Hi, The "lockmass" is a separate scan filter in Thermo files that you can see in qualbrowser. If the lock mass is present throughout the experiment you get a single scan filter. When the lock mass isn't present throughout the whole experiment you get to filters, "lockmass" and "fullms". One of these scans contains all the data, and one contains just the parts relating to the specific scan header, but it seems to vary which is which. I think it is whichever if the most common throughout the experiment.
I'm pretty sure we had this problem with readw but I don't ever remember having it with msconvert, although I do remember having a conversation with someone and I've never contacted the readw people. This ring any bells with you Matt? Anas, does the mzXML file contain all of the positive scans? If you are running pos/neg switching they'll either be all the odd or all the even numbers if you only have two scan events. Cheers, Gavin. -----Original Message----- From: Andris Jankevics [mailto:[email protected]] Sent: 01 November 2012 15:17 To: Anas Cc: proteowizard-support; Chang, Zhenyu (charlie); Matthew Chambers; [email protected] Subject: Re: [proteowizard-support] ReadW and Orbitrap Exactive output files Hi Anas, I believe that all measured masses are corrected on the fly during measurement (at least Waters machines does so), and stored lock-mass scans usually can be discarded by using "scanEvent" filter. Best Regards, Andris Jankevics (1) Groningen Bioinformatics Center, University of Groningen, The Netherlands (2) Systems Biology lab, Joseph Black Building Room B3.9, University Avenue, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK On Thu, Nov 1, 2012 at 3:08 PM, Matthew Chambers <[email protected]> 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] >> https://lists.sourceforge.net/lists/listinfo/proteowizard-support >> > ------------------------------------------------------------------------------ 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] 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.
