I have some single quad GC-MS data, in which part of the dataset was run using one autotune and the remaing using a different autotune. As a result, the masses are shifted in half the dataset. Oddly enough by a pretty large margin (which I can't explain) - about 0.4-0.5 Da. I looked into the XCMS options and found what I thought would be the savior for this dataset, in the calibrate() function. However, I cannot get it to work for me. I am using a subset of the dataset, five files from tune one, five files from tune two. I use this code:
Time range: 601.8-2482.9 seconds (10-41.4 minutes) Mass range: 50.2301-649.5369 m/z Peaks: 71753 (about 7175 per sample) Peak Groups: 0 Sample classes: GC-MS_masscorrection
Profile settings: method = bin step = 0.5
Memory usage: 8.38 MB
I then try to apply the m/z correction using the calibrate function using the command: xset2<- calibrate(xset, calibrants=147.1, method="shift", mzabs=1, neighbours=3, plotres=TRUE)
Error in .local(object, ...) : No masses close enough!
I know for a fact that there are plenty of masses near this mass in the dataset, but I can't seem to find them. In fact, even if I expand the mzabs to 10, I receive the same message. If I expand the mzabs value to 100, it works, and actuall does seem to shift all the masses by 100da (note the mass range)
> xset2 An "xcmsSet" object with 10 samples
Time range: 601.8-2482.9 seconds (10-41.4 minutes) Mass range: 144.0489-743.6364 m/z Peaks: 71753 (about 7175 per sample) Peak Groups: 0 Sample classes: GC-MS_masscorrection
Profile settings: method = bin step = 0.5
Memory usage: 8.38 MB >
I am misusing 'calibrate' or misunderstanding? What am I missing? Thanks, Corey
This did answer my question. I don't know exactly what format I need yet, but just good to know that there is a function to get this data out. On a related subject - when CAMERA is selecting spectra for plotting pseudospectra, what is this selection process based on?
Is it possible to export a text formatted pseodospectrum? I am interested in trying CAMERA's grouping functions as an alternate to AMDIS. Having a text export option would potentially allow to integrate CAMERA output with NIST/custom database searches. Thanks.
> plotEICs(an4, pspec=1000, maxlabel=10) Error in pks[, 1] : incorrect number of dimensions
> packageVersion("CAMERA") [1] ‘1.9.3’
> an4 An "xsAnnotate" object! With 2237 groups (pseudospectra) With 84 samples and 9528 peaks Using automatic sample selection Annotated isotopes: 251 Memory usage: 134 MB
Thanks for looking into it. I get the impression that this error occurs most frequently when there are few (or only one) features in a particular pseudospectrum group.
I was just hoping to avoid having to convert to yet another format. MassLynx databridge doesn't covert to mzXML, so I now have another step and another (roughly) doubling of hardrive space for each dataset. I will try it though.
I am playing with XCMS v 1.27.4. I am having an issue with a dataset that I started working with. If i use the matchedFilter peak detection, the process goes smoothly. If I use the centWave method:
" 11-07-18_test_005501: Detecting mass traces at 25 ppm ... % finished: 0 10 20 30 40 50 60 Error in .local(object, ...) : m/z sort assumption violated ! (scan 670, p 129, current 170.1777 (I=5.06), last 170.1777) In addition: Warning messages: 1: closing unused connection 6 (<-PMFLAB-04.cvmbs.ColoState.EDU:10187) 2: closing unused connection 5 (<-PMFLAB-04.cvmbs.ColoState.EDU:10187) 3: closing unused connection 4 (<-PMFLAB-04.cvmbs.ColoState.EDU:10187) 4: closing unused connection 3 (<-PMFLAB-04.cvmbs.ColoState.EDU:10187) " where 11-07-18_test_005501 is the problem filename. When I use the nSlaves option, I end up with, this message
" Error in checkForRemoteErrors(val) : 5 nodes produced errors; first error: m/z sort assumption violated ! (scan 670, p 129, current 170.1777 (I=5.06), last 170.1777) "
So apparently there are something about a few of these files that centWave does not like, but matchedFilter is OK with. These are cdf files produced by Markerlynx DataBridge from waters raw files. I am using R 3.13.1. Anyone seen this issue previously?
I am getting all up to date on the current XCMS and CAMERA versions, and found that while the mulitcore function is presumably activated (nSlaves doesn't generate an 'not functional' message, as it did in older CAMERA versions), it generates an error message indicating that it is dependent on Rmpi, which there is no Windows 64bit version of. Does this sound right or am I missing something? Strangely enough, the nSlaves option works for XCMS.
package 'CAMERA' successfully unpacked and MD5 sums checked
The downloaded packages are in C:UserscbroecklAppDataLocalTempRtmpvQ5TAbdownloaded_packages
I noticed at the bioconductor site that I should be downloading v1.8.2, but it is listed as 32bit only. Is my issue that I am on a 64 bit computer? If so, any plans for 64bit CAMERA soon?
Regarding the ruleset table, I have CAMERA installed on two different computers, and neither installation has a file called "primary_adducts_pos.csv". Nor is there a 'rules' folder. I can find the list folder with 'ions.csv' etc., but this doesn't have the detail that the 7 columns of the ruleset described previously. Am I missing something silly, or is the primary_adducts_pos file obselete? I am using section six from the pdf linked from the bioconductor site dated Apr 28, 2011. Thanks.
I don't think I ran the isotope annotation for that spectrum first. I will keep trying. And I will look at the vignette to check out the annotation rules. I appreciate the quick response.
