[spctools-discuss] How to determine (retrieve) charge information from jrap's Scan object
Hi there, I'm using jrap to parse mzxml file generated from Thermo's raw file. How can I retrieve charge state information from the Scan project? Thanks, David -- 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/-/UIa_G9DomgIJ. To post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
[spctools-discuss] Having trouble parsing latest Xcalibur 2.2 generated mzXML (q-executive) using Jrap
Hi there, I'm having trouble parsing the latest Xcalibur 2.2 generated mzXML (q-executive) using Jrap: for some scans, scan.getMassIntensityList method returns negative float values for m/z and intensities. Has anybody seen this before? I realized that we're using jrap-0.1.jar, just downloaded jrap-3.0.jar, but still getting negative values. Thanks, David -- 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/-/bpZuwduVT9gJ. To post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
Re: [spctools-discuss] Re: JRAP question
At this point, you can probably not worry about jrap not being updated because the mzXML format isn't really in flux. But if you want to look for alternatives ... Quite a few folks here would tell you to look at ProteoWizard http://proteowizard.sourceforge.net/ Possibly look into OpenMS (I honestly have no clue how pertinent this is): http://open-ms.sourceforge.net/ Also MSToolkit: https://code.google.com/p/mstoolkit/ Other folks should chime in if there are other parsing libraries out there (which I know there are). On Tue, Jan 15, 2013 at 7:20 PM, David Zhao weizhao6...@gmail.com wrote: Thanks Jimmy! So it sounds like jrap is not being updated anymore. If i'd like to keep up to date with a mzXML parser, which library should I follow? Thanks, David On Tuesday, January 15, 2013 7:14:17 PM UTC-8, Jimmy Eng wrote: I'm not a jrap user nor do I know what file are associated with what versions. But if you are looking for jrap_3.0.jar and jakarta-regexp-1.4.jar, you can find them here: http://sashimi.svn.** sourceforge.net/viewvc/**sashimi/trunk/jrap/sax2/http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/jrap/sax2/ -- You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
RE: [spctools-discuss] Re: JRAP question
And if you’re in the market for a Java implementation (like JRAP), then I’d recommend jmzreader: http://code.google.com/p/jmzreader/ Cheers, Eric *From:* spctools-discuss@googlegroups.com [mailto: spctools-discuss@googlegroups.com] *On Behalf Of *Jimmy Eng *Sent:* Tuesday, January 15, 2013 9:18 PM *To:* spctools-discuss@googlegroups.com *Subject:* Re: [spctools-discuss] Re: JRAP question At this point, you can probably not worry about jrap not being updated because the mzXML format isn't really in flux. But if you want to look for alternatives ... Quite a few folks here would tell you to look at ProteoWizard http://proteowizard.sourceforge.net/ Possibly look into OpenMS (I honestly have no clue how pertinent this is): http://open-ms.sourceforge.net/ Also MSToolkit: https://code.google.com/p/mstoolkit/ Other folks should chime in if there are other parsing libraries out there (which I know there are). On Tue, Jan 15, 2013 at 7:20 PM, David Zhao weizhao6...@gmail.com wrote: Thanks Jimmy! So it sounds like jrap is not being updated anymore. If i'd like to keep up to date with a mzXML parser, which library should I follow? Thanks, David On Tuesday, January 15, 2013 7:14:17 PM UTC-8, Jimmy Eng wrote: I'm not a jrap user nor do I know what file are associated with what versions. But if you are looking for jrap_3.0.jar and jakarta-regexp-1.4.jar, you can find them here: http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/jrap/sax2/ -- You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. 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 post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
