unreliable peak intensity in report table

Topic: unreliable peak intensity in report table (Read 16075 times) previous topic - next topic

Re: unreliable peak intensity in report table

Reply #15 – July 31, 2015, 03:42:58 AM

mmmmhh I see. We are using proteowizard to convert the raw data into mzXML, using the peakpicking filter (I thought it convert profile data into centroided ones?), such as:

converter <- c("D:/Pwiz/msconvert.exe")
FILES <- list.files(recursive=TRUE,full.names=TRUE,pattern="\.raw")

for (i in 1:length(FILES)){system (paste(converter," --mzXML --32 --filter "peakPicking true 1" --filter "polarity negative" -o Negative -v",FILES))}
for (i in 1:length(FILES)){
system (paste(converter," --mzXML --32 --filter "peakPicking true 1" --filter "polarity positive" -o Positive -v",FILES))}

but obviously it's not correct

what do you think?
many thanks again
jc

Re: unreliable peak intensity in report table

Reply #16 – July 31, 2015, 04:29:11 AM

I don't know why that doesn't work... I tried re-converting your files and I cannot get it to centroid the data either... You'd probably have to ask the proteowizard people. Sorry.

Re: unreliable peak intensity in report table

Reply #17 – July 31, 2015, 07:23:10 AM

Jan
I just used another version of proteowizard than the one we previously utilized to generate the files I'm working on, and this time it worked well, converting the data into the centroid mode (12Mo instead of 163Mo!, with m/z with zero line witdhs). The good version of proteowizard to use would be 3.0.6994 and over.
I must admit that we should have looked at the size of the files generated after proteowizard,
I'll keep you posted on our continuation
by the way, I finished to succesfully install chemhelper and all dependancies
thanks anyway
jc