It sounds like you got the newest pwiz but you're executing an older version (perhaps the one you
got with TPP). The latest error message should be:
[Reader_ABI::ctor] Reading ABI WIFF files requires Protein Pilot 3.0 or Skyline to be installed.
Skyline is freely available
at:\nhttps://brendanx-uw1.gs.washington.edu/labkey/project/home/software/Skyline/begin.view
So it points you at Skyline, which is still available. It should work seamlessly once Skyline is
installed (please let me know if it doesn't).
-Matt
On 1/17/2011 5:42 PM, bobxiong wrote:
Hi Matt,
Thanks for your reply and suggestion.
I downloaded pwiz-bin-windows-x86-vc90-release-2_1_2467.tar.bz2 to get
msconvert. However, when I ran the command 'msconvert
my_fullscan.wiff' on the command line, I got the error msg '...
requires Protein Pilot 3.0...'. Unfortunately, Protein Pilot 3.0
(trial version) doesn't seem to be available from ABI's download
portal. (part # 1036426 listed on ABI's website but nothing matches
it). So I probably need an alternate solution. Can you give me another
pointer?
Thanks,
Bob
On Jan 17, 2:26 pm, Matthew Chambers<[email protected]>
wrote:
I don't know why mzWiff isn't writing a peaks element, but msconvert will.
-Matt
On 1/17/2011 11:29 AM, bobxiong wrote:
I'm using TPP v4.4 VUVUZELA rev 1, Build 201010121551 (MinGW) to
convert wiff raw data to mzXML. The command executed in TPP was
c:\Inetpub\tpp-bin\mzWiff -v --mzXML -c1 -g -G --Analyst c:/Inetpub/
wwwroot/ISB/data/my_fullscan.wiff.
An excerpt of the output is shown below:
<scan num="1"
msLevel="1"
peaksCount="140"
polarity="+"
scanType="Q1 Scan"
retentionTime="PT0.001S"
lowMz="106.7"
highMz="1206.8"
basePeakMz="115.9"
basePeakIntensity="3.24903e+006"
totIonCurrent="3.06962e+007">
</scan>
I wonder if I could use some sort of advanced option (that I'm not
aware of) to extract info (mz, intensity and retention time) for ALL
the peaks contained in the wiff file rather than for the base peak
only (shown above). If this is not feasible using mzWiff, are there
other tools available to do what I needed? Any advice would be greatly
appreciated.
Bob- Hide quoted text -
- Show quoted text -
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