Hi,

I'm trying to msnbase to process my itraq data. I'm getting an error message when I try to add identification data. Please see my code and error message below. My raw data input is mzXML files  (.raw converted to mzXML using Proteowizard) and my mzIdent files are from Mascot.

files=dir("/Users/kasojimd/Projects/ccrifx-541/Raw2mzXML",full.names=T,patter="mzXML")

rawdata=readMSData(files)

identFile=list.files(pattern=".mzid$")

msexp <- addIdentificationData(rawdata, filenames = identFile, verbose = FALSE)
Error in basename(id$spectrumFile) : a character vector argument expected

Any suggestions on how to get past this will be appreciated! I am new to proteomics data, so any other bioconductor package option suggestions will be appreciated too. I have already tried isobar, however I have come across  much difficulty when trying to use it.

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

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   base     

other attached packages:
[1] MSnbase_1.12.1       mzR_1.10.8           Rcpp_0.11.3          ggplot2_1.0.0        BiocInstaller_1.14.3 isobar_1.10.0       
[7] plyr_1.8.1           Biobase_2.24.0       BiocGenerics_0.10.0 

loaded via a namespace (and not attached):
 [1] affy_1.42.3              affyio_1.32.0            codetools_0.2-9          colorspace_1.2-4         digest_0.6.8            
 [6] distr_2.5.3              doParallel_1.0.8         foreach_1.4.2            grid_3.1.0               gtable_0.1.2            
[11] impute_1.38.1            IRanges_1.22.10          iterators_1.0.7          labeling_0.3             lattice_0.20-29         
[16] limma_3.20.9             MASS_7.3-37              munsell_0.4.2            mzID_1.2.1               pcaMethods_1.54.0       
[21] preprocessCore_1.26.1    proto_0.3-10             reshape2_1.4.1           scales_0.2.4             sfsmisc_1.0-27          
[26] startupmsg_0.9           stats4_3.1.0             stringr_0.6.2            SweaveListingUtils_0.6.2 tools_3.1.0             
[31] vsn_3.32.0               XML_3.98-1.1             zlibbioc_1.10.0         

I think your should not have this error any more with a recent version of MSnbase. From the NEWS file, I can see

CHANGES IN VERSION 1.15.1
-------------------------
 o Fixing error when id file has no spectrumFile info (see issue #39)
   and return a warning (instead of an error) when the file used to
   create the MSnExp/MSnSet and mzid file were different
   [2014-10-15 Wed]

However, this corresponds to the current development version. There are several options:

1. You install the development version of R, which will get you the Bioc devel and MSnbase 1.15.3. Beforehand, feel free to share the data with me and I will test it for you. I might actually even be possible (without guarantee, however) for you to continue with the object I create on your system.
2. You use the bioconductor/devel_proteomics docker container to get up and running with devel in no time without messing up with your current installation.
3. (I port the fix to release, but that will require some time.)

Option 2 is the fastest for you. Option 1 will take a bit of time.

Your is the previous stable version, so I would suggest you update anyway.

Laurent