Hi Matt,
I applied multiple filters to pick peaks and keep all the peaks that
are at least 25% of the intensity of the base peak (command shown
below).
msconvert my_fullscan.wiff --filter "peakPicking true 1-" --filter
"threshold bpi-relative .25 most-intense"
(msconvert in ProteoWizard release 2.1.2465 (2011-1-13))
But I only saw basePeakMz, basePeakIntensity and retentionTime.
(output excerpt shown below, peaksCount=16)
<scan num="6947"
scanType="FULL"
centroided="1"
msLevel="1"
peaksCount="16"
polarity="+"
retentionTime="PT13984.6S"
lowMz="101.90000000000001"
highMz="1250"
basePeakMz="583.29999999999995"
basePeakIntensity="7366390.5"
totIonCurrent="1421788123">
<peaks compressedLen="0"
precision="64"
byteOrder="network"
pairOrder="m/z-
int">QG4WZmZmZmZBPevYgAAAAEBuIAAAAAAAQTz0wQAAAABAcNZmZmZmZkFCQEgAAAAAQHhRmZmZmZpBSXI9AAAAAEB89mZmZmZmQVsML6AAAABAfQTMzMzMzUFWMxyAAAAAQH0UzMzMzM1BSuTgQAAAAECCOmZmZmZmQVwZvaAAAABAgkQAAAAAAEFWjPaAAAAAQIJKZmZmZmZBTkWygAAAAECDCzMzMzMzQVE4V6AAAABAgxQAAAAAAEFCxw8AAAAAQIN4AAAAAABBUA61gAAAAECDgzMzMzMzQT62AwAAAABAhJJmZmZmZkFLBpIAAAAAQIj3MzMzMzNBRKoCwAAAAA==</
peaks>
</scan>
Did I apply the filters incorrectly?
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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