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M0000.Rmd
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---
title: "Molecule Details"
output:
html_document:
toc: true
toc_float: true
params:
metabolite: "M0000"
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE)
```
```{r}
library(plotly)
library(Spectra)
library(xcms)
library(MsCoreUtils)
```
`r paste0(m[i], ": ", cmps$name[cmps$compound_id == m[i]])`
`r paste("Formula:", cmps$formula[cmps$compound_id == m[i]])`
`r paste("Exact mass:", round(cmps$exactmass[cmps$compound_id == m[i]], 5))`
# Average Spectra
```{r comment=NA, results='asis'}
tmp_sps <- sps[sps$compound_id == m[i]]
tmp_sps <- tmp_sps[tmp_sps$raw_spectra == 0]
a <- unique(tmp_sps$adduct)
k <- 1
tmp_sps2 <- tmp_sps[tmp_sps$adduct == a[k]]
cat(paste(tmp_sps2$adduct, round(precursorMz(tmp_sps2), 5)))
tmp_dt <- data.frame(
mz = unlist(mz(tmp_sps2)),
int = unlist(intensity(tmp_sps2))
)
tmp_dt <- tmp_dt[tmp_dt$mz <= precursorMz(tmp_sps2), ]
tmp_dt <- rbind(tmp_dt, c(precursorMz(tmp_sps2), 0))
tmp_dt$mz1 <- round(tmp_dt$mz, 4)
tmp_dt$mz <- tmp_dt$mz
tmp_dt$nl <- precursorMz(tmp_sps2) - tmp_dt$mz
tmp_dt$ann <- NA
tmp_nl <- nl[nl$polarity == tmp_sps2$polarity, ]
tmp_ions <- ions[ions$polarity == tmp_sps2$polarity,]
if(m[i] %in% c("M0004", "M0005")){
tmp_ions <- tmp_ions[!grepl("Leu", tmp_ions$name),]
} else if(m[i] == "M0007"){ # Phenylalanine
tmp_ions <- tmp_ions[!grepl("Phe", tmp_ions$name),]
} else if(m[i] == "M0009"){
tmp_ions <- tmp_ions[!grepl("Val", tmp_ions$name),]
}
for(j in seq(nrow(tmp_dt))){
idx <- which(between(tmp_nl$mass, tmp_dt$nl[j] + 0.01 * c(-1, 1)))
if(length(idx) > 0){
tmp_dt$ann[j] <- paste(tmp_nl$name[idx], collapse = "-")
}
idx <- which(between(tmp_ions$mass, tmp_dt$mz[j] + 0.01 * c(-1, 1)))
if(length(idx) > 0){
tmp_dt$ann[j] <- paste(tmp_ions$name[idx], collapse = "-")
}
idx <- which(between(precursorMz(tmp_sps2), tmp_dt$mz[j] + 0.01 * c(-1, 1)))
if(length(idx) > 0){
tmp_dt$ann[j] <- tmp_sps2$adduct
}
}
tmp_dt$mz1[(tmp_dt$int / max(tmp_dt$int) < 0.05) & is.na(tmp_dt$ann)] <- ""
tmp_dt$ann[is.na(tmp_dt$ann)] <- ""
htmltools::tagList(
#plot_ly(data = tmp_dt, x = ~mz, y = ~int, type = "bar",
# hovertext = ~mz1, hoverinfo = "text") %>%
plot_ly(tmp_dt) %>%
add_trace(data = tmp_dt, x = ~mz, y = ~int, type = "bar",
hovertext = ~mz1, hoverinfo = "text", width = 0.05) %>%
add_text(x = ~mz, y = ~int,
text = paste(tmp_dt$mz1, "\n", tmp_dt$ann), hoverinfo = 'none',
textposition = 'top') %>%
layout(title = 'MS/MS Spectrum', showlegend = FALSE,
xaxis = list(title = "m/z", range = list(50, precursorMz(tmp_sps))),
yaxis = list(
title = "intensity",
range = list(0, max(tmp_dt$int) + max(tmp_dt$int)*10/100)))
)
if(length(a) > 1){
for(k in 2:length(a)){
tmp_sps2 <- tmp_sps[tmp_sps$adduct == a[k]]
if(length(tmp_sps2$raw_spectra) > 1){
print(paste("Warning!! There is >1 average spectra for", a[k], "!!!"))
} else {
cat(paste(tmp_sps2$adduct, round(precursorMz(tmp_sps2), 5)))
tmp_dt <- data.frame(
mz = unlist(mz(tmp_sps2)),
int = unlist(intensity(tmp_sps2))
)
tmp_dt <- tmp_dt[tmp_dt$mz <= precursorMz(tmp_sps2), ]
tmp_dt <- rbind(tmp_dt, c(precursorMz(tmp_sps2), 0))
tmp_dt$mz1 <- round(tmp_dt$mz, 4)
tmp_dt$mz <- tmp_dt$mz
tmp_dt$nl <- precursorMz(tmp_sps2) - tmp_dt$mz
tmp_dt$ann <- NA
tmp_nl <- nl[nl$polarity == tmp_sps2$polarity, ]
tmp_ions <- ions[ions$polarity == tmp_sps2$polarity,]
if(m[i] == "M0007"){ # Phenylalanine
tmp_ions <- tmp_ions[!grepl("Phe", tmp_ions$name),]
}
for(j in seq(nrow(tmp_dt))){
idx <- which(between(tmp_nl$mass, tmp_dt$nl[j] + 0.01 * c(-1, 1)))
if(length(idx) > 0){
tmp_dt$ann[j] <- paste(tmp_nl$name[idx], collapse = "-")
}
idx <- which(between(tmp_ions$mass, tmp_dt$mz[j] + 0.01 * c(-1, 1)))
if(length(idx) > 0){
tmp_dt$ann[j] <- paste(tmp_ions$name[idx], collapse = "-")
}
idx <- which(between(precursorMz(tmp_sps2), tmp_dt$mz[j] + 0.01 * c(-1, 1)))
if(length(idx) > 0){
tmp_dt$ann[j] <- tmp_sps2$adduct
}
}
tmp_dt$mz1[(tmp_dt$int / max(tmp_dt$int) < 0.05) & is.na(tmp_dt$ann)] <- ""
tmp_dt$ann[is.na(tmp_dt$ann)] <- ""
print(htmltools::tagList(
plot_ly(tmp_dt) %>%
add_trace(data = tmp_dt, x = ~mz, y = ~int, type = "bar",
hovertext = ~mz1, hoverinfo = "text", width = 0.05) %>%
add_text(x = ~mz, y = ~int,
text = paste(tmp_dt$mz1, "\n", tmp_dt$ann), hoverinfo = 'none',
textposition = 'top') %>%
layout(title = 'MS/MS Spectrum', showlegend = FALSE,
xaxis = list(title = "m/z", range = list(50, precursorMz(tmp_sps))),
yaxis = list(
title = "intensity",
range = list(0, max(tmp_dt$int) + max(tmp_dt$int)*10/100)))
))
}
}
}
```
# Individual Spectra
```{r, results='asis'}
tmp_sps <- sps[sps$compound_id == m[i]]
tmp_sps <- tmp_sps[tmp_sps$raw_spectra == 1]
do <- unique(tmp_sps$dataOrigin)
for(k in seq(length(do))){
tmp_sps2 <- tmp_sps[tmp_sps$dataOrigin == do[k],]
ms1 <- readMSData(do[k], mode = "inMemory", msLevel. = 1L)
a <- unique(tmp_sps2$adduct)
for(l in seq(length(a))){
tmp_sps3 <- tmp_sps2[tmp_sps2$adduct == a[l],]
tmp_sps3 <- tmp_sps3[order(rtime(tmp_sps3))]
chr <- chromatogram(ms1, mz = mean(precursorMz(tmp_sps3)) + 0.01 * c(-1, 1))
dt1 <- data.frame(rt = rtime(chr[[1]]),
int = intensity(chr[[1]]))
dt1$int[is.na(dt1$int)] <- 0
dt2 <- data.frame(rt = rtime(tmp_sps3))
dt2$int <- dt1$int[closest(dt2$rt, dt1$rt)]
cat(paste0(
basename(do[k]), ": ", round(mean(precursorMz(tmp_sps3)), 4),
" ", tmp_sps3$adduct[1]))
print(htmltools::tagList(
plot_ly(data = dt1, x = ~rt/60, y = ~int, mode = "lines",
type = "scatter") %>%
add_trace(data = dt2, x = ~rt/60, y = ~int, mode = "markers",
text= paste("Scan N.", tmp_sps3$scanIndex)) %>%
layout(title = "EIC",
yaxis = list(title = "intensity"),
xaxis = list(title = "RT (min)"), showlegend = FALSE)
))
for(j in seq(length(tmp_sps3))){
tmp_dt <- data.frame(
mz = mz(tmp_sps3)[[j]],
int = intensity(tmp_sps3)[[j]]
)
tmp_dt <- tmp_dt[tmp_dt$mz <= precursorMz(tmp_sps3)[j], ]
tmp_dt <- rbind(tmp_dt, c(precursorMz(tmp_sps3)[j], 0))
tmp_dt$mz1 <- round(tmp_dt$mz, 4)
#tmp_dt$mz <- as.factor(tmp_dt$mz)
fig1 <- plotly_empty() %>%
add_text(x = 1, y = 1, textposition = "right", text =
paste("\n Scan Number:", tmp_sps3$scanIndex[j], "\n",
"Precursor:", round(precursorMz(tmp_sps3)[j], 4), "\n",
"Retention time:", round(rtime(tmp_sps3)[j]/60, 2), "\n",
"Collision energy:", tmp_sps3$collisionEnergy[j]))
fig2 <- plot_ly(data = tmp_dt, x = ~mz, y = ~int, type = "bar",
hovertext = ~mz1, hoverinfo = "text") %>%
layout(title = 'MS/MS Spectrum', showlegend = FALSE,
yaxis = list(title = "intensity"),
xaxis = list(title = "m/z", showticklabels = TRUE,
range = list(50, precursorMz(tmp_sps3)[j]))) %>%
add_text(text = tmp_dt$mz1, hoverinfo = 'none', textposition = 'top')
print(htmltools::tagList(
subplot(fig1, fig2, widths = c(0.4, 0.6))
))
}
}
}
```
**Last update:** `r format(Sys.time(), "%d %b %Y")`