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Topic: Peak - adduct relationships (Read 3589 times) previous topic - next topic

Peak - adduct relationships

Hello all,

In working with CAMERA data I have been attempting to find hydrogen adducts and their corresponding sodium adducts.  I am wondering if this relationship is stored in the xsAnnotate object anywhere or if I should just repeat the search myself.

I currently find sodium adducts via rule_id as stored in an@derivativeIons.  I can then find hydrogen adducts within that psg in the same manner.  I am wondering if the information linking a specific M+H to its M+Na (or eg. M+Na to M+K) is stored anywhere?  I havent been able to find it - an@annoID$parentID isn't populated and no other an@derivativeIons fields seem applicable.

Thanks for the help,

Re: Peak - adduct relationships

Reply #1
This got several views so I got around to doing this and here is my solution.

an@derivativeIons is a list with each item corresponding to a peak from the xcmsSet peaktable.  It contains a rule-based annotation for each peak as an adduct, NL, etc.  Each of these annotations links an ion in a dataset a (Eg. M+H) to a corresponding neutral mass (M).  I was hoping to retrieve these relationships, specifically the M+H and M+Na that both predict the same mass (M), rather than the isolated peak's annotation as found in an@derivativeIons.

In case anyone else wants to do this, here is a simple search for these relationships.

First we collect all the annotations and their predicted neutral masses:

Code: [Select]
  an = xsAnnotate
  all_masses ="rbind", lapply(1:length(an@pspectra), function(x) {
    neutral_masses ="rbind", lapply(an@pspectra[[x]], function(y) {"rbind", lapply(an@derivativeIons[[y]], function(z) {
        cbind(neutral = z$mass, rule = z$rule_id, peaknum=y, psg = x)

This looks like:

Code: [Select]
> head(all_masses)
      neutral rule peaknum psg
mass 401.3136    7    234  1
mass 670.6027    1    236  1
mass 401.3136    1    248  1
mass 670.6027  37    259  2
mass 498.3887  12    274  2
mass 451.3561    7    281  3

This is then easy to search however you like.  To find all the M-H and M+Cl's that predict the same parent mass (and are in the same psg).

Code: [Select]
  withinppm = function(m1, m2, ppm=20) {   abs(m1-m2)/m1*1E6 < 20   }

  hcl_pairs ="rbind",lapply(which(all_masses[,"rule"] == 1), function(x) {
    mh = all_masses[x,,drop=F]
    a_pair = all_masses[
                      all_masses[,"psg"] == mh[,"psg"] &
                      withinppm(all_masses[,"neutral"], mh[,"neutral"]) &
                      all_masses[,"rule"] == 7,
    if(nrow(a_pair) < 1) {return(NULL)}
    cbind(neutral=mh[,"neutral"],psg = mh[,"psg"], mh_peaknum = mh[,"peaknum"], mcl_peaknum = a_pair[,"peaknum"])

This looks like:

Code: [Select]
> head(hcl_pairs)
  neutral psg mh_peaknum mcl_peaknum
 401.3136  1        248        234
 882.6437  3      9228        9193
 856.5924  4      1946        1982
 886.5545  4      1981        1984
 713.4113  7      9483        9397
 443.3272  8      3144        2666

Disclaimer: This isn't an optimized way to search, but its functional and fast enough on my laptop.  I'm also not an R guru so suggestions are welcome.