For a more detailed explanation of the filters, use msconvert
--help. But yes, mzWindow and scanTime will do what you need, except
it's still extracting raw spectra within those criteria, not making
an intensity vs retention time chromatogram. If you want to make a
chromatogram, try msaccess' "slice" command. All of the tools will
give you unprocessed data unless you tell them otherwise. Your
confusion stems from the fact that your file was acquired with some
centroid-only spectra (I'm guessing MS2s). You can't get the profile
data back for those spectra. But if you're making a chromatogram,
you don't really need profile data anyway.
The SHA-1 is part of the mzML standard and is required to make it a
valid file. It's useful for checking that the file that was
converted has not been corrupted or changed, or indeed checking if
the file is a different one that's been evilly renamed. Make sure
you're using the very latest msconvert. I recently fixed a severe
performance issue that has been in effect since I made the SHA-1
tool we use work for UTF-8 filenames.
Hope this helps,
On 7/2/2014 6:27 PM, James Yuan wrote:
I have been tasked with extracting specific windows of data
from raw profile data collected on an Agilent instrument. I need
to extract data based on a specific retention time window and
specific mz window. The output should be intensity vs retention
time for that window.
I was originally going to use the Reader API to manipulate
the files directly but I noticed there were two filter options
in msconvert called “scanTime” and “mzWindow”
I just need to confirm does calling:
msconvert example_data.d --filter
“scanTime [a,b]” --filter “mzWindow [x,z]”
do what I want? When I run this command does msconvert use
the raw profile data in the directory or the centroid data? And
does msconvert automatically do any extra processing (eg.
centroiding) to the output or does it simply convert the raw
profile data from the Agilent format into mzML? I want to
extract the pure untouched profile data.
I did a test run and in the mzML file I noticed the following
name="total ion current
name="total ion current
Does this mean the data that I have in the mzML file is
not from the profile spectrum? The file that contains
profile data is called “MSProfile.bin” and not
“MSScan.bin”. Do I need to change the command I’m using to
extract data from the correct file? I have attached the
full mzML file for you to look at. It seems the file is a
little small considering the original binary file was
1.7GB although I did choose a relatively small window to
use for this test.
Also what is the purpose of performing the SHA-1 hash
and is there any way to skip it?
Thanks for your help,
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