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:>> 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 view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/GucbfkxmNLAJ. 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.
