Greetings, I am working on a project that requires a detailed audit of the entire MS processing chain, including the conversion of the Finnigan raw data into mzXML.
I've got a question about the source of precursor intensity values in MS2 scans obtained with Thermo instruments. Because precursor intensity is not be found anywhere in the Finnigan files (not as a named attribute), but it is found in the profile data, I assume readw (or the Thermo library it uses -- not sure how the code is divided between them) searches the parent scan's profile to find the intensity corresponding to the precursor mass. Q1: If that's what it does, what is the algorithm? Q2: Does it always do that correctly? A case in point: http://www.pil.sdu.dk/1/MSQuant/LTQ-FTsampleDataSet1,2004-02-14.zip readw v. 4.3.1 generates the following data set for the first MS2 scan in this file: <scan num="395" msLevel="2" peaksCount="184" polarity="+" scanType="Full" filterLine="ITMS + c ESI d Full ms2 [email protected] [90.00-755.00]" retentionTime="PT904.361S" lowMz="110.959" highMz="474" basePeakMz="354.963" basePeakIntensity="1354.62" totIonCurrent="6636.68" collisionEnergy="27" > <precursorMz precursorIntensity="574.678" activationMethod="CID" >370.12</precursorMz> . . . The naïve way to do it (and I can think of no other) would be to take the stated precursor mass (370.121154785156) and look for a matching bin value in the parent scan's profile (in this case, scan 394): 370.117473251246 2696.37426757812 370.119133095675 6863.94091796875 370.120792954993 9653.3193359375 370.122452829198 8103.22998046875 In this case, I would simply grab the value at 370.120792954993. Readw, however, picks 574.678. Where does it get it? I do a search across the entire file and find matching values at four locations: addr hex decimal 72d24a 6AAB0F44 574.6783 1731572 65AB0F44 574.678 32c86ce 67AB0F44 574.6782 33de66a 60AB0F44 574.6777 Of these, only the first one seems to be relevant, as it happens to be in the profile data for scan 393 -- the one immediately preceding my parent scan: 370.112977204668 432.1953125 370.116296831858 565.481323242188 370.119616518597 574.678344726562 370.122936264888 449.774383544922 Is this a common array indexing error, or is there some magic I fail to understand? Thanks, --Gene -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
