Hi, I would use xcmsFragments() to collect all the MSMS spectra from my samples:

files <- list.files(pattern="mzXML", full.names=FALSE, recursive=TRUE)

xs <- xcmsSet(files, method="MS1")

xfrg <- xcmsFragments(xs)

> xfrg
An "xcmsFragments" object with  408600  peaks in 77569 Spectra
From Level 1 to 2 Number of Samples:  4 .

Sample 1 :
    16441 Peaks in Level 1
    83365 Peaks in Level 2

Sample 2 :
    17192 Peaks in Level 1
    86170 Peaks in Level 2

Sample 3 :
    17147 Peaks in Level 1
    89497 Peaks in Level 2

Sample 4 :
    16548 Peaks in Level 1
    82240 Peaks in Level 2

Memory usage: 28.1 MB

but it seems I haven't MSMS spectra:

> str(xfrg)
Formal class 'xcmsFragments' [package "xcms"] with 3 slots
  ..@ peaks   : num [1:408600, 1:9] 1 2 3 4 5 6 7 8 9 10 ...
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : NULL
  .. .. ..$ : chr [1:9] "peakID" "MSnParentPeakID" "msLevel" "rt" ...
  ..@ MS2spec : NULL
  ..@ specinfo: NULL

How can I get them? How can I extract the MSMS spectra according to the precustor ID (xfrg@peaks[,"peakID"])?