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Spectra MsBackend for Thermo Fisher Scientific's New RawFileReader

Home Page: https://bioconductor.org/packages/MsBackendRawFileReader/

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jorainer rogerginber

msbackendrawfilereader's Issues

call the test suite to check if their backend is compatible with the expectations.

see rformassspectrometry/Spectra#227

raw file spec. meta data

thermo raw files contain lots of metadata in different containers. This issue will deal with how to make them accessible in R using the Spectra class or a raw specific extension.

Missing link to package at https://www.rformassspectrometry.org/contributions/

https://www.rformassspectrometry.org

does not mention this package at all. There is also no link to your name in the contribution section @cpanse. This should really change!

implement lazy evaluation for scan metadata

@lgatto @jorainer We were wondering if you already have an estimated time of submission to bioc/cran for the Spectra package? @cpanse is almost ready with the MSBackendRawFileReader code, so a back-to-back submission might be a cool thing.

Error with 'spectraData(S)'

hi,
i'm getting an error when calling the function 'spectraData()', as follows:

library(MsBackendRawFileReader)

fls <- file.path(path.package(package = 'MsBackendRawFileReader'),
                      'extdata', 'sample.raw')
be <- backendInitialize(MsBackendRawFileReader(), files = fls, extra=TRUE)
S <- Spectra(be)
S
MSn data (Spectra) with 574 spectra in a MsBackendRawFileReader backend:
filename:       /opt/R/R-devel/lib/R/library/MsBackendRawFileReader/extdata/sample.raw
creation date:  2/13/2018 11:09:03 AM
first scan:     1
last scan:      574
model:  Q Exactive HF-X Orbitrap
name:   Q Exactive HF-X Orbitrap
SerialNumber:   Exactive Series slot #6114 

Processing:

df <- spectraData(S)
Error in internal <- ccall(obj, fun, list(...)) :
  System.ArgumentException: cannot find matching method: getFirstScanNumber, within: MsBackendRawFileReader.Rawfile, requested with 0 params
  at bridge.common.reflection.ReflectUtils.CallMethod (System.Object obj, System.String name, System.Object[] parameters) [0x00069] in <91361fa098404b9790c079edab938b6d>:0
    at bridge.embedded.CLRBridgeEmbedded.CallMethod (System.Object obj, System.String name, System.Object[] parameters) [0x00001] in <91361fa098404b9790c079edab938b6d>:0
    at bridge.server.CLRBridgeServerClient.HandleCallMethod (bridge.server.ctrl.CLRCallMethodMessage req) [0x00022] in <91361fa098404b9790c079edab938b6d>:0

here is the traceback:

traceback()
17: stop(e)
16: value[[3L]](cond)
15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch({
          FUN(...)
              }, error = handle <- error)
12: withCallingHandlers({
          tryCatch({
                        FUN(...)
                                }, error = handle <- error)
              }, warning = handle <- warning)
11: FUN(...)
10: FUN(X[[i]], ...)
9: lapply(X, FUN <- , ...)
8: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = param)
7: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = param)
6: bplapply(split(object@backend, f), function(z, queue) {
                     .apply <- processing <- queue(as.list(z), msLevel(z), centroided(z),
                                                              queue = queue)
                        }, queue = pqueue, BPPARAM = BPPARAM)
5: bplapply(split(object@backend, f), function(z, queue) {
                     .apply <- processing <- queue(as.list(z), msLevel(z), centroided(z),
                                                              queue = queue)
                        }, queue = pqueue, BPPARAM = BPPARAM)
4: .peaksapply(object)
3: .local(object, ...)
2: spectraData(S)

Here's my session information:

sessionInfo()
R Under development (unstable) (2019-11-05 r77372)                              
Platform: x86_64-apple-darwin16.7.0 (64-bit)                                    
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS:   /opt/R/R-devel/lib/R/lib/libRblas.dylib                                
LAPACK: /opt/R/R-devel/lib/R/lib/libRlapack.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] stats4    parallel  stats     graphics  grDevices utils     datasets       
[8] methods   base     

other attached packages:
 [1] MsBackendRawFileReader_0.0.2 rDotNet_0.9.1                                
 [3] Spectra_0.3.0                ProtGenerics_1.19.0                          
 [5] IRanges_2.21.2               S4Vectors_0.25.6                             
 [7] BiocGenerics_0.33.0          BiocParallel_1.21.0                          
 [9] nvimcom_0.9-28               colorout_1.2-2                               

loaded via a namespace (and not attached):                                     
[1] Rcpp_1.0.3        R6_2.4.1          magrittr_1.5      MsCoreUtils_0.0.2    
[5] rlang_0.4.2       testthat_2.3.1    tools_4.0.0       compiler_4.0.0

thanks!!

robert.

consider rawFile.IncludeReferenceAndExceptionData = true;

https://github.com/cpanse/MsBackendRawFileReader/blob/63d90b342cce3552b51ccca73b2adcad1eadc3b6/src/MsBackendRawFileReader.cs#L59

#R

# BiocManager::install('cpanse/MsBackendRawFileReader')
library(MsBackendRawFileReader)

rawfile <- "AC0040V1_pos.RAW"

xic5 <- readXICs(rawfile, 143.10666, 5)
xic10 <- readXICs(rawfile, 143.10666, 10)


par(mfrow=c(2,1))
plot(xic5[[1]]$times, xic5[[1]]$intensities, type='l')
plot(xic10[[1]]$times, xic10[[1]]$intensities, type='l')
sessionInfo()

R --no-save < code.R

R> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.4

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.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] stats4    parallel  stats     graphics  grDevices utils    
[7] datasets  methods   base     

other attached packages:
[1] MsBackendRawFileReader_0.0.4 rDotNet_0.9.1               
[3] Spectra_0.3.0                ProtGenerics_1.18.0         
[5] IRanges_2.20.2               S4Vectors_0.24.3            
[7] BiocGenerics_0.32.0          BiocParallel_1.20.1         

loaded via a namespace (and not attached):
[1] Rcpp_1.0.3        R6_2.4.1          magrittr_1.5     
[4] MsCoreUtils_0.0.2 rlang_0.4.4       testthat_2.3.1   
[7] tools_3.6.2       compiler_3.6.2   
R>

rawFile.IncludeReferenceAndExceptionData = false;

rawFile.IncludeReferenceAndExceptionData = true;

The RAW file has data from 1 instruments
General File Information:
   RAW file: AC0040V1_pos.RAW
   RAW file version: 66
   Creation date: 08/13/2019 15:05:45
   Operator: ExactiveUser
   Number of instruments: 1
   Description: 
   Instrument model: Q Exactive Plus Orbitrap
   Instrument name: Q Exactive Plus Orbitrap
   Serial number: Exactive Series slot #1234
   Software version: 2.9-290204/2.9.3.2948
   Firmware version: rev. 1
   Units: None
   Mass resolution: 0.500 
   Number of scans: 392
   Number of ms2 scans: 0
   Scan range: 1 - 392
   Time range: 0.01 - 7.75
   Mass range: 85.0000 - 600.0000

Sample Information:
   Sample name: 
   Sample id: 
   Sample type: Unknown
   Sample comment: 
   Sample vial: 
   Sample volume: 0
   Sample injection volume: 0
   Sample row number: 0
   Sample dilution factor: 0

Filter Information:
   Scan filter (first scan): FTMS + p ESI Full lock ms [85.0000-600.0000]
   Scan filter (last scan): FTMS + p ESI Full lock ms [85.0000-600.0000]
   Total number of filters: 1

ACK
[email protected]

Implement access to all coreSpectraVariables()

Hi @cpanse!

I was trying to expand the spectraData currently retrieved from the raw files to include relevant variables in Spectra::coreSpectraVariables() like collisionEnergy, polarity, isolationWindow, etc. For context, our group is currently working with stepped-energy HCD MS2 spectra, but conversion to mzML always removes this info and leaves us with only one collision energy.

From what I've seen, it seems that all this data is in each rawrrSpectrum (ie. not in the header), so my idea would be to retrieve the spectra in groups at some point during .backendInitialize, extract the relevant information and add it to what's already in the spectraData DFrame.

Does that sound good? Would you be interested in a PR?

Cheers,
Roger

add tiny raw|mzXML file for Fusion|Lumos instruments

just for unit testing

Note: spectraData,MsBackend renamed to asDataFrame,MsBackend

Just a note: we've recently renamed the spectraData,MsBackend method into asDataFrame,MsBackend. This should not affect your package, since I haven't seen any implementation/usage of this method in your package but I still wanted to let you know.

add test cases - MsBackendMzR versus MsBackendRawFileReader

generate sample.mzXML
use testthat to compare Spectra objects

MsBackendMzR versus MsBackendRawFileReader

compare profile to centroid methods

#R

# Orbitrap Fusion Lumos FSN20242
rawfile <- "/Users/cp/Downloads/p2722/stds_pos_neg_MS_highconc_UVPD_50_300.raw"


library(MsBackendRawFileReader)

be <- backendInitialize(MsBackendRawFileReader(), files = rawfile)
(SP <- Spectra(be))

i.p <- Spectra::intensity(SP)
m.p <- Spectra::mz(SP)

SC <- Spectra::pickPeaks(SP)
i.c <- Spectra::intensity(SC)
m.c <- Spectra::mz(SC)


idx.ms2 <-  which(msLevel(SP) == 2)

# BiocManager::install('cpanse/protViz')
# protViz package version >= 0.3.6
library(protViz)

rv <- lapply(idx.ms2, function(i){
        profile <- data.frame(mZ=m.p[[i]], intensity=i.p[[i]])
        rv.protViz <- protViz::centroid(m.p[[i]], i.p[[i]])
        rv.spectra  <- data.frame(mZ=m.c[[i]], intensity=i.c[[i]])

        if (nrow(rv.protViz) == nrow(rv.spectra )){
                fit <- lm(rv.protViz$mZ ~ rv.spectra$mZ)
        list(profile, rv.protViz, rv.spectra, fit)
        }
        list(profile, rv.protViz, rv.spectra)

})

implement `filterScan`

MsBackendRawFileReader funding

In the README file, I saw that you have an internal FGCZ project p3181 application for R MsBackendRawFileReader. I am writing a grant proposal to hire somebody full time on the R for Mass Spectrometry project, and I am asked to mention any existing support related to the project. I would like to know if I can mention the internal application. If so, would it be possible to get the duration and possibly even amount?

Thank you in advance!