Metabolomics Xcms Preprocessing

Load Raw Data

library(xcms)
library(MSnbase)

raw_files <- list.files('raw_data', pattern = '\\.(mzML|mzXML)$', full.names = TRUE)
raw_data <- readMSData(raw_files, mode = 'onDisk')

Define Sample Groups

sample_info <- data.frame(
    sample_name = basename(raw_files),
    sample_group = c(rep('Control', 5), rep('Treatment', 5), rep('QC', 3)),
    injection_order = 1:length(raw_files)
)
pData(raw_data) <- sample_info

Peak Detection (CentWave — Centroided Data)

cwp <- CentWaveParam(
    peakwidth = c(5, 30),       # Peak width range in seconds
    ppm = 15,                    # m/z tolerance
    snthresh = 10,               # Signal-to-noise threshold
    prefilter = c(3, 1000),      # Min peaks and intensity
    mzdiff = 0.01,               # Minimum m/z difference
    noise = 1000,                # Noise level
    integrate = 1                # Integration method
)

xdata <- findChromPeaks(raw_data, param = cwp)
cat('Peaks found:', nrow(chromPeaks(xdata)), '\n')

Peak Detection (MatchedFilter — Profile Data)

mfp <- MatchedFilterParam(
    binSize = 0.1, fwhm = 30, snthresh = 10, step = 0.1, mzdiff = 0.8
)
xdata_profile <- findChromPeaks(raw_data, param = mfp)

Retention Time Alignment (Obiwarp)

obp <- ObiwarpParam(
    binSize = 0.5, response = 1, distFun = 'cor_opt',
    gapInit = 0.3, gapExtend = 2.4
)
xdata <- adjustRtime(xdata, param = obp)
plotAdjustedRtime(xdata)

Peak Correspondence (Grouping)

pdp <- PeakDensityParam(
    sampleGroups = pData(xdata)$sample_group,
    bw = 5,                      # RT bandwidth
    minFraction = 0.5,           # Min fraction of samples
    minSamples = 1,              # Min samples per group
    binSize = 0.025              # m/z bin size
)
xdata <- groupChromPeaks(xdata, param = pdp)
cat('Features:', nrow(featureDefinitions(xdata)), '\n')

Gap Filling

fpp <- ChromPeakAreaParam()
xdata <- fillChromPeaks(xdata, param = fpp)

Extract Feature Table

feature_values <- featureValues(xdata, method = 'maxint', value = 'into')
feature_defs <- as.data.frame(featureDefinitions(xdata))
feature_defs$feature_id <- rownames(feature_defs)

feature_table <- cbind(feature_defs[, c('feature_id', 'mzmed', 'rtmed')], feature_values)
write.csv(feature_table, 'feature_table.csv', row.names = FALSE)

CAMERA Annotation (Isotopes/Adducts)

library(CAMERA)

xsa <- xsAnnotate(as(xdata, 'xcmsSet'))
xsa <- groupFWHM(xsa, perfwhm = 0.6)
xsa <- findIsotopes(xsa, mzabs = 0.01, ppm = 10)
xsa <- findAdducts(xsa, polarity = 'positive')
camera_results <- getPeaklist(xsa)

Quality Control

# TIC for each sample
tic <- chromatogram(raw_data, aggregationFun = 'sum')
plot(tic)

# Peak count per sample
peak_counts <- table(chromPeaks(xdata)[, 'sample'])
barplot(peak_counts, main = 'Peaks per sample')

# PCA of features
library(pcaMethods)
log_values <- log2(feature_values + 1)
log_values[is.na(log_values)] <- 0
pca <- pca(t(log_values), nPcs = 3, method = 'ppca')
plotPcs(pca, col = as.factor(pData(xdata)$sample_group))

Export for MetaboAnalyst

export_data <- t(feature_values)
colnames(export_data) <- paste0('M', round(feature_defs$mzmed, 4), 'T', round(feature_defs$rtmed, 1))
export_df <- data.frame(Sample = rownames(export_data), Group = pData(xdata)$sample_group, export_data)
write.csv(export_df, 'metaboanalyst_input.csv', row.names = FALSE)

Parameters

Why This Exists

• Without it: Raw mzML/mzXML profiles are just unaligned 3D data clouds of m/z, intensity, and time
• With it: Sophisticated algorithms detect true chemical peaks, correct temporal drift (Obiwarp), and map features across runs
• Why OmicsClaw: Avoids verbose R scripts with a hyper-optimized parameter wrapper for XCMS3

Workflow

1. Calculate: Fit moving mathematical wavelets to detect peaks (CentWave).
2. Execute: Align retention times dynamically across all mass spec runs.
3. Assess: Group congruent features and integrate signal caps for missing zones.
4. Generate: Output structural correspondence matrices (feature tables).
5. Report: Synthesize Total Ion Chromatogram (TIC) and aligned retention deviation plots.

Example Queries

• "Preprocess these mzML files using XCMS"
• "Detect peaks and align retention times"

Output Structure

output_directory/
├── report.md
├── result.json
├── feature_table.csv
├── figures/
│   ├── tic_overlay.png
│   └── retention_deviation.png
├── tables/
│   └── grouped_features.csv
└── reproducibility/
    ├── commands.sh
    ├── requirements.txt
    └── checksums.sha256

Safety

• Local-first: Strict offline processing without external upload.
• Disclaimer: Requires OmicsClaw reporting structures and disclaimers.
• Audit trail: Hyperparameters and operational flow states are logged fully.

Integration with Orchestrator

Trigger conditions:

• Automatically invoked dynamically based on tool metadata and user intent matching.

Chaining partners:

• met-normalize — Downstream data scaling
• met-annotate — Downstream explicit matching to spectra

Version Compatibility

Reference examples tested with: xcms 4.0+, MSnbase 2.28+

Dependencies

Required: xcms, MSnbase (R/Bioconductor) Optional: CAMERA, pcaMethods

Citations

• XCMS — Smith et al., Analytical Chemistry 2006
• CentWave — Tautenhahn et al., BMC Bioinformatics 2008
• CAMERA — Kuhl et al., Analytical Chemistry 2012

Related Skills

• met-annotate — Identify metabolites
• met-normalize — Normalize feature table
• met-diff — Differential analysis