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Re: [Psidev-ms-dev] use case: FT transient data
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From: Kessner, D. E. <Dar...@cs...> - 2008-02-21 19:33:42
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Actually, I agree with Matt here -- allowing a <binaryDataArray> to override the <spectrum> 'arrayLength' is a simple solution to allow these auxilliary arrays to have a different length from the main m/z-intensity arrays. Another issue with using two <spectrum> elements for a single scan is that it has to be decided whether to duplicate scan metadata. If the metadata is not to be duplicated, it is essential to have cross-references between the <spectrum> elements. Darren -----Original Message----- From: psi...@li... [mailto:psi...@li...] On Behalf Of Matthew Chambers Sent: Thursday, February 21, 2008 11:15 AM To: Mass spectrometry standard development Subject: Re: [Psidev-ms-dev] use case: FT transient data It's a neat use case and would like to see it supported, but am I the only one that thinks this would be better as an auxiliary binaryDataArray element inside the same spectrum element? This implementation seems much more complicated and verbose than an equivalent implementation supported by binaryDataArray elements with varying length. -Matt Kessner, Darren E. wrote: > > Hi all, > > > > Here is a <spectrumList> fragment to illustrate the encoding of FT > transient data, as requested by Eric during the conference call. > > > > Some notes: > > > > The <spectrum> attribute 'index' indicates the 0-based index into the > <spectrumList>. There are two scans (17 and 18), each with an > m/z-intensity <spectrum> followed by a transient intensity > <spectrum>. The Thermo scan number is encoded as <acquisition> > attribute 'number' as suggested by Randy. > > > > I'm not sure whether we would want an additional CV term for > "transient intensity array", which is a time-based intensity array. > We would need a CV term for "acquisition time" to describe how long > the signal is being observed in the FT cell. There would be some > other terms for metadata values associated with the transient as > well. Note that there is no array for time points -- it is assumed > that the time spacing is regular, and calculated by the array size and > "acquisition time" (this may be encoded differently by different vendors). > > > > I don't immediately see a way to pair the m/z spectrum with the > transient spectrum -- it would be nice to have a general <spectrumRef> > from one <spectrum> to another (not just to a precursor), so that you > can find e.g. the transient data associated with an m/z spectrum or > vice versa. > > > > > > <spectrumList count="4"> > > > > <spectrum id="S17" index="0" msLevel="1" arrayLength="1313"> > > <cvParam cvLabel="MS" accession="MS:1000580" name="MSn > spectrum" value=""/> > > <spectrumDescription> > > <acquisitionList count="1"> > > <acquisition number="17" spectrumRef="?" > sourceFileRef="?"/> > > </acquisitionList> > > ... > > </spectrumDescription> > > <binaryDataArray encodedLength="5000" > dataProcessingRef="Xcalibur Processing"> > > ... > > <cvParam cvLabel="MS" accession="MS:1000514" name="m/z > array" value=""/> > > <binary>...</binary> > > </binaryDataArray> > > <binaryDataArray encodedLength="5000"> > > ... > > <cvParam cvLabel="MS" accession="MS:1000515" > name="intensity array" value=""/> > > <binary>...</binary> > > </binaryDataArray> > > </spectrum> > > > > <spectrum id="S17_transient" index="1" msLevel="1" arrayLength="1234"> > > <cvParam cvLabel="MS" accession="MS:1000xxx" name="MSn > transient spectrum ?" value=""/> > > <spectrumDescription> > > <acquisitionList count="1"> > > <acquisition number="17" spectrumRef="?" > sourceFileRef="?"/> > > </acquisitionList> > > ... > > <cvParam cvLabel="MS" accession="MS:1000xxx" > name="acquisition time" value=".768" unitAccession="MS:1000039" > > unitName="second"/> > > </spectrumDescription> > > <binaryDataArray encodedLength="5000" > dataProcessingRef="Xcalibur Processing"> > > ... > > <cvParam cvLabel="MS" accession="MS:1000xxx" > name="transient intensity array ?" value=""/> > > <binary>...</binary> > > </binaryDataArray> > > </spectrum> > > > > <spectrum id="S18" index="2" msLevel="1" arrayLength="1400"> > > <cvParam cvLabel="MS" accession="MS:1000580" name="MSn > spectrum" value=""/> > > <spectrumDescription> > > <acquisitionList count="1"> > > <acquisition number="18" spectrumRef="?" > sourceFileRef="?"/> > > </acquisitionList> > > ... > > </spectrumDescription> > > <binaryDataArray encodedLength="5000" > dataProcessingRef="Xcalibur Processing"> > > ... > > <cvParam cvLabel="MS" accession="MS:1000514" name="m/z > array" value=""/> > > <binary>...</binary> > > </binaryDataArray> > > <binaryDataArray encodedLength="5000"> > > ... > > <cvParam cvLabel="MS" accession="MS:1000515" > name="intensity array" value=""/> > > <binary>...</binary> > > </binaryDataArray> > > </spectrum> > > > > <spectrum id="S18_transient" index="3" msLevel="1" arrayLength="2345"> > > <cvParam cvLabel="MS" accession="MS:1000xxx" name="MSn > transient spectrum ?" value=""/> > > <spectrumDescription> > > <acquisitionList count="1"> > > <acquisition number="18" spectrumRef="?" > sourceFileRef="?"/> > > </acquisitionList> > > ... > > <cvParam cvLabel="MS" accession="MS:1000xxx" > name="acquisition time" value=".768" unitAccession="MS:1000039" > > unitName="second"/> > > </spectrumDescription> > > <binaryDataArray encodedLength="5000" > dataProcessingRef="Xcalibur Processing"> > > ... > > <cvParam cvLabel="MS" accession="MS:1000xxx" > name="transient intensity array ?" value=""/> > > <binary>...</binary> > > </binaryDataArray> > > </spectrum> > > > > </spectrumList> > > > > > > Darren > > > > IMPORTANT WARNING: This message is intended for the use of the person > or entity to which it is addressed and may contain information that is > privileged and confidential, the disclosure of which is governed by > applicable law. If the reader of this message is not the intended > recipient, or the employee or agent responsible for delivering it to > the intended recipient, you are hereby notified that any > dissemination, distribution or copying of this information is STRICTLY > PROHIBITED. > > If you have received this message in error, please notify us immediately > by calling (310) 423-6428 and destroy the related message. Thank You > for your cooperation. > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ - > This SF.net email is sponsored by: Microsoft > Defy all challenges. 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If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is STRICTLY PROHIBITED. If you have received this message in error, please notify us immediately by calling (310) 423-6428 and destroy the related message. Thank You for your cooperation. |
