Extracted Ion Chromatogram from MS2 data

[michaelwitting]

Hi,

I encountered another issue working with the SWATH data: Creating an EIC for the MS2 data.
Following error pops up when trying to create a chromatogram:

Warning message:
In .extractMultipleChromatograms(object, rt = rt, mz = mz, aggregationFun = aggregationFun, :
No MS 1 data present.

Data is the same as in my last issue posted. I wanted execute the following Code line:

bpis <- chromatogram(xrms_ms2_swath[[10]], mz = c(184.0, 184.1), aggregationFun = "max")

Thank you very much!

Best regards,

Michael

[jorainer]

Yup, sorry. I'll fix that. There will be soon a parameter msLevel that allows to specify from which MS level you want to extract the chromatogram.

[jorainer]

OK, my pull request has been merged into MSnbase (lgatto/MSnbase#247). If you install the latest MSnbase you can use chromatogram(object, msLevel = 2) to extract a chromatogram of MS level 2.

[michaelwitting]

bpis <- chromatogram(ms2data[[2]], msLevel = 2)

throws following error:

Error in .local(object, ...) : unused argument (msLevel = 2)

Same for bpis <- MSnbase::chromatogram(ms2data[[2]], msLevel = 2)

used versions are

xcms_2.99.7
MSnbase_2.3.10 (freshly installed from GitHub today)
mzR_2.10.0

[jorainer]

This is very strange. I've just installed MSnbase from github (devtools::install_github("lgatto/MSnbase", version is still 2.3.10) and that version does support the msLevel argument in chromatogram. Can you try to re-install the package please? Note that you will have to restart R or detach and reload the package if you want to use a newly installed/updated package.

[michaelwitting]

Just removed and re-installed MSnbase... Still the same error. Same after restarting R...

[jorainer]

That's strange. This is what I did:

> remove.packages("MSnbase")
Removing package from ‘/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/library’
(as ‘lib’ is unspecified)
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
> library(MSnbase)
Error in library(MSnbase) : there is no package called ‘MSnbase’
> devtools::install_github("lgatto/MSnbase")
Downloading GitHub repo lgatto/MSnbase@master
from URL https://api.github.com/repos/lgatto/MSnbase/zipball/master
Installing MSnbase
'/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/bin/R' --no-site-file  \
  --no-environ --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/_2/xgzjxb8j6jg467lqv1j19cpr0000gn/T/RtmpaZPoZc/devtools11d9d5c59f4dc/lgatto-MSnbase-ffaa210'  \
  --library='/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/library'  \
  --install-tests 

* installing *source* package ‘MSnbase’ ...
** libs
*** arch - x86_64
clang++  -I/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/include -I/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/include/x86_64 -DNDEBUG  -I"/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/library/Rcpp/include" -D__ACCELERATE__   -fPIC  -g -O2  -c RcppExports.cpp -o RcppExports.o
clang -I/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/include -I/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/include/x86_64 -DNDEBUG  -I"/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/library/Rcpp/include" -D__ACCELERATE__   -fPIC  -g -O2  -c Spectrum1_class.c -o Spectrum1_class.o
clang -I/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/include -I/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/include/x86_64 -DNDEBUG  -I"/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/library/Rcpp/include" -D__ACCELERATE__   -fPIC  -g -O2  -c Spectrum2_class.c -o Spectrum2_class.o
clang++  -I/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/include -I/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/include/x86_64 -DNDEBUG  -I"/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/library/Rcpp/include" -D__ACCELERATE__   -fPIC  -g -O2  -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
clang -I/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/include -I/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/include/x86_64 -DNDEBUG  -I"/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/library/Rcpp/include" -D__ACCELERATE__   -fPIC  -g -O2  -c utils.c -o utils.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/lib/x86_64 -L/usr/local/lib -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -L/Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/lib/x86_64 -lR -Wl,-framework -Wl,CoreFoundation
installing to /Users/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/library/MSnbase/libs/x86_64
** R
** data
*** moving datasets to lazyload DB
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** inst
** tests
** preparing package for lazy loading
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSnbase)
> library(MSnbase)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
    colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
fLoading required package: ProtGenerics

This is MSnbase version 2.3.10 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: ‘MSnbase’

The following object is masked from ‘package:stats’:

    smooth

The following object is masked from ‘package:base’:

    trimws

> cdfs <- dir(system.file("cdf/KO/", package = "faahKO"), full.names = TRUE)
> tmp <- readMSData(cdfs, mode = "onDisk")
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
> chromatogram(tmp, msLevel = 2)
Chromatograms with 0 rows and 6 columns
phenoData with 1 variables
Warning message:
In .extractMultipleChromatograms(object, rt = rt, mz = mz, aggregationFun = aggregationFun,  :
  No MS 2 data present.
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin16.7.0/x86_64 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] MSnbase_2.3.10      ProtGenerics_1.9.0  BiocParallel_1.11.6
[4] mzR_2.11.7          Rcpp_0.12.12        Biobase_2.37.2     
[7] BiocGenerics_0.23.0

loaded via a namespace (and not attached):
 [1] BiocInstaller_1.27.3  compiler_3.4.1        git2r_0.19.0         
 [4] plyr_1.8.4            iterators_1.0.8       zlibbioc_1.23.0      
 [7] tools_3.4.1           MALDIquant_1.16.2     digest_0.6.12        
[10] memoise_1.1.0         tibble_1.3.4          preprocessCore_1.39.0
[13] gtable_0.2.0          lattice_0.20-35       rlang_0.1.2          
[16] foreach_1.4.3         curl_2.8.1            withr_2.0.0          
[19] httr_1.3.1            knitr_1.17            IRanges_2.11.12      
[22] S4Vectors_0.15.5      devtools_1.13.3       stats4_3.4.1         
[25] grid_3.4.1            impute_1.51.0         R6_2.2.2             
[28] XML_3.98-1.9          limma_3.33.7          ggplot2_2.2.1        
[31] scales_0.4.1          pcaMethods_1.69.0     codetools_0.2-15     
[34] mzID_1.15.0           colorspace_1.3-2      affy_1.55.0          
[37] doParallel_1.0.10     lazyeval_0.2.0        munsell_0.4.3        
[40] vsn_3.45.2            affyio_1.47.0        

of course I can't extract MS level > 1 from the CDF files, but the msLevel parameter is supported. What is the class of your ms2data[[2]]?

[michaelwitting]

Well it looks like that is the problem:

> ms2data[[2]]
MSn experiment data ("XCMSnExp")
Object size in memory: 0.14 Mb
- - - Spectra data - - -
 MS level(s): 2 
 Number of spectra: 551 
 MSn retention times: 0:18 - 10:1 minutes
- - - Processing information - - -
Data loaded [Tue Aug 22 13:17:40 2017] 
Filter: select MS level(s) 2 [Tue Aug 22 13:17:46 2017] 
Filter: select MS level(s) 2 [Tue Aug 22 13:18:32 2017] 
 MSnbase version: 2.3.10 
- - - Meta data  - - -
phenoData
  rowNames: Bruker.mzML
  varLabels: sampleNames
  varMetadata: labelDescription
Loaded from:
  Bruker.mzML 
protocolData: none
featureData
  featureNames: F1.S00091 F1.S00120 ... F1.S16041 (551 total)
  fvarLabels: fileIdx spIdx ... spectrum (26 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave 
 19 peaks identified in 1 samples.
 On average 19 chromatographic peaks per sample.

on xrms_ms2_swath it is working.

> xrms_ms2_swath[[2]]
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 0.14 Mb
- - - Spectra data - - -
 MS level(s): 2 
 Number of spectra: 551 
 MSn retention times: 0:18 - 10:1 minutes
- - - Processing information - - -
Data loaded [Tue Aug 22 13:17:40 2017] 
Filter: select MS level(s) 2 [Tue Aug 22 13:17:46 2017] 
 MSnbase version: 2.3.10 
- - - Meta data  - - -
phenoData
  rowNames: Bruker.mzML
  varLabels: sampleNames
  varMetadata: labelDescription
Loaded from:
  Bruker.mzML 
protocolData: none
featureData
  featureNames: F1.S00091 F1.S00120 ... F1.S16041 (551 total)
  fvarLabels: fileIdx spIdx ... spectrum (26 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'

if I use ms1data for extracting a chromatogram it is working although it is XCMSnExp

Hope that makes things clear???

[jorainer]

Thanks for the info! So sorry, it's my fault. I completely forgot that I have a chromatogram,XCMSnExp method in xcms. That one didn't have (yet) the msLevel argument. Now, with the most recent version in the xcms3 branch there is the parameter.

devtools::install_github("sneumann/xcms", ref = "xcms3")

[michaelwitting]

Now it's working. Thank you very much!