Hi Mike, Thank you for the quick reply. This does indeed seem to be the problem so I will have to recalculate the offset.... I'll report back when completed in case others have a similar problem.
Thanks! Connor On Monday, August 7, 2017 at 6:09:29 PM UTC-5, Michael Hoopmann wrote: > > Hi Connor, > > In the example file you provided, I see that your > <indexListOffset>761801</indexListOffset> points to the middle of the > intensity array of scan 100 and not to the start of the indexList. > > > > Your actual indexListOffset looks to be 769983. The error message is > because the indexListOffset needs to be set to the correct position. > > > > Similarly, all your scan indexes listed in the <offset> tags point to the > wrong places. You can’t see that yet because the TPP stopped reading the > file when it gave you the first error message. > > > > I am not sure what openMS does when a bad index is found; perhaps it just > recomputes it on the fly at your expense without notifying you. This is > probably undesired behavior if your goal is to reduce overhead. I will see > if I can get the TPP to output more verbose error messages in the future, > to perhaps notify you of the specific problem with the index. > > > > Cheers, > > Mike > > > > *From:* spctools...@googlegroups.com <javascript:> [mailto: > spctools...@googlegroups.com <javascript:>] *On Behalf Of *Connor Hoffmann > *Sent:* Monday, August 07, 2017 3:26 PM > *To:* spctools-discuss > *Subject:* [spctools-discuss] TPP Search Software not working with > generated mzML files > > > > Hi all, > > > > My group is working on software capable of generating mzML files that can > be searched/viewed with TPP and other software. > > > > The mzML files we generate are openable and viewable in programs like > seeMS. MS/MS searches can also be conducted on our generated files in > programs like Mascot (through their server) and MSGF+. > > > > The issue is that when I try to run out mzML file in a comet search(or any > other search part of the TPP pipeline) this error is thrown: > > > > > test.mzml(1) : error 2: Syntax error parsing XML. > > > > I understand that this is probably an error with how the mzML files are > getting formatted. Does anyone have any advice as to why our files can be > searched in other software that's not part of the TPP? Do searches like > Comet have more strict formatting standards? > > > > Also our generated mzML files pass xml and mzML validation put out by > openMS. > > > > I know a workaround is to convert the mzML into a TPP comatible mzML using > MsConvert, however if at possible I would like if our generated files were > compatible with TPP searches without the added overhead of converting them. > > > > I have attached an example of one of our generated mzML files should you > like yo view it. > > > > Thank you! > > > > Connor Hoffmann > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to spctools-discu...@googlegroups.com <javascript:>. > To post to this group, send email to spctools...@googlegroups.com > <javascript:>. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
