LC-MS/MS data analysis with xcms
4 March 2020
Package
xcms 3.8.2
Package: xcms
Authors: Johannes Rainer, Michael Witting
Modified: 2019-11-15 16:45:50
Compiled: Wed Mar 4 19:24:28 2020
1 Introduction
Metabolite identification is an important step in non-targeted metabolomics and requires different steps. One involves the use of tandem mass spectrometry to generate fragmentation spectra of detected metabolites (LC-MS/MS), which are then compared to fragmentation spectra of known metabolites. Different approaches exist for the generation of these fragmentation spectra, whereas the most used is data dependent acquisition (DDA) also known as the top-n method. In this method the top N most intense m/z values from a MS1 scan are selected for fragmentation in the next N scans before the cycle starts again. This method allows to generate clean MS2 fragmentation spectra on the fly during acquisition without the need for further experiments, but suffers from poor coverage of the detected metabolites (since only a limited number of ions are fragmented).
Data independent approaches (DIA) like Bruker bbCID, Agilent AllIons or Waters MSe don’t use such a preselection, but rather fragment all detected molecules at once. They are using alternating schemes with scan of low and high collision energy to collect MS1 and MS2 data. Using this approach, there is no problem in coverage, but the relation between the precursor and fragment masses is lost leading to chimeric spectra. Sequential Window Acquisition of all Theoretical Mass Spectra (or SWATH [1]) combines both approaches through a middle-way approach. There is no precursor selection and acquisition is independent of acquired data, but rather than isolating all precusors at once, defined windows (i.e. ranges of m/z values) are used and scanned. This reduces the overlap of fragment spectra while still keeping a high coverage.
This document showcases the analysis of two small LC-MS/MS data sets using r Biocpkg("xcms"). The data files used are reversed-phase LC-MS/MS runs from the
Agilent Pesticide mix obtained from a Sciex 6600 Triple ToF operated in SWATH
acquisition mode. For comparison a DDA file from the same sample is included.
2 Analysis of DDA data
Below we load the example DDA data set using the readMSData function from the
MSnbase package.
library(xcms)
dda_file <- system.file("TripleTOF-SWATH/PestMix1_DDA.mzML",
package = "msdata")
dda_data <- readMSData(dda_file, mode = "onDisk")The variable dda_data contains now all MS1 and MS2 spectra from the specified
mzML file. The number of spectra for each MS level is listed below.
table(msLevel(dda_data))##
## 1 2
## 1504 2238Next we perform the chromatographic peak detection on the MS level 1 data with
the findChromPeaks method. Below we define the settings for a centWave-based
peak detection and perform the analysis.
cwp <- CentWaveParam(snthresh = 5, noise = 100, ppm = 10,
peakwidth = c(3, 30))
dda_data <- findChromPeaks(dda_data, param = cwp)In total 112 peaks were identified in the present data set.
The advantage of LC-MS/MS data is that (MS1) ions are fragmented and the
corresponding MS2 spectra measured. Thus, for some of the ions (identified as
MS1 chromatographic peaks) MS2 spectra are available. These can facilitate the
annotation of the respective MS1 chromatographic peaks (or MS1 features after a
correspondence analysis). MS2 spectra for identified chromatographic peaks can
be extracted with the chromPeakSpectra method which returns a Spectra object
of MS2 spectra associated with a chromatographic peak (i.e. with their retention
time within the retention time window of a chromatographic peak and their
precursor m/z within the m/z range of the same chromatographic peak.
dda_spectra <- chromPeakSpectra(dda_data)
dda_spectra## Spectra with 150 spectra and 1 metadata column(s):
## msLevel rtime peaksCount | peak_id
## <integer> <numeric> <integer> | <character>
## CP004.F1.S1812 2 237.869 1489 | CP004
## CP004.F1.S1846 2 241.299 1807 | CP004
## CP005.F1.S2446 2 326.583 21 | CP005
## CP006.F1.S2450 2 327.113 85 | CP006
## CP006.F1.S2502 2 330.273 168 | CP006
## ... ... ... ... . ...
## CP100.F1.S5110 2 574.725 890 | CP100
## CP100.F1.S5115 2 575.255 1042 | CP100
## CP101.F1.S5272 2 596.584 196 | CP101
## CP102.F1.S5236 2 592.424 12 | CP102
## CP102.F1.S5266 2 596.054 88 | CP102The metadata column "peak_id" contains the identifiers of the chromatographic
peaks the MS2 spectrum is associated with.
We next use the MS2 information to aid in the annotation of a chromatographic peak. As an example we use a chromatographic peak of an ion with an m/z of 304.1131 which we extract in the code block below.
ex_mz <- 304.1131
chromPeaks(dda_data, mz = ex_mz, ppm = 20)## mz mzmin mzmax rt rtmin rtmax into intb
## CP057 304.1133 304.1126 304.1143 425.024 417.985 441.773 13040.8 12884.14
## maxo sn sample
## CP057 3978.987 79 1A search of potential ions with a similar m/z in a reference database (e.g. Metlin) returned a large list of potential hits, most with a very small ppm. For two of the hits, Flumazenil (Metlin ID 2724) and Fenamiphos (Metlin ID 72445) experimental MS2 spectra are available. Thus, we could match the MS2 spectrum for the identified chromatographic peak against these to annotate our ion. Below we extract all MS2 spectra that were associated with the candidate chromatographic peak using the ID of the peak in the present data set.
ex_id <- rownames(chromPeaks(dda_data, mz = ex_mz, ppm = 20))
ex_spectra <- dda_spectra[mcols(dda_spectra)$peak_id == ex_id]
ex_spectra## Spectra with 5 spectra and 1 metadata column(s):
## msLevel rtime peaksCount | peak_id
## <integer> <numeric> <integer> | <character>
## CP057.F1.S3505 2 418.926 10 | CP057
## CP057.F1.S3510 2 419.306 30 | CP057
## CP057.F1.S3582 2 423.036 694 | CP057
## CP057.F1.S3603 2 423.966 783 | CP057
## CP057.F1.S3609 2 424.296 753 | CP057There are 5 MS2 spectra representing fragmentation of the ion(s) measured
in our candidate chromatographic peak. We next reduce this to a single MS2
spectrum using the combineSpectra method employing the consensusSpectrum
function to determine which peaks to keep in the resulting spectrum.
ex_spectrum <- combineSpectra(ex_spectra, method = consensusSpectrum, mzd = 0,
ppm = 20, minProp = 0.8, weighted = FALSE,
intensityFun = median, mzFun = median)
ex_spectrum## Spectra with 1 spectra and 1 metadata column(s):
## msLevel rtime peaksCount | peak_id
## <integer> <numeric> <integer> | <character>
## CP057.F1.S3505 2 418.926 24 | CP057Mass peaks from all input spectra with a difference in m/z smaller 20 ppm
(parameter ppm) were combined into one peak and the median m/z and intensity
is reported for these. Due to parameter minProp = 0.8, the resulting MS2
spectrum contains only peaks that were present in 80% of the input spectra.
A plot of this consensus spectrum is shown below.
plot(ex_spectrum[[1]])
Figure 1: Consensus MS2 spectrum created from all measured MS2 spectra for ions of chromatographic peak CP53
We could now match the consensus spectrum against a database of MS2 spectra. In our example we simply load MS2 spectra for the two compounds with matching m/z exported from Metlin. For each of the compounds MS2 spectra created with collision energies of 0V, 10V, 20V and 40V are available. Below we import the respective data and plot our candidate spectrum against the MS2 spectra of Flumanezil and Fenamiphos (from a collision energy of 20V).
flumanezil <- spectra(readMgfData(
system.file("mgf/metlin-2724.mgf", package = "xcms")))
fenamiphos <- spectra(readMgfData(
system.file("mgf/metlin-72445.mgf", package = "xcms")))
par(mfrow = c(1, 2))
plot(ex_spectrum[[1]], flumanezil[[3]], main = "against Flumanezil",
tolerance = 40e-6)
plot(ex_spectrum[[1]], fenamiphos[[3]], main = "against Fenamiphos",
tolerance = 40e-6)
Figure 2: Mirror plots for the candidate MS2 spectrum against Flumanezil (left) and Fenamiphos (right)
The upper panel represents the candidate MS2 spectrum, the lower the target MS2 spectrum. Matching peaks are indicated with a dot.
Our candidate spectrum matches Fenamiphos, thus, our example chromatographic
peak represents signal measured for this compound. In addition to plotting the
spectra, we can also calculate similarities between them with the
compareSpectra method (e.g. using the dotproduct method as shown below).
compareSpectra(ex_spectrum[[1]], flumanezil[[3]], binSize = 0.02,
fun = "dotproduct")## [1] 0.005350294compareSpectra(ex_spectrum[[1]], fenamiphos[[3]], binSize = 0.02,
fun = "dotproduct")## [1] 0.9092189Clearly, the candidate spectrum does not match Flumanezil, while it has a high
similarity to Fenamiphos. While we performed here the MS2-based annotation on a
single chromatographic peak, this could be easily extended to the full list of
MS2 spectra (returned by chromPeakSpectra) for all chromatographic peaks in an
experiment. Respective code facilitating this will be implemented in future.
In the present example we used only a single data file and we did thus not need
to perform a sample alignment and correspondence analysis. These tasks could
however be performed similarly to plain LC-MS data, retention times of
recorded MS2 spectra would however also be adjusted during alignment based on
the MS1 data. After correspondence analysis (peak grouping) MS2 spectra for
features can be extracted with the featureSpectra function which returns all
MS2 spectra associated with any chromatographic peak of a feature.
Note also that this workflow can be included into the Feature-Based Molecular Networking FBMN to match MS2 spectra against GNPS. See here for more details and examples.
3 SWATH data analysis
In this section we analyze a small SWATH data set consisting of a single mzML
file with data from the same sample analyzed in the previous section but
recorded in SWATH mode. We again read the data with the readMSData
function. The resulting object will contain all recorded MS1 and MS2
spectra in the specified file.
swath_file <- system.file("TripleTOF-SWATH",
"PestMix1_SWATH.mzML",
package = "msdata")
swath_data <- readMSData(swath_file, mode = "onDisk")Below we determine the number of MS level 1 and 2 spectra in the present data set.
table(msLevel(swath_data))##
## 1 2
## 444 3556As described in the introduction, in SWATH mode all ions within pre-defined
isolation windows are fragmented and MS2 spectra measured. The definition of
these isolation windows (SWATH pockets) is imported from the mzML files and
stored in the object’s fData (which provides additional annotations for each
individual spectrum). Below we inspect the respective information for the first
few spectra. The upper and lower isolation window m/z can be extracted with the
isolationWindowLowerMz and isolationWindowUpperMz.
head(fData(swath_data)[, c("isolationWindowTargetMZ",
"isolationWindowLowerOffset",
"isolationWindowUpperOffset",
"msLevel", "retentionTime")])## isolationWindowTargetMZ isolationWindowLowerOffset
## F1.S2000 208.95 21.95
## F1.S2001 244.05 14.15
## F1.S2002 270.85 13.65
## F1.S2003 299.10 15.60
## F1.S2004 329.80 16.10
## F1.S2005 367.35 22.45
## isolationWindowUpperOffset msLevel retentionTime
## F1.S2000 21.95 2 200.084
## F1.S2001 14.15 2 200.181
## F1.S2002 13.65 2 200.278
## F1.S2003 15.60 2 200.375
## F1.S2004 16.10 2 200.472
## F1.S2005 22.45 2 200.569head(isolationWindowLowerMz(swath_data))## [1] 187.0 229.9 257.2 283.5 313.7 344.9head(isolationWindowUpperMz(swath_data))## [1] 230.9 258.2 284.5 314.7 345.9 389.8In the present data set we use the value of the isolation window target m/z to define the individual SWATH pockets. Below we list the number of spectra that are recorded in each pocket/isolation window.
table(isolationWindowTargetMz(swath_data))##
## 163.75 208.95 244.05 270.85 299.1 329.8 367.35 601.85
## 444 445 445 445 445 444 444 444We have thus 1,000 MS2 spectra measured in each isolation window.
3.1 Chromatographic peak detection in MS1 and MS2 data
Similar to a conventional LC-MS analysis, we perform first a chromatographic
peak detection (on the MS level 1 data) with the findChromPeaks method. Below
we define the settings for a centWave-based peak detection and perform the
analysis.
cwp <- CentWaveParam(snthresh = 5, noise = 100, ppm = 10,
peakwidth = c(3, 30))
swath_data <- findChromPeaks(swath_data, param = cwp)Next we perform a chromatographic peak detection in the MS level 2 data of each
isolation window. We use the findChromPeaksIsolationWindow function employing
the same peak detection algorithm reducing however the required signal-to-noise
ratio. The isolationWindow parameter allows to specify which MS2 spectra
belong to which isolation window and hence defines in which set of MS2 spectra
chromatographic peak detection should be performed. While the default value for
this parameter uses isolation windows provided by calling
isolationWindowTargetMz on the object, it would also be possible to manually
define the isolation windows, e.g. if the corresponding information is not
available in the input mzML files.
cwp <- CentWaveParam(snthresh = 3, noise = 10, ppm = 10,
peakwidth = c(3, 30))
swath_data <- findChromPeaksIsolationWindow(swath_data, param = cwp)The findChromPeaksIsolationWindow function added all peaks identified in the
individual isolation windows to the chromPeaks matrix containing already the
MS1 chromatographic peaks. These newly added peaks can be identified by the
value of the "isolationWindow" column in the corresponding row in
chromPeakData, which lists also the MS level in which the peak was identified.
chromPeakData(swath_data)## DataFrame with 368 rows and 6 columns
## ms_level is_filled isolationWindow isolationWindowTargetMZ
## <integer> <logical> <factor> <numeric>
## CP01 1 FALSE NA NA
## CP02 1 FALSE NA NA
## CP03 1 FALSE NA NA
## CP04 1 FALSE NA NA
## CP05 1 FALSE NA NA
## ... ... ... ... ...
## CP364 2 FALSE 601.85 601.85
## CP365 2 FALSE 601.85 601.85
## CP366 2 FALSE 601.85 601.85
## CP367 2 FALSE 601.85 601.85
## CP368 2 FALSE 601.85 601.85
## isolationWindowLowerMz isolationWindowUpperMz
## <numeric> <numeric>
## CP01 NA NA
## CP02 NA NA
## CP03 NA NA
## CP04 NA NA
## CP05 NA NA
## ... ... ...
## CP364 388.8 814.9
## CP365 388.8 814.9
## CP366 388.8 814.9
## CP367 388.8 814.9
## CP368 388.8 814.9Below we count the number of chromatographic peaks identified within each isolation window (the number of chromatographic peaks identified in MS1 is 62).
table(chromPeakData(swath_data)$isolationWindow)##
## 163.75 208.95 244.05 270.85 299.1 329.8 367.35 601.85
## 2 38 32 14 105 23 61 31We thus successfully identified chromatographic peaks in the different MS levels and isolation windows, but don’t have any actual MS2 spectra yet. These have to be reconstructed from the available chromatographic peak data which we will done in the next section.
3.2 Reconstruction of MS2 spectra
Identifying the signal of the fragment ions for the precursor measured by each MS1 chromatographic peak is a non-trivial task. The MS2 spectrum of the fragment ion for each MS1 chromatographic peak has to be reconstructed from the available MS2 signal (i.e. the chromatographic peaks identified in MS level 2). For SWATH data, fragment ion signal should be present in the isolation window that contains the m/z of the precursor ion and the chromatographic peak shape of the MS2 chromatographic peaks of fragment ions of a specific precursor should have a similar retention time and peak shape than the precursor’s MS1 chromatographic peak.
After detection of MS1 and MS2 chromatographic peaks has been performed, we can
reconstruct the MS2 spectra using the reconstructChromPeakSpectra
function. This function defines an MS2 spectrum for each MS1 chromatographic
peak based on the following approach:
- Identify MS2 chromatographic peaks in the isolation window containing the m/z
of the ion (the MS1 chromatographic peak) that have approximately the same
retention time than the MS1 chromatographic peak (the accepted difference in
retention time can be defined with the
diffRtparameter). - Extract the MS1 chromatographic peak and all MS2 chromatographic peaks
identified by the previous step and correlate the peak shapes of the candidate
MS2 chromatographic peaks with the shape of the MS1 peak. MS2 chromatographic
peaks with a correlation coefficient larger than
minCorare retained. - Reconstruct the MS2 spectrum using the m/z of all above selected MS2 chromatographic peaks and their intensity; each MS2 chromatographic peak selected for an MS1 peak will thus represent one mass peak in the reconstructed spectrum.
To illustrate this process we perform the individual steps on the example of Fenamiphos (exact mass 303.105800777 and m/z of [M+H]+ adduct 304.113077). As a first step we extract the chromatographic peak for this ion.
fenamiphos_mz <- 304.113077
fenamiphos_ms1_peak <- chromPeaks(swath_data, mz = fenamiphos_mz, ppm = 2)
fenamiphos_ms1_peak## mz mzmin mzmax rt rtmin rtmax into intb
## CP34 304.1124 304.1121 304.1126 423.945 419.445 428.444 10697.34 10688.34
## maxo sn sample
## CP34 2401.849 618 1Next we identify all MS2 chromatographic peaks that were identified in the
isolation window containing the m/z of Fenamiphos. The information on the
isolation window in which a chromatographic peak was identified is available in
the chromPeakData (which contains arbitrary additional annotations to each
individual chromatographic peak).
keep <- chromPeakData(swath_data)$isolationWindowLowerMz < fenamiphos_mz &
chromPeakData(swath_data)$isolationWindowUpperMz > fenamiphos_mzWe also require the retention time of the MS2 chromatographic peaks to be similar to the retention time of the MS1 peak and extract the corresponding peak information.
keep <- keep &
chromPeaks(swath_data)[, "rtmin"] < fenamiphos_ms1_peak[, "rt"] &
chromPeaks(swath_data)[, "rtmax"] > fenamiphos_ms1_peak[, "rt"]
fenamiphos_ms2_peak <- chromPeaks(swath_data)[which(keep), ]In total 24 MS2 chromatographic peaks match all the
above condition. Next we extract their corresponding ion chromatograms, as well
as the ion chromatogram of the MS1 peak. Note that we extend the retention time
range by 1 seconds on both sides. In addition we have to filter the object
first by isolation window, keeping only spectra that were measured in that
specific window and to specify to extract the chromatographic data from MS2
spectra (with msLevel = 2L).
rtr <- fenamiphos_ms1_peak[, c("rtmin", "rtmax")]
rtr[1] <- rtr[1] - 1
rtr[2] <- rtr[2] + 1
mzr <- fenamiphos_ms1_peak[, c("mzmin", "mzmax")]
fenamiphos_ms1_chr <- chromatogram(swath_data, rt = rtr, mz = mzr)
rtr <- fenamiphos_ms2_peak[, c("rtmin", "rtmax")]
rtr[, 1] <- rtr[, 1] - 1
rtr[, 2] <- rtr[, 2] + 1
mzr <- fenamiphos_ms2_peak[, c("mzmin", "mzmax")]
fenamiphos_ms2_chr <- chromatogram(
filterIsolationWindow(swath_data, mz = fenamiphos_mz),
rt = rtr, mz = mzr, msLevel = 2L)We can now plot the extracted ion chromatogram of the MS1 and the extracted MS2 data.
plot(rtime(fenamiphos_ms1_chr[1, 1]),
intensity(fenamiphos_ms1_chr[1, 1]),
xlab = "retention time [s]", ylab = "intensity", pch = 16,
ylim = c(0, 5000), col = "blue", type = "b", lwd = 2)
#' Add data from all MS2 peaks
tmp <- lapply(fenamiphos_ms2_chr@.Data,
function(z) points(rtime(z), intensity(z),
col = "#00000080",
type = "b", pch = 16))