Can XCMS search Metlin using MS/MS spectra and provide a similarity score?
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dannel025 ▴ 20
@dannel025-9710
Last seen 5.2 years ago

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 • 1.4k views
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@wssdandan2009-11216
Last seen 3.3 years ago

Have you resolved this problem now? Thank you~~

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