[BioC] XCMS query regarding mzXML

[Laurent Gatto]

Dear Reema,

On 6 August 2013 10:22, Reema Singh <reema28sep at gmail.com> wrote:
> Dear All,
>
> I am trying to import .mzXML files using XCMS package. I have tried it with
> two different data set (
> ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/PAe000030 ) and
> ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/PAe0000<ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/PAe000030>02).
>  After extracting .mzXML files, when i tried to import them using XCMS, I
> got this output.
> *PAe000002*
> files <- list.files("TEST", recursive=TRUE,full.names=TRUE)
>> xr<-xcmsRaw(files[1])
>> xr
> An "xcmsRaw" object with 2070 mass spectra
>
> Time range: 120-5879.1 seconds (2-98 minutes)
> Mass range: 400.0667-1399.9995 m/z
> Intensity range: 1-465033000
>
> MSn data on  0  mass(es)
> with  0  MSn spectra
> Profile method: bin
> Profile step: 1 m/z (1001 grid points from 400 to 1400 m/z)
>
> Memory usage: 34.4 MB
>
> *PAe000030*
>
>> files1 <- list.files("TEST1", recursive=TRUE,full.names=TRUE)
>> xr1<-xcmsRaw(files1[1])
> Warning message:
> In `profStep<-`(`*tmp*`, value = 1) :
>   MS1 scans empty. Skipping profile matrix calculation.
>> xr1
> An "xcmsRaw" object with 0 mass spectra
>
> MSn data on  0  mass(es)
> with  0  MSn spectra
> Profile method: bin
> Profile step: no profile data
>
> Memory usage: 0.00481 MB
>>
>
> Now My question is Why One dataset is successfulyy imported, whereas in the
> same dataset got some warnings and datset with zero masses?.
>
> I would appreciate any help.

First, we do not know exactly what files you are using for your test.
Reading all of the PAe000030 mzXML files works well on my computer,
indicating that it is likely not a mzXML issue as such.

As the warning message suggests, the MS1 scans of that particular
mzXML file are empty, which terminates the processing. Have you had
more luck with another file from that experiment? You might want to
check the offending mzXML file - it might indeed be valid yet 'empty'.

Hope this helps,

Laurent

> Kind Regards
>
>
> --
> Reema Singh
> PhD Scholar
> Computational Biology and Bioinformatics
> School of Computational and Integrative Sciences
> Jawaharlal Nehru University
> New Delhi-110067
> INDIA
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
Laurent Gatto
- http://proteome.sysbiol.cam.ac.uk/lgatto/
Cambridge Centre for Proteomics
- http://www.bio.cam.ac.uk/proteomics
Using R/Bioconductor for proteomics data analysis
- http://lgatto.github.io/RforProteomics/