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Mass fragmentation collections of each full scan

Source: R/Spectra-functions.R
fragmentGroupIndex.Rd

This function generates an integer index grouping MS^n spectra (MS level > 1) with their corresponding MS1 spectra based on acquisition order. Each group contains exactly one MS1 spectrum and all subsequent higher-level spectra (MS2, MS3, ...) acquired until the next MS1 scan. MS1-only spectra are also assigned sequential group IDs.

Note that this function:

  • does not consider the direct relationship between a precursor scan and the associated product scans,

  • and does not distinguish between different fragmentation trees.

For example, all MS3 scans measured after a given MS1 are grouped together with all MS2 scans from that MS1, regardless of which MS2 spectrum they originated from. See filterPrecursorScan() for a function that considers relationships between fragment and precursor scans.

Usage

fragmentGroupIndex(object, BPPARAM = SerialParam())

Arguments

object

A Spectra object (from the Spectra package) containing MS data. Must include at least two MS levels (msLevel) and be ordered by acquisitionNum within each dataOrigin.

BPPARAM

A BiocParallelParam object for parallel execution. Defaults to SerialParam().

Value

An integer vector of the same length as object. Each element gives the group index associated with the corresponding spectrum (MS1 or MS^n). Group indices are unique across all files (dataOrigin values).

Note

  • Each file (dataOrigin) must contain at least one MS1 spectrum.

  • If a group contains only MS1 spectra, each MS1 is assigned a unique group ID.

  • The user is responsible for ensuring that spectra are correctly ordered. Improper ordering may lead to incorrect groupings.

See also

filterPrecursorScan() for a function that instead returns a Spectra object containing each parent (e.g., MS1) and its direct child scans (e.g., MS2) according to their acquisition numbers.

Author

Philippine Louail

Examples


fl_ms3 <- system.file("proteomics", "MS3TMT11.mzML", package = "msdata")
sps_dda <- Spectra(fl_ms3)
idx <- fragmentGroupIndex(sps_dda)
head(idx)
#>             
#> 1 1 1 1 1 1