Hi Anas, Just looked at the files. The working one is ok because the lock mass scan filter doesn’t appear at any point in the data (as far as I can see), but the corrupted file does have this scan filter for several scans and so causes this problem.
As Matt said, MSConvert should solve the problem for you. Cheers, Gavin. From: Anas [mailto:[email protected]] Sent: 01 November 2012 16:00 To: [email protected] Cc: proteowizard-support; Chang, Zhenyu (charlie); [email protected]; Anas Subject: Re: [proteowizard-support] ReadW and Orbitrap Exactive output files Matt,Gavin, thanks for the quick reply, Matt, I meant to say lockmass filter (function in Waters terms), it is not a separate scan event, I just turned it on to improve mass accuracy, all the scans were MS1, but Thermo decided to mix the two filters together, I am using ReAdW to convert o mzXML as I need centroid data, an option deleted by Thermo from Exactive and can`t find support for it in msconvert, here is an example of a working (lockmass off) and a corrupted file (converted by ReAdW) it`s certainly a Thermo bug, msconvert is not the culprit :), Gavin, No switching, a single polarity data, https://icseclzt.cc.ic.ac.uk/pickup.php?claimID=YZ6QXbK3ojWU3z9D&claimPasscode=ufAeKModjUaB3ZFH&emailAddr=mkamleh%40imperial.ac.uk On Thursday, November 1, 2012 4:08:04 PM UTC+1, matt.chambers wrote: Hi Anas, I don't know what a "lockmass function" is in the context of a Thermo instrument. Do you have it set up as a separate scan event? I thought lockmass was calibrated based on finding the given masses inside normal MS1 scans. Msconvert will certainly export ALL scan events by default, so if XCMS isn't picking some of them up that's not an msconvert bug. :) If you WANT to export just certain scan events, use the scanEvent filter: # skip scan event 5 --filter "scanEvent 1-4 6-" Hope this helps, -Matt On 11/1/2012 9:57 AM, Anas wrote: > Hi all, > How did this problem got solved eventually ? I have acquired Q-Exactive data > with lockmass on (for > metabolomics uses) and the lockmass functions seems the only one to be > recognized by xcms, > I appreciate your help, > Cheers, > Anas > > On Friday, June 25, 2010 11:36:27 PM UTC+2, Matt Chambers wrote: > > Hi Andris and Charlie, > > Overdue support for filter lines found in Exactive files has finally been > added to ProteoWizard > (as of r2087). Also there was a problem with parsing the > instrument model and that should also be fixed. > > Thanks for your reports and for uploading the files. > -Matt > > On 6/24/2010 3:46 PM, Zhenyu Chang wrote: > However, I have encountered the following problem when using msconvert > tool. I was trying to > convert a .RAW data generated by Thermo Fisher Exactive instrument > to mzML 1.1 data format. > > > On 11/17/2009 3:19 AM, Andris Jankevics wrote: > > Hi Matt. > > > > Thank you for your work, these data will be mostly metabolomics data > > sets which will be analyzed by XCMS and several other software tools. > > It would be nice to have functionality in ReAdW to extract only mzXML > > file by based on scan event (for example only lock mass corrected > > positive slice), but this is not so essential. > > > > best regards, > > Andris > > > > On Mon, Nov 16, 2009 at 8:36 PM, Matthew Chambers > > <[email protected] > <javascript:<mailto:[email protected]%20%3cjavascript:>>> wrote: > >> That file requires Xcalibur 2.1, which doesn't run on Windows 7 > x64...I > >> had to use a Windows VM to view it. It indeed appears they've put scan > >> segment and scan event in the filter line, and have added a new > keyword > >> ("lock"). The lock keyword appears to only be applied if at least one > of > >> the configured lock masses was found in the spectrum, in which case > some > >> adjustment has been applied; otherwise, it won't have the lock keyword > >> and no adjustment is applied. It shouldn't be difficult to add support > >> for these changes, although I'm curious what you're planning to do > with > >> this data once it's in mzXML format. > >> > >> -Matt > > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_sfd2d_oct > > > > _______________________________________________ > proteowizard-support mailing list > [email protected]<javascript:> > https://lists.sourceforge.net/lists/listinfo/proteowizard-support > -- 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.
