Question: Can XCMS search Metlin using MS/MS spectra and provide a similarity score?
2
gravatar for dannel025
3.6 years ago by
dannel02520
dannel02520 wrote:

As a beginner in Metabolomics and R, I'm trying to identify hundreds of peaks generated by LC-MS/MS. The xcms package tutorial shows how to process tandem MS data, but no information on identification is given. Another helpful tutorial, named "XCMS2: A Howto"(https://masspec.scripps.edu/xcms/download/XCMS2_howto.pdf), mentioned a function called "searchMetlin", which is not included in xcms package(1.47.2). So it puzzles me and need help to get me through it or provide some suggestions on how to identify peaks using tandem MS information.

The details about my R environment are listed below:

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936
[2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936   
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
[4] LC_NUMERIC=C                                                   
[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936    

attached base packages:
[1] parallel  stats     graphics  grDevices utils    
[6] datasets  methods   base     

other attached packages:
[1] xcms_1.47.2         Biobase_2.30.0     
[3] ProtGenerics_1.2.1  BiocGenerics_0.16.1
[5] mzR_2.4.0           Rcpp_0.12.3        

loaded via a namespace (and not attached):
[1] tools_3.2.3        RColorBrewer_1.1-2 codetools_0.2-14  
[4] grid_3.2.3         lattice_0.20-33   
>
xcms • 1.3k views
ADD COMMENTlink modified 2.2 years ago by wssdandan20090 • written 3.6 years ago by dannel02520
Answer: Can XCMS search Metlin using MS/MS spectra and provide a similarity score?
0
gravatar for wssdandan2009
2.2 years ago by
wssdandan20090 wrote:

Have you resolved this problem now? Thank you~~

ADD COMMENTlink written 2.2 years ago by wssdandan20090
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 176 users visited in the last hour