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.

Kind Regards


-- 
Reema Singh
PhD Scholar
Computational Biology and Bioinformatics
School of Computational and Integrative Sciences
Jawaharlal Nehru University
New Delhi-110067
INDIA

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