtcluster = 49,main = 'Retention time group 49')
    plotstdrt(std,rtcluster = 6,main = 'Retention time group 6')

### Extra filter with correlation coefficient cutoff

Original GlobalStd algorithm only use mass to charge ratio and retention time of peaks to select independent peaks. However, if intensity data across samples are available, correlation coefficient of paired ions could be used to further filter the random noise in high frequency PMDs. You could set up cutoff of Pearson Correlation Coefficient between peaks to refine the peaks selected by GlobalStd within same retention time groups. In this case, the numbers of selected independent peaks will be further reduced. When you use this parameter, make sure the intensity data are from real samples instead of blank samples, which will affect the calculation of correlation coefficient.

    std2 <- getstd(pmd,corcutoff = 0.9)
    #> 8 retention group(s) have single peaks. 14 23 32 33 54 55 56 75
    #> 23 group(s) with multiple peaks while no isotope/paired relationship 2 4 5 7 8 10 11 15 18 26 35 39 41 42 49 50 59 62 68 69 70 72 73
    #> 14 group(s) with multiple peaks with isotope without paired relationship 9 12 22 24 27 28 34 51 52 57 60 64 66 71
    #> 3 group(s) with paired relationship without isotope 1 53 74
    #> 27 group(s) with paired relationship and isotope 3 6 13 16 17 19 20 21 25 29 30 31 36 37 38 40 43 44 45 46 47 48 58 61 63 65 67
    #> 120 std mass found.

## Validation by principal components analysis(PCA)

You need to check the GlobalStd algorithm’s results by principal components analysis(PCA). If we removed too much peaks containing information, the score plot of reduced data set would show great changes.

    library(enviGCMS)
    par(mfrow = c(2,2),mar = c(4,4,2,1)+0.1)
    plotpca(std$data,lv = as.numeric(as.factor(std$group$sample_group)),main = "all peaks")
    plotpca(std$data[std$stdmassindex,],lv = as.numeric(as.factor(std$group$sample_group)),main = paste(sum(std$stdmassindex),"independent peaks"))
    plotpca(std2$data[std2$stdmassindex,],lv = as.numeric(as.factor(std$group$sample_group)),main = paste(sum(std2$stdmassindex),"reduced independent peaks"))

You might find original GlobalStd algorithm show a similar PCA score plot with original data while GlobalStd algorithm considering intensity data seems change the profile. The major reason is that correlation coefficient option in the algorithm will remove the paired ions without strong correlation. It will be aggressive to remove low intensity peaks, which are vulnerable by baseline noise. However, such options would be helpful if you only concern high quality peaks for following analysis. Otherwise, original GlobalStd will keep the most information for explorer purpose.

## Comparison with other pseudo spectra extraction method

GlobalStd algorithm in `pmd` package could be treated as a method to extract pseudo spectra. You could use `getcluster` to get peaks groups information for all GlobalStd peaks. This function would consider the merge of GlobalStd peaks when certain peak is involved in multiple clusters. Then you could choose export peaks with the highest intensities or base peaks in each GlobalStd merged peaks groups. Meanwhile, you could also include the correlation coefficient cutoff to further improve the data quality.

    stdcluster <- getcluster(std)
    # extract pseudospectra for std peak 71
    idx <- unique(stdcluster$cluster$largei[stdcluster$cluster$i==71])
    plot(stdcluster$cluster$mz[stdcluster$cluster$largei==idx],stdcluster$cluster$ins[stdcluster$cluster$largei==idx],type = 'h',xlab = 'm/z',ylab = 'intensity',main = 'pseudo spectra for GlobalStd peak 71')

    # export peaks with the highest intensities in each GlobalStd peaks groups.
    data <- stdcluster$data[stdcluster$stdmassindex2,]
    # considering the correlation coefficient cutoff
    stdcluster2 <- getcluster(std, corcutoff = 0.9)
    # considering the correlation coefficient cutoff for both psedospectra extraction and GlobalStd algorithm
    stdcluster3 <- getcluster(std2, corcutoff = 0.9)

We supplied `getcorcluster` to find peaks groups by correlation analysis only. The base peaks of correlation cluster were selected to stand for the compounds.

    corcluster <- getcorcluster(spmeinvivo)
    #> 75 retention time cluster found.
    # extract pseudospectra 1@46
    peak <- corcluster$cluster[corcluster$cluster$largei == '1@46',]
    plot(peak$ins~peak$mz,type = 'h',xlab = 'm/z',ylab = 'intensity',main = 'pseudo spectra for correlation cluster')

Then we could compare the compare reduced result using PCA similarity factor. A good peak selection algorithm could show a high PCA similarity factor compared with original data set while retain the minimized number of peaks.

    par(mfrow = c(3,3),mar = c(4,4,2,1)+0.1)
    plotpca(std$data[std$stdmassindex,],lv = as.numeric(as.factor(std$group$sample_group)),main = paste(sum(std$stdmassindex),"independent peaks"))
    plotpca(std$data[stdcluster$stdmassindex2,],lv = as.numeric(as.factor(std$group$sample_group)),main = paste(sum(stdcluster$stdmassindex2),"independent base peaks"))
    plotpca(std$data[stdcluster2$stdmassindex2,],lv = as.numeric(as.factor(std$group$sample_group)),main = paste(sum(stdcluster2$stdmassindex2),"independent reduced base peaks"))
    plotpca(std$data[corcluster$stdmassindex,],lv = as.numeric(as.factor(std$group$sample_group)),main = paste(sum(corcluster$stdmassindex),"peaks without correlationship"))
    plotpca(std$data[corcluster$stdmassindex2,],lv = as.numeric(as.factor(std$group$sample_group)),main = paste(sum(corcluster$stdmassindex2),"base peaks without correlationship"))
    plotpca(std$data,lv = as.numeric(as.factor(std$group$sample_group)),main = paste(nrow(std$data),"all peaks"))
    plotpca(std$data[stdcluster3$stdmassindex2,],lv = as.numeric(as.factor(std$group$sample_group)),main = paste(sum(stdcluster3$stdmassindex2),"reduced independent base peaks"))
    pcasf(std$data, std$data[std$stdmassindex,])
    #>     pcasf
    #> 0.9993497
    pcasf(std$data, std$data[stdcluster$stdmassindex2,])
    #>     pcasf
    #> 0.9993578
    pcasf(std$data, std$data[stdcluster2$stdmassindex2,])
    #>    pcasf
    #> 0.999346
    pcasf(std$data, std$data[corcluster$stdmassindex,])
    #>     pcasf
    #> 0.9471586
    pcasf(std$data, std$data[corcluster$stdmassindex2,])
    #>     pcasf
    #> 0.9497193
    pcasf(std$data, std$data[stdcluster3$stdmassindex2,])
    #>    pcasf
    #> 0.713527

In this case, five peaks selection algorithms are fine to stand for the original peaks with PCA similarity score larger than 0.9. However, the independent base peaks retain the most information with relative low numbers of peaks.

## Structure/Reaction directed analysis

`getsda` function could be used to perform Structure/reaction directed analysis. The cutoff of frequency is automate found by PMD network analysis with the largest mean distance of all nodes.

    sda <- getsda(std)
    #> PMD frequency cutoff is 6 by PMD network analysis with largest network average distance 6.67 .
    #> 53 groups were found as high frequency PMD group.
    #> 0 was found as high frequency PMD.
    #> 1.98 was found as high frequency PMD.
    #> 2.01 was found as high frequency PMD.
    #> 2.02 was found as high frequency PMD.
    #> 6.97 was found as high frequency PMD.
    #> 11.96 was found as high frequency PMD.
    #> 12 was found as high frequency PMD.
    #> 13.98 was found as high frequency PMD.
    #> 14.02 was found as high frequency PMD.
    #> 14.05 was found as high frequency PMD.
    #> 15.99 was found as high frequency PMD.
    #> 16.03 was found as high frequency PMD.
    #> 19.04 was found as high frequency PMD.
    #> 28.03 was found as high frequency PMD.
    #> 30.05 was found as high frequency PMD.
    #> 31.99 was found as high frequency PMD.
    #> 33.02 was found as high frequency PMD.
    #> 37.02 was found as high frequency PMD.
    #> 42.05 was found as high frequency PMD.
    #> 48.04 was found as high frequency PMD.
    #> 48.98 was found as high frequency PMD.
    #> 49.02 was found as high frequency PMD.
    #> 54.05 was found as high frequency PMD.
    #> 56.06 was found as high frequency PMD.
    #> 56.1 was found as high frequency PMD.
    #> 58.04 was found as high frequency PMD.
    #> 58.08 was found as high frequency PMD.
    #> 58.11 was found as high frequency PMD.
    #> 63.96 was found as high frequency PMD.
    #> 66.05 was found as high frequency PMD.
    #> 68.06 was found as high frequency PMD.
    #> 70.04 was found as high frequency PMD.
    #> 70.08 was found as high frequency PMD.
    #> 74.02 was found as high frequency PMD.
    #> 80.03 was found as high frequency PMD.
    #> 82.08 was found as high frequency PMD.
    #> 88.05 was found as high frequency PMD.
    #> 91.1 was found as high frequency PMD.
    #> 93.12 was found as high frequency PMD.
    #> 94.1 was found as high frequency PMD.
    #> 96.09 was found as high frequency PMD.
    #> 101.05 was found as high frequency PMD.
    #> 108.13 was found as high frequency PMD.
    #> 110.11 was found as high frequency PMD.
    #> 112.16 was found as high frequency PMD.
    #> 116.08 was found as high frequency PMD.
    #> 122.15 was found as high frequency PMD.
    #> 124.16 was found as high frequency PMD.
    #> 126.14 was found as high frequency PMD.
    #> 144.18 was found as high frequency PMD.
    #> 148.04 was found as high frequency PMD.
    #> 150.2 was found as high frequency PMD.
    #> 173.18 was found as high frequency PMD.

Such largest mean distance of all nodes is calculated for top 1 to 100 (if possible) high frequency PMDs. Here is a demo for the network generation process.

    library(igraph)
    #>
    #> Attaching package: 'igraph'
    #> The following objects are masked from 'package:stats':
    #>
    #>     decompose, spectrum
    #> The following object is masked from 'package:base':
    #>
    #>     union
    cdf <- sda$sda
    # get the PMDs and frequency
    pmds <- as.numeric(names(sort(table(cdf$diff2),decreasing = T)))
    freq <- sort(table(cdf$diff2),decreasing = T)
    # filter the frequency larger than 10 for demo
    pmds <- pmds[freq>10]
    cdf <- sda$sda[sda$sda$diff2 %in% pmds,]
    g <- igraph::graph_from_data_frame(cdf,directed = F)
    l <- igraph::layout_with_fr(g)
    for(i in 1:length(pmds)){
      g2 <- igraph::delete_edges(g,which(E(g)$diff2%in%pmds[1:i]))
      plot(g2,edge.width=1,vertex.label="",vertex.size=1,layout=l,main=paste('Top',length(pmds)-i,'high frequency PMDs'))
    }

Here we could find more and more compounds will be connected with more high frequency PMDs. Meanwhile, the mean distance of all network nodes will increase. However, some PMDs are generated by random combination of ions. In this case, if we included those PMDs for the network, the mean distance of all network nodes will decrease. Here, the largest mean distance means no more information will be found for certain data set and such value is used as the cutoff for high frequency PMDs selection.

You could use `plotstdsda` to show the distribution of the selected paired peaks.

    plotstdsda(sda)

You could also use index to show the distribution of certain PMDs.

    par(mfrow = c(1,3),mar = c(4,4,2,1)+0.1)
    plotstdsda(sda,sda$sda$diff2 == 2.02)
    plotstdsda(sda,sda$sda$diff2 == 28.03)
    plotstdsda(sda,sda$sda$diff2 == 58.04)

Structure/reaction directed analysis could be directly performed on all the peaks, which is slow to process:

    sdaall <- getsda(spmeinvivo)
    #> PMD frequency cutoff is 104 by PMD network analysis with largest network average distance 14.06 .
    #> 6 groups were found as high frequency PMD group.
    #> 0 was found as high frequency PMD.
    #> 2.02 was found as high frequency PMD.
    #> 28.03 was found as high frequency PMD.
    #> 31.01 was found as high frequency PMD.
    #> 58.04 was found as high frequency PMD.
    #> 116.08 was found as high frequency PMD.
    par(mfrow = c(1,3),mar = c(4,4,2,1)+0.1)
    plotstdsda(sdaall,sdaall$sda$diff2 == 2.02)
    plotstdsda(sdaall,sdaall$sda$diff2 == 28.03)
    plotstdsda(sdaall,sdaall$sda$diff2 == 58.04)

### Extra filter with correlation coefficient cutoff

Structure/Reaction directed analysis could also use correlation to restrict the paired ions. However, similar to GlobalStd algorithm, such cutoff will remove low intensity data. Researcher should have a clear idea to use this cutoff.

    sda2 <- getsda(std, corcutoff = 0.9)
    #> PMD frequency cutoff is 6 by PMD network analysis with largest network average distance 6.67 .
    #> 41 groups were found as high frequency PMD group.
    #> 0 was found as high frequency PMD.
    #> 1.98 was found as high frequency PMD.
    #> 2.01 was found as high frequency PMD.
    #> 2.02 was found as high frequency PMD.
    #> 11.96 was found as high frequency PMD.
    #> 12 was found as high frequency PMD.
    #> 13.98 was found as high frequency PMD.
    #> 14.02 was found as high frequency PMD.
    #> 14.05 was found as high frequency PMD.
    #> 15.99 was found as high frequency PMD.
    #> 16.03 was found as high frequency PMD.
    #> 19.04 was found as high frequency PMD.
    #> 28.03 was found as high frequency PMD.
    #> 30.05 was found as high frequency PMD.
    #> 31.99 was found as high frequency PMD.
    #> 33.02 was found as high frequency PMD.
    #> 42.05 was found as high frequency PMD.
    #> 48.98 was found as high frequency PMD.
    #> 49.02 was found as high frequency PMD.
    #> 54.05 was found as high frequency PMD.
    #> 56.06 was found as high frequency PMD.
    #> 58.04 was found as high frequency PMD.
    #> 58.08 was found as high frequency PMD.
    #> 63.96 was found as high frequency PMD.
    #> 66.05 was found as high frequency PMD.
    #> 68.06 was found as high frequency PMD.
    #> 70.08 was found as high frequency PMD.
    #> 74.02 was found as high frequency PMD.
    #> 80.03 was found as high frequency PMD.
    #> 82.08 was found as high frequency PMD.
    #> 88.05 was found as high frequency PMD.
    #> 93.12 was found as high frequency PMD.
    #> 94.1 was found as high frequency PMD.
    #> 96.09 was found as high frequency PMD.
    #> 108.13 was found as high frequency PMD.
    #> 110.11 was found as high frequency PMD.
    #> 112.16 was found as high frequency PMD.
    #> 116.08 was found as high frequency PMD.
    #> 122.15 was found as high frequency PMD.
    #> 124.16 was found as high frequency PMD.
    #> 126.14 was found as high frequency PMD.
    plotstdsda(sda2)

### Structure/reaction directed analysis for peaks/compounds only data

When you only have data of peaks without retention time or compounds list, structure/reaction directed analysis could also be done by `getrda` function.

    sda <- getrda(spmeinvivo$mz)
    #> 164462 pmd found.
    #> 20 pmd used.
    # check high frequency pmd
    colnames(sda)
    #>  [1] "0"       "1.001"   "1.002"   "1.003"   "1.004"   "2.015"   "2.016"
    #>  [8] "14.015"  "17.026"  "18.011"  "21.982"  "28.031"  "28.032"  "44.026"
    #> [15] "67.987"  "67.988"  "88.052"  "116.192" "135.974" "135.975"
    # get certain pmd related m/z
    idx <- sda[,'2.016']
    # show the m/z
    spmeinvivo$mz[idx]
    #>  [1] 118.0651 118.0652 120.0812 159.1575 162.0552 170.0330 170.0932 170.1541
    #>  [9] 174.1363 174.9917 175.0873 176.0305 176.0418 181.9872 184.1695 188.6484
    #> [17] 192.1487 192.1604 226.9522 226.9523 228.1969 228.1973 259.1148 261.1317
    #> [25] 270.3185 271.3217 272.3230 272.3234 273.8902 274.8744 284.2955 285.3002
    #> [33] 285.3002 286.3101 286.3101 291.0712 293.1755 294.9392 296.2961 304.3081
    #> [41] 305.2480 305.3118 308.0889 308.2953 308.2954 309.1672 309.2046 315.1781
    #> [49] 317.9344 319.3005 319.3002 319.9302 320.3041 320.3322 321.3165 322.3185
    #> [57] 323.3221 324.3266 325.3294 327.2022 327.3449 329.0052 331.0031 350.3426
    #> [65] 352.3214 352.3215 353.3244 354.3365 355.0696 359.2410 361.2353 372.3197
    #> [73] 375.3066 383.2804 383.3723 384.3350 385.2753 385.3480 387.2851 397.1907
    #> [81] 399.3274 400.9174 401.3420 403.2859 432.8860 433.2781 445.8289 447.1173
    #> [89] 451.3633 462.8615 522.3557 524.1178 525.9831 526.4841 705.7223 708.8218
    #> [97] 976.3139 976.8122 982.7763

## Wrap function for GlobalStd algorithm

`globalstd` function is a wrap function to process GlobalStd algorithm and structure/reaction directed analysis in one line. All the plot function could be directly used on the `list` objects from `globalstd` function. If you want to perform structure/reaction directed analysis, set the `sda=T` in the `globalstd` function.

    result <- globalstd(spmeinvivo, sda=FALSE)
    #> 75 retention time cluster found.
    #> 369 paired masses found
    #> 5 unique within RT clusters high frequency PMD(s) used for further investigation.
    #> The unique within RT clusters high frequency PMD(s) is(are)  28.03 21.98 44.03 17.03 18.01.
    #> 719 isotopologue(s) related paired mass found.
    #> 492 multi-charger(s) related paired mass found.
    #> 8 retention group(s) have single peaks. 14 23 32 33 54 55 56 75
    #> 11 group(s) with multiple peaks while no isotope/paired relationship 4 5 7 8 11 41 42 49 68 72 73
    #> 9 group(s) with multiple peaks with isotope without paired relationship 2 9 22 26 52 62 64 66 70
    #> 4 group(s) with paired relationship without isotope 1 10 15 18
    #> 43 group(s) with paired relationship and isotope 3 6 12 13 16 17 19 20 21 24 25 27 28 29 30 31 34 35 36 37 38 39 40 43 44 45 46 47 48 50 51 53 57 58 59 60 61 63 65 67 69 71 74
    #> 291 std mass found.

## Use independent peaks for MS/MS validation (PMDDA)

Independent peaks are supposing generated from different compounds. We could use those peaks for MS/MS analysis instead of DIA or DDA. Here we need multiple injections for one sample since it might be impossible to get all ions’ fragment ions in one injection with good sensitivity. You could use `gettarget` to generate the index for the injections and output the peaks for each run.

    # you need retention time for independent peaks
    index <- gettarget(std$rt[std$stdmassindex])
    #> You need 10 injections!
    # output the ions for each injection
    table(index)
    #> index
    #>  1  2  3  4  5  6  7  8  9 10
    #> 24 41 25 37 17 28 26 34 29 30
    # show the ions for the first injection
    std$mz[index==1]
    #>   [1] 112.0183 134.1185 137.9879 140.0600 149.0236 149.9530 158.9617 161.0600
    #>   [9] 161.0967 165.0787 170.1541 175.0873 181.1597 186.1854 198.1854 206.0898
    #>  [17] 214.9181 226.1822 244.0288 245.0787 252.0721 255.9443 258.8998 259.1148
    #>  [25] 265.4216 270.3185 270.3184 271.3217 273.1854 273.8902 282.9806 283.2838
    #>  [33] 283.3000 285.3002 293.1755 299.1113 304.9038 307.9421 315.1781 320.3040
    #>  [41] 328.0132 335.1258 352.3214 353.3244 359.0292 364.3575 365.3196 366.3006
    #>  [49] 372.3197 383.3313 386.3523 389.2529 394.4045 394.8754 404.2360 405.2616
    #>  [57] 406.2651 410.2585 416.8073 421.2521 429.3192 431.0687 445.2767 447.3469
    #>  [65] 460.3112 472.9023 507.3409 512.4158 522.1371 528.4989 533.9698 534.9708
    #>  [73] 541.3942 557.0950 560.3877 562.1811 566.8886 567.1783 580.1907 581.1925
    #>  [81] 581.3659 586.4524 599.4366 607.4028 616.4645 622.4229 643.4632 651.8520
    #>  [89] 665.4664 675.6790 704.6384 707.6675 712.8208 723.4865 730.6517 731.7391
    #>  [97] 744.8477 765.5253 771.8544 773.3274 779.3404 779.5153 794.6305 795.6669
    #> [105] 797.5461 803.5434 815.4180 831.6037 839.3409 845.5232 870.7857 873.4237
    #> [113] 884.7221 900.8085 946.7398 949.3083 973.4945 982.7763 984.7703 985.7859
    std$rt[index==1]
    #>   [1]   85.3860  355.8470  165.4680  511.0515  583.7690 1079.6400  154.9830
    #>   [8]  620.6270  645.5280  511.3690  638.9930  511.2940  615.0530  501.3300
    #>  [15]  415.9985  583.3410   76.9220  416.1050  212.6665  511.0800  678.3130
    #>  [22]   76.7060  217.2010  144.0380  145.8285  838.9070  465.0070  744.1460
    #>  [29]  581.1950  145.9680  146.0980  595.2325  679.6010  716.7800  553.5540
    #>  [36]  447.6060  145.4960  146.3215  401.2135  622.7700  509.1510  581.4100
    #>  [43]  582.4820  582.4830  717.0520  616.7710  656.2235  561.9110  659.8815
    #>  [50]  656.0300  644.4580  383.1060  682.3135  217.1550  601.4480  547.3380
    #>  [57]  547.4460  633.9130  503.1515  634.3425  557.1970  762.3630  421.8915
    #>  [64]  711.4240  169.9670  213.7270  422.9630  550.3385  762.5750  643.4925
    #>  [71]  639.2075  639.0995  628.3425  762.5765  533.3660  762.3630  213.7720
    #>  [78]  762.3630  762.3610  762.4690  533.7950  439.2500  454.9350  434.9630
    #>  [85]  454.9350  455.1500  449.3200  215.7110  528.0080  638.8870  639.0980
    #>  [92]  594.4830  214.7985  463.1855  594.6980  659.2430  214.3560  773.7190
    #>  [99]  213.7720  370.5620  214.9615  519.6690  613.5560  643.3860  519.7585
    #> [106]  665.0290  490.4010  503.6870  213.6370  517.5090  216.5120  471.3075
    #> [113]  632.0920  213.7720  800.2900  214.8495  500.9015  640.2780  215.0690
    #> [120]  215.0680

## Shiny application

An interactive document has been included in this package to perform PMD analysis. You need to prepare a csv file with m/z and retention time of peaks. Such csv file could be generated by run `enviGCMS::getcsv()` on the `list` object from `enviGCMS::getmzrt(xset)` function. The `xset` should be `XCMSnExp` object or `xcmsSet` object. You could also generate the csv file by `enviGCMS::getmzrt(xset,name = 'test')`. You will find the csv file in the working dictionary named `test.csv`.

Then you could run `runPMD()` to start the Graphical user interface(GUI) for GlobalStd algorithm and structure/reaction directed analysis.

## Conclusion

`pmd` package could be used to reduce the redundancy peaks for GC/LC-MS based research and perform structure/reaction directed analysis to screen known and unknown important compounds or reactions.