Absolutely right! I should have said that at least we encounter non-indexed mzML files much more often than non-indexed mzXML files (for instance in compassXport 3.0.5 the default is indices with mzXML, no indices with mzML...). We did some benchmarking with our parsers and having the indices do make a difference, although not as much as a factor 7.
Cheers, Magnus On Thursday, 30 August 2012 18:11:40 UTC+2, Brian Pratt wrote: > > Actually the index is an optional element in mzXML, too - a proper > mzXML parser will function without it. > > - Brian > > On Thu, Aug 30, 2012 at 9:03 AM, [email protected] <javascript:> > <[email protected] <javascript:>> wrote: > > Hi Thomas, > > > > Was the mzML file indexed or not? This can sometimes make a big > difference > > if the program you use accesses the data randomly (or one spectra at a > > time). The mzXML files always have indices, but for mzML they are > optional. > > Then the mzML parser must also make use of the indices of course - see > > previous comment. > > > > > > Cheers, > > > > Magnus > > > > On Thursday, 30 August 2012 17:37:42 UTC+2, Brian Pratt wrote: > >> > >> Quite a lot of performance work was done in pwiz in late 2011 - do you > >> know what version of pwiz is in use? > >> > >> Brian Pratt > >> > >> On Thu, Aug 30, 2012 at 2:16 AM, Thomas Dybdal Pedersen > >> <[email protected]> wrote: > >> > Hi > >> > > >> > I've recently begun to investigate whether it was time to change our > >> > pipeline from mxXML to mxML format. Our pipeline is partly based on > xcmd > >> > which uses RAMP to read in ms data. I quick comparison of the parsing > >> > speed > >> > between mzML and mzXML showed that mzML was slower by a factor ~7. > This > >> > is > >> > quite substantial especially for larger files. > >> > > >> > I understand that the mzML parsing is based on pwiz instead of > >> > implemented > >> > from the ground, which is probably the cause for the difference. Is > >> > there > >> > any effort in creating a more effecient parser for the mzML format as > >> > this > >> > format increase in relevance? > >> > > >> > with best wishes > >> > > >> > Thomas > >> > > >> > -- > >> > You received this message because you are subscribed to the Google > >> > Groups > >> > "spctools-discuss" group. > >> > To view this discussion on the web visit > >> > https://groups.google.com/d/msg/spctools-discuss/-/sDYMC6Ynd3cJ. > >> > 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. > > > > -- > > You received this message because you are subscribed to the Google > Groups > > "spctools-discuss" group. > > To view this discussion on the web visit > > https://groups.google.com/d/msg/spctools-discuss/-/gFktILjGAOAJ. > > > > To post to this group, send email to > > [email protected]<javascript:>. > > > To unsubscribe from this group, send email to > > [email protected] <javascript:>. > > For more options, visit this group at > > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/a9cJ4jx27R4J. 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.
