If you're getting that old error message it means you're executing the wrong version. You can very
it by running msconvert without arguments. At the bottom of the usage output will be version
information. Try specifying an absolute path to the new msconvert like:
C:\path\to\new\msconvert.exe <args>
-Matt
On 1/18/2011 1:46 PM, bobxiong wrote:
Hi Matt,
Thanks again for your insight.
I ran the command 'msconvert my_fullscan.wiff' in the directory pwiz-
bin-windows-x86-vc90-release-2_1_2465 and here is the complete error
msg.
[Reader_ABI::ctor] Reading ABI WIFF files requires Protein Pilot 3.0
to be installed. A trial version is available for download at:
https://licensing.appliedbiosystems.com/download/ProteinPilot/3.0
Error processing file my_fullscan.wiff
I got the same error msg when running the same command in the tpp-bin
directory.
Now I have both Protein Pilot 4.0 and Skyline 0.7.0.2342 installed on
my Windows XP. But the error msg remains unchanged.
(The web installation of Skyline was successful. But it looked bizzare
when I fired it up. It displayed no tool bar whatsoever. The only
thing displayed were several dots followed by a small gray box.
Something must be wrong either with the build or my system, which is
Windows XP Professional Version 2002, Service Pack 2)
Thanks for your time,
Bob
On Jan 18, 10:36 am, Matthew Chambers<[email protected]>
wrote:
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/S...
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 -
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