Hi Ludovic, The Agilent scanIds are the numbers used by the raw file and the API. It's not a bug.
One of my primary requirements for ids is being able to unambiguously find the raw spectrum given the id, whether it's been converted to mzML, mzXML, or whatever. Artificially forcing the scan numbers to be consecutive violates that for several vendor formats (not to mention filtering by MS level, activation type, or sorting on something other than time, etc.).
I think TPP has some refresh program to force the numbers to be consecutive but I'll let someone more familiar with TPP answer that; I remember this issue came up a while ago. I never noticed the correlation between scan time and scanId before, that's interesting! I suppose that at least for your instrument, the (micro?)scan rate was close to 1000/sec.
HTH, -Matt On 2/7/2011 9:56 AM, lgillet wrote:
Dear group, While trying to search files obtained upon conversion of Agilent QTOF .d files to mzXML with msconvert, I realized that the .dta files created for Sequest search were very few and had a very strange numbering. (Windows XP, msconvert version tried: Build_12_ProteoWizard_r2127 or pwiz-bin-windows-x86-vc90-1_6_1386 or pwiz-bin-windows-x86-vc90- release-shared-2_1_2485). Upon investigating a bit, it seems that msconvert performs a wrong numbering of the scans from the .d files. Here is an example of the 2 first scans obtained from an mzXML files from msconvert: As you may realize, the scan numbers from the msconver conversion are actually, for whatever reason, the time in milli-seconds?!? (e.g. scan 1<=> 2.56sec<=> scan num="2567" !!!!!) So here are my questions: 1) is there a script (I think there is but I cannot put hands on it anymore) among the TPP executables to renumber the scans consecutively? 2) Could you release a fix for this Agilent file conversion in a future msconvert release? Thanks in advance for you inputs, Best, Ludovic
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