I am well aware of this issue, but there's no schematic rule about the file being in retention time
order. And there is no scan number for a WIFF scan (since it uses the arbitrary index that pwiz
translates to, that part at least actually does increase monotonically). Use mzML and nativeID! :)
The problem is the WiffFileReader API takes a relative eternity to switch between experiments. It's
quite slow enough as it is. :) You'll be happy to hear that the new API does not have the same
problem. With the current API it would be faster (except possibly with huge profile data) to first
convert to XML and then use a sorting filter to convert the XML to another file sorted by retention
time. Currently there is a sorting filter, but no built-in predicates that use it are accessible
from the command-line.
I'm not actually sure HOW to tell which scan is the precursor scan. In Thermo, figuring out the
precursor scan with certainty without parsing the scan event list (which comes in a fascinating
variety of formats) can be quite tricky. I don't know if the same problems exist in ABI and there's
no scan event list to check (AFAIK), so I punted.
-Matt
On 1/19/2011 11:34 AM, Nathan Edwards wrote:
I've had this problem with a variety of tools and their handling .wiff
data file from Analyst, and now having gotten msconvert to work
(thanks Matt) I was hoping that msconvert did it "right".
Unfortunately, it doesn't seem so.
I believe that the scan number and retention times should increase
monotonically in the mzXML file and in a tandem mass-spectrometry
experiment, I expect the MS1 scan to be immediately followed by the MS/
MS scans whose precursors are derived from the MS1 scan.
A number (n>= 2) of converters (msconvert& ABI's) for .wiff files do
not respect this file structure and output the spectra by experiment
and cycle, with all experiment 1 (MS1 spectra) first, then all
experiment 2 (MS/MS from first selected precursor peak from each MS1
spectrum), then all experiment 3, etc.
In the msconvert mzXML output, there isn't even any reference in the
MS2 spectra to assist in determining the correct MS1 spectrum to
associate with the MS2 spectrum.
It is possible to use various tricks to try and determine cycle,
experiment, and MS1/MS2 relationships but at the least these require
sorting (globally) on retentionTime, an expensive proposition for
large mzXML files.
I'd be happy to provide an example mzXML output to demonstrate the
issue.
- n
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