Type: Package
Title: Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted Analysis and Reactomics Analysis
Version: 0.2.7
Description: Paired mass distance (PMD) analysis proposed in Yu, Olkowicz and Pawliszyn (2018) <doi:10.1016/j.aca.2018.10.062> and PMD based reactomics analysis proposed in Yu and Petrick (2020) <doi:10.1038/s42004-020-00403-z> for gas/liquid chromatography–mass spectrometry (GC/LC-MS) based non-targeted analysis. PMD analysis including GlobalStd algorithm and structure/reaction directed analysis. GlobalStd algorithm could found independent peaks in m/z-retention time profiles based on retention time hierarchical cluster analysis and frequency analysis of paired mass distances within retention time groups. Structure directed analysis could be used to find potential relationship among those independent peaks in different retention time groups based on frequency of paired mass distances. Reactomics analysis could also be performed to build PMD network, assign sources and make biomarker reaction discovery. GUIs for PMD analysis is also included as 'shiny' applications.
URL: https://yufree.github.io/pmd/
BugReports: https://github.com/yufree/pmd/issues
License: GPL-2
Encoding: UTF-8
LazyData: true
Suggests: knitr, shiny, rmarkdown
VignetteBuilder: knitr
Depends: R (≥ 3.5.0)
Imports: RColorBrewer, stats, graphics, utils, igraph, enviGCMS
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2025-01-15 18:31:33 UTC; yufree
Author: Miao YU ORCID iD [aut, cre]
Maintainer: Miao YU <yufreecas@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-15 19:40:05 UTC

mass spectrometry contaminants database for PMD check

Description

mass spectrometry contaminants database for PMD check

Usage

data(MaConDa)

Format

A data frame from doi:10.1093/bioinformatics/bts527 with 308 rows and 5 variables:

id

MaConDa ID

name

contaminants

formula

contaminants fomula

exact_mass

exact mass of contaminants

type_of_contaminant

type of contaminant

Perform correlation directed analysis for peaks list.

Description

Perform correlation directed analysis for peaks list.

Usage

getcda(list, corcutoff = 0.9, rtcutoff = 10, accuracy = 4)

Arguments

list

a list with mzrt profile

corcutoff

cutoff of the correlation coefficient, default NULL

rtcutoff

cutoff of the distances in retention time hierarchical clustering analysis, default 10

accuracy

measured mass or mass to charge ratio in digits, default 4

Value

list with correlation directed analysis results

See Also

getsda,getrda

Examples

data(spmeinvivo)
cluster <- getcorcluster(spmeinvivo)
cbp <- enviGCMS::getfilter(cluster,rowindex = cluster$stdmassindex2)
cda <- getcda(cbp)

Get reaction chain for specific mass to charge ratio

Description

Get reaction chain for specific mass to charge ratio

Usage

getchain(
  list,
  diff,
  mass,
  digits = 2,
  accuracy = 4,
  rtcutoff = 10,
  corcutoff = 0.6,
  ppm = 25
)

Arguments

list

a list with mzrt profile

diff

paired mass distance(s) of interests

mass

a specific mass for known compound or a vector of masses. You could also input formula for certain compounds

digits

mass or mass to charge ratio accuracy for pmd, default 2

accuracy

measured mass or mass to charge ratio in digits, default 4

rtcutoff

cutoff of the distances in retention time hierarchical clustering analysis, default 10

corcutoff

cutoff of the correlation coefficient, default 0.6

ppm

all the peaks within this mass accuracy as seed mass or formula

Value

a list with mzrt profile and reaction chain dataframe

Examples

data(spmeinvivo)
# check metabolites of C18H39NO
pmd <- getchain(spmeinvivo,diff = c(2.02,14.02,15.99),mass = 286.3101)
# remove the retention time for mass only data
spmeinvivo$rt <- NULL
pmd <- getchain(spmeinvivo,diff = c(2.02,14.02,15.99),mass = 286.3101)

Get Pseudo-Spectrum as peaks cluster based on pmd analysis.

Description

Get Pseudo-Spectrum as peaks cluster based on pmd analysis.

Usage

getcluster(list, corcutoff = NULL, accuracy = 4)

Arguments

list

a list from getstd function

corcutoff

cutoff of the correlation coefficient, default NULL

accuracy

measured mass or mass to charge ratio in digits, default 4

Value

list with Pseudo-Spectrum index

See Also

getpaired,getstd,plotstd

Examples

data(spmeinvivo)
re <- getpaired(spmeinvivo)
re <- getstd(re)
cluster <- getcluster(re)

Get Pseudo-Spectrum as peaks cluster based on correlation analysis.

Description

Get Pseudo-Spectrum as peaks cluster based on correlation analysis.

Usage

getcorcluster(list, corcutoff = 0.9, rtcutoff = 10, accuracy = 4)

Arguments

list

a list with peaks intensity

corcutoff

cutoff of the correlation coefficient, default 0.9

rtcutoff

cutoff of the distances in cluster, default 10

accuracy

measured mass or mass to charge ratio in digits, default 4

Value

list with Pseudo-Spectrum index

Examples

data(spmeinvivo)
cluster <- getcorcluster(spmeinvivo)

read in MSP file as list for ms/ms annotation

Description

read in MSP file as list for ms/ms annotation

Usage

getms2pmd(file, digits = 2, icf = 10)

Arguments

file

the path to your MSP file

digits

mass or mass to charge ratio accuracy for pmd, default 2

icf

intensity cutoff, default 10 percentage

Value

list a list with MSP information for MS/MS annotation

read in MSP file as list for EI-MS annotation

Description

read in MSP file as list for EI-MS annotation

Usage

getmspmd(file, digits = 2, icf = 10)

Arguments

file

the path to your MSP file

digits

mass or mass to charge ratio accuracy for pmd, default 0

icf

intensity cutoff, default 10 percentage

Value

list a list with MSP information for EI-MS annotation

Filter ions/peaks based on retention time hierarchical clustering, paired mass distances(PMD) and PMD frequency analysis.

Description

Filter ions/peaks based on retention time hierarchical clustering, paired mass distances(PMD) and PMD frequency analysis.

Usage

getpaired(
  list,
  rtcutoff = 10,
  ng = NULL,
  digits = 2,
  accuracy = 4,
  mdrange = NULL
)

Arguments

list

a list with mzrt profile

rtcutoff

cutoff of the distances in retention time hierarchical clustering analysis, default 10

ng

cutoff of global PMD's retention time group numbers, If ng = NULL, 20 percent of RT cluster will be used as ng, default NULL.

digits

mass or mass to charge ratio accuracy for pmd, default 2

accuracy

measured mass or mass to charge ratio in digits, default 4

mdrange

mass defect range to ignore. Default NULL and c(0.25,0.9) to retain the possible reaction related paired mass

Value

list with tentative isotope, multi-chargers, adducts, and neutral loss peaks' index, retention time clusters.

See Also

getstd,getsda,plotpaired

Examples

data(spmeinvivo)
pmd <- getpaired(spmeinvivo)

Get pmd for specific reaction

Description

Get pmd for specific reaction

Usage

getpmd(list, pmd, rtcutoff = 10, corcutoff = NULL, digits = 2, accuracy = 4)

Arguments

list

a list with mzrt profile

pmd

a specific paired mass distance or a vector of pmds

rtcutoff

cutoff of the distances in retention time hierarchical clustering analysis, default 10

corcutoff

cutoff of the correlation coefficient, default NULL

digits

mass or mass to charge ratio accuracy for pmd, default 2

accuracy

measured mass or mass to charge ratio in digits, default 4

Value

list with paired peaks for specific pmd or pmds.

See Also

getpaired,getstd,getsda,getrda

Examples

data(spmeinvivo)
pmd <- getpmd(spmeinvivo,pmd=15.99)

Get pmd details for specific reaction after the removal of isotopouge.

Description

Get pmd details for specific reaction after the removal of isotopouge.

Usage

getpmddf(mz, group = NULL, pmd = NULL, digits = 2, mdrange = c(0.25, 0.9))

Arguments

mz

a vector of mass to charge ratio.

group

mass to charge ratio group from either retention time or mass spectrometry imaging segmentation.

pmd

a specific paired mass distance or a vector of pmds

digits

mass or mass to charge ratio accuracy for pmd, default 2.

mdrange

mass defect range to ignore. Default c(0.25,0.9) to retain the possible reaction related paired mass.

Value

dataframe with paired peaks for specific pmd or pmds. When group is provided, a column named net will be generated to show if certain pmd will be local(within the same group) or global(across the groups)

See Also

getpaired,getstd,getsda,getrda

Examples

data(spmeinvivo)
pmddf <- getpmddf(spmeinvivo$mz,pmd=15.99)

Link pos mode peak list with neg mode peak list by pmd.

Description

Link pos mode peak list with neg mode peak list by pmd.

Usage

getposneg(pos, neg, pmd = 2.02, digits = 2)

Arguments

pos

a list with mzrt profile collected from positive mode.

neg

a list with mzrt profile collected from negative mode.

pmd

numeric or numeric vector

digits

mass or mass to charge ratio accuracy for pmd, default 2

Value

dataframe with filtered positive and negative peak list

Perform structure/reaction directed analysis for mass only.

Description

Perform structure/reaction directed analysis for mass only.

Usage

getrda(
  mz,
  pmd = NULL,
  freqcutoff = 10,
  digits = 3,
  top = 20,
  formula = NULL,
  mdrange = c(0.25, 0.9),
  verbose = FALSE
)

Arguments

mz

numeric vector for independent mass or mass to charge ratio. Mass to charge ratio from GlobalStd algorithm is suggested. Isomers would be excluded automated

pmd

a specific paired mass distance or a vector of pmds, default NULL

freqcutoff

pmd frequency cutoff for structures or reactions, default 10

digits

mass or mass to charge ratio accuracy for pmd, default 3

top

top n pmd frequency cutoff when the freqcutoff is too small for large data set

formula

vector for formula when you don't have mass or mass to charge ratio data

mdrange

mass defect range to ignore. Default c(0.25,0.9) to retain the possible reaction related paired mass

verbose

logic, if TURE, return will be llist with paired mass distances table. Default FALSE.

Value

logical matrix with row as the same order of mz or formula and column as high frequency pmd group when verbose is FALSE

See Also

getsda

Examples

data(spmeinvivo)
pmd <- getpaired(spmeinvivo)
std <- getstd(pmd)
sda <- getrda(spmeinvivo$mz[std$stdmassindex])
sda <- getrda(spmeinvivo$mz, pmd = c(2.016,15.995,18.011,14.016))

Get quantitative paired peaks list for specific reaction/pmd

Description

Get quantitative paired peaks list for specific reaction/pmd

Usage

getreact(
  list,
  pmd,
  rtcutoff = 10,
  digits = 2,
  accuracy = 4,
  cvcutoff = 30,
  outlier = FALSE,
  method = "static",
  ...
)

Arguments

list

a list with mzrt profile and data

pmd

a specific paired mass distances

rtcutoff

cutoff of the distances in retention time hierarchical clustering analysis, default 10

digits

mass or mass to charge ratio accuracy for pmd, default 2

accuracy

measured mass or mass to charge ratio in digits, default 4

cvcutoff

ratio or intensity cv cutoff for quantitative paired peaks, default 30

outlier

logical, if true, outlier of ratio will be removed, default False.

method

quantification method can be 'static' or 'dynamic'. See details.

...

other parameters for getpmd

Details

PMD based reaction quantification methods have two options: 'static' will only consider the stable mass pairs across samples and such reactions will be limited by the enzyme or other factors than substrates. 'dynamic' will consider the unstable paired masses by normalization the relatively unstable peak with stable peak between paired masses and such reactions will be limited by one or both peaks in the paired masses.

Value

list with quantitative paired peaks.

See Also

getpaired,getstd,getsda,getrda,getpmd,

Examples

data(spmeinvivo)
pmd <- getreact(spmeinvivo,pmd=15.99)

Perform structure/reaction directed analysis for peaks list.

Description

Perform structure/reaction directed analysis for peaks list.

Usage

getsda(
  list,
  rtcutoff = 10,
  corcutoff = NULL,
  digits = 2,
  accuracy = 4,
  freqcutoff = NULL
)

Arguments

list

a list with mzrt profile

rtcutoff

cutoff of the distances in retention time hierarchical clustering analysis, default 10

corcutoff

cutoff of the correlation coefficient, default NULL

digits

mass or mass to charge ratio accuracy for pmd, default 2

accuracy

measured mass or mass to charge ratio in digits, default 4

freqcutoff

pmd frequency cutoff for structures or reactions, default NULL. This cutoff will be found by PMD network analysis when it is NULL.

Value

list with tentative isotope, adducts, and neutral loss peaks' index, retention time clusters.

See Also

getpaired,getstd,plotpaired

Examples

data(spmeinvivo)
pmd <- getpaired(spmeinvivo)
std <- getstd(pmd)
sda <- getsda(std)

Find the independent ions for each retention time hierarchical clustering based on PMD relationship within each retention time cluster and isotope and return the index of the std data for each retention time cluster.

Description

Find the independent ions for each retention time hierarchical clustering based on PMD relationship within each retention time cluster and isotope and return the index of the std data for each retention time cluster.

Usage

getstd(list, corcutoff = NULL, digits = 2, accuracy = 4)

Arguments

list

a list from getpaired function

corcutoff

cutoff of the correlation coefficient, default NULL

digits

mass or mass to charge ratio accuracy for pmd, default 2

accuracy

measured mass or mass to charge ratio in digits, default 4

Value

list with std mass index

See Also

getpaired,getsda,plotstd

Examples

data(spmeinvivo)
pmd <- getpaired(spmeinvivo)
std <- getstd(pmd)

Get multiple injections index for selected retention time

Description

Get multiple injections index for selected retention time

Usage

gettarget(rt, drt = 10, n = 6)

Arguments

rt

retention time vector for peaks in seconds

drt

retention time drift for targeted analysis in seconds, default 10.

n

max ions numbers within retention time drift windows

Value

index for each injection

Examples

data(spmeinvivo)
pmd <- getpaired(spmeinvivo)
std <- getstd(pmd)
index <- gettarget(std$rt[std$stdmassindex])
table(index)

GlobalStd algorithm with structure/reaction directed analysis

Description

GlobalStd algorithm with structure/reaction directed analysis

Usage

globalstd(
  list,
  rtcutoff = 10,
  ng = NULL,
  corcutoff = NULL,
  digits = 2,
  accuracy = 4,
  freqcutoff = NULL,
  mdrange = NULL,
  sda = FALSE
)

Arguments

list

a peaks list with mass to charge, retention time and intensity data

rtcutoff

cutoff of the distances in cluster, default 10

ng

cutoff of global PMD's retention time group numbers, If ng = NULL, 20 percent of RT cluster will be used as ng, default NULL.

corcutoff

cutoff of the correlation coefficient, default NULL

digits

mass or mass to charge ratio accuracy for pmd, default 2

accuracy

measured mass or mass to charge ratio in digits, default 4

freqcutoff

pmd frequency cutoff for structures or reactions, default NULL. This cutoff will be found by PMD network analysis when it is NULL.

mdrange

mass defect range to ignore. Default NULL and c(0.25,0.9) to retain the possible reaction related paired mass

sda

logical, option to perform structure/reaction directed analysis, default FALSE.

Value

list with GlobalStd algorithm processed data.

See Also

getpaired,getstd,getsda,plotstd,plotstdsda,plotstdrt

Examples

data(spmeinvivo)
re <- globalstd(spmeinvivo)

A dataframe containing HMDB with unique accurate mass pmd with three digits frequency larger than 1 and accuracy percentage larger than 0.9.

Description

A dataframe containing HMDB with unique accurate mass pmd with three digits frequency larger than 1 and accuracy percentage larger than 0.9.

Usage

data(hmdb)

Format

A dataframe with atoms numbers of C, H, O, N, P, S

percentage

accuracy of atom numbers prediction

pmd2

pmd with two digits

pmd

pmd with three digits

A dataframe containing reaction related accurate mass pmd and related reaction formula with KEGG ID

Description

A dataframe containing reaction related accurate mass pmd and related reaction formula with KEGG ID

Usage

data(keggrall)

Format

A dataframe with KEGG reaction, their realted pmd and atoms numbers of C, H, O, N, P, S

ID

KEGG reaction ID

pmd

pmd with three digits

A dataframe containing multiple reaction database ID and their related accurate mass pmd and related reactions

Description

A dataframe containing multiple reaction database ID and their related accurate mass pmd and related reactions

Usage

data(omics)

Format

A dataframe with reaction and their realted pmd

KEGG

KEGG reaction ID

RHEA_ID

RHEA_ID

DIRECTION

reaction direction

MASTER_ID

master reaction RHEA ID

ec

ec reaction ID

ecocyc

ecocyc reaction ID

macie

macie reaction ID

metacyc

metacyc reaction ID

reactome

reactome reaction ID

compounds

reaction related compounds

pmd

pmd with two digits

pmd2

pmd with three digits

Compare matrices using PCA similarity factor

Description

Compare matrices using PCA similarity factor

Usage

pcasf(x, y, dim = NULL)

Arguments

x

Matrix with sample in column and features in row

y

Matrix is compared to x.

dim

number of retained dimensions in the comparison. Defaults to all.

Value

Ratio of projected variance to total variance

Author(s)

Edgar Zanella Alvarenga

References

Singhal, A. and Seborg, D. E. (2005), Clustering multivariate time-series data. J. Chemometrics, 19: 427-438. doi: 10.1002/cem.945

Examples

c1 <- matrix(rnorm(16),nrow=4)
c2 <- matrix(rnorm(16),nrow=4)
pcasf(c1, c2)

plot PMD KEGG network for certain compounds and output network average distance and degree

Description

plot PMD KEGG network for certain compounds and output network average distance and degree

Usage

plotcn(formula, name, pmd)

Arguments

formula

Chemical formula

name

Compound name

pmd

specific paired mass distances

Examples

plotcn('C6H12O6','Glucose',c(2.016,14.016,15.995))

Plot the mass pairs and high frequency mass distances

Description

Plot the mass pairs and high frequency mass distances

Usage

plotpaired(list, index = NULL, ...)

Arguments

list

a list from getpaired function

index

index for PMD value

...

other parameters for plot function

See Also

getpaired, globalstd

Examples

data(spmeinvivo)
pmd <- getpaired(spmeinvivo)
plotpaired(pmd)

Plot the retention time group

Description

Plot the retention time group

Usage

plotrtg(list, ...)

Arguments

list

a list from getpaired function

...

other parameters for plot function

See Also

getpaired, globalstd

Examples

data(spmeinvivo)
pmd <- getpaired(spmeinvivo)
plotrtg(pmd)

Plot the specific structure directed analysis(SDA) groups

Description

Plot the specific structure directed analysis(SDA) groups

Usage

plotsda(list, ...)

Arguments

list

a list from getpmd function

...

other parameters for plot function

See Also

getstd, globalstd,plotstd,plotpaired,plotstdrt

Examples

data(spmeinvivo)
re <- getpmd(spmeinvivo,pmd=78.9)
plotsda(re)

Plot the std mass from GlobalStd algorithm

Description

Plot the std mass from GlobalStd algorithm

Usage

plotstd(list)

Arguments

list

a list from getstd function

See Also

getstd, globalstd

Examples

data(spmeinvivo)
pmd <- getpaired(spmeinvivo)
std <- getstd(pmd)
plotstd(std)

Plot the std mass from GlobalStd algorithm in certain retention time groups

Description

Plot the std mass from GlobalStd algorithm in certain retention time groups

Usage

plotstdrt(list, rtcluster, ...)

Arguments

list

a list from getstd function

rtcluster

retention time group index

...

other parameters for plot function

See Also

getstd, globalstd,plotstd,plotpaired,plotstdsda

Examples

data(spmeinvivo)
pmd <- getpaired(spmeinvivo)
std <- getstd(pmd)
plotstdrt(std,rtcluster = 6)

Plot the std mass from GlobalStd algorithm in structure directed analysis(SDA) groups

Description

Plot the std mass from GlobalStd algorithm in structure directed analysis(SDA) groups

Usage

plotstdsda(list, index = NULL, ...)

Arguments

list

a list from getsda function

index

index for PMD value

...

other parameters for plot function

See Also

getstd, globalstd,plotstd,plotpaired,plotstdrt

Examples

data(spmeinvivo)
re <- globalstd(spmeinvivo, sda=TRUE)
plotstdsda(re)

Shiny application for PMD analysis

Description

Shiny application for PMD analysis

Usage

runPMD()

Shiny application for PMD network analysis

Description

Shiny application for PMD network analysis

Usage

runPMDnet()

A dataset containing common Paired mass distances of substructure, ions replacements, and reaction

Description

A dataset containing common Paired mass distances of substructure, ions replacements, and reaction

Usage

data(sda)

Format

A data frame with 94 rows and 4 variables:

PMD

Paired mass distances

origin

potential sources

Ref.

references

mode

positive, negative or both mode to find corresponding PMDs

A peaks list dataset containing 9 samples from 3 fish with triplicates samples for each fish from LC-MS.

Description

A peaks list dataset containing 9 samples from 3 fish with triplicates samples for each fish from LC-MS.

Usage

data(spmeinvivo)

Format

A list with 4 variables from 1459 LC-MS peaks:

mz

mass to charge ratios

rt

retention time

data

intensity matrix

group

group information