Re: [spctools-discuss] Re: AB-Sciex TripleTOF wiff files to MGFs
A well constructed mzXML file would normally be somewhat smaller than its mzML equivalent - make sure you've got peaklist compression turned on (IIRC the msconvert default is no compression, which seems like a Bad Thing to me but there you have it). On Wed, Mar 2, 2011 at 10:37 PM, ben benane...@gmail.com wrote: I wanted to provide an update. First, it appears that the export mgf function from within peak view isn't very good and talking to AB folks it seems more like a left over beta function. Second, the AB folks have unanimously confirmed that the mascot.dlll script shouldn't be used in this case (Analyst TF 1.5 with TripleTOF data), and based on the resulting mgfs and mascot results, I agree. Lastly, I was able to join the beta and the converter has the ability to easily generate an mgf which is exactly what proteinpilot then sends to the Mascot server, albeit without any profile data. It also has an option to make an mzML which works great, only takes about 30 minutes, and results in a ~2 GB file. I am still struggling with how to get this mzML file to mzXML since certain programs (Progenesis LC-MS, VIPER, MAVEN, etc.) take mzXML not mzML. When I convert the mzML file with msconvert, so far it simply stalls out though the file appears to be about 6GB large. If anyone has any clue about this or would like an example mzML to play with, please let me know. Thanks again for all the helpful feedback, especially about the beta. On Feb 22, 5:59 pm, ben benane...@gmail.com wrote: I didn't realize that about PeakView. So I am generating mgfs from a single wiff 4 ways right now: dll script within Analyst, dll script within Daemon, through PeakView (which took about two seconds), and using Distiller (going on 3 hours right now). Then I will compare them. Thanks for all the ideas, and for the updates about msconvert. Am bugging our AB-Sciex guy about the purported standalone converter. - Ben On Feb 22, 1:55 pm, lgillet gil...@imsb.biol.ethz.ch wrote: Hi Ben, I do not know how you look at your runs, but the PeakView software (I use Version 1.1) that open the raw data wiff files can actually export mgf format. You need to open the IDA runs with the IDA explorer, select filtering criteria you want (rt, spectra quality) and then right click on the map and export to mgf. You can even get consensus spectra during the mgf export (the software pre-compiles MSMS spectra of close m/z and rt from parameters you can set yourself). Hope that helps. Ludovic On Feb 22, 4:17 pm, Matt Chambers matt.chamber...@gmail.com wrote: ProteinPilot 3 doesn't support the 5200 or 5600 afaik so neither can msconvert. We're helping to test a new api that will add that support but it won't be available until the testing is over (probably another month or so). In the meantime, try to get a copy of the AB's new beta standalone converter that Eric mentioned. -Matt On Feb 22, 2011 2:55 AM, Eric Deutsch edeut...@systemsbiology.org wrote: Hi Ben, we have had some trouble with msconvert and TripleTOF. It seems that the ProteinPilot dll calls that msconvert uses does not get the precursor m/zs right. At least this happened at one time, I'm not certain this is still a problem. However, AB is beta testing a converter tool that will convert a TripleTOF file to an MGF. I don't know about it speed. But you might ask them if you can be a beta tester. Regards, Eric -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools- disc...@googlegroups.com] On Behalf Of ben Sent: Monday, February 21, 2011 11:04 AM To: spctools-discuss Subject: [spctools-discuss] AB-Sciex TripleTOF wiff files to MGFs Just wanted to get an idea about what other people get for processing time when converting wiff files to other formats. Presently I am using the mascot.dll script within AnalystTF as well as within Mascot Daemon (the latter taking roughly 4 hours for a single wiff). I am wondering if using msconvert is the route I should go. Matt seems to recommend this based on some threads in this group I saw from January, and it would probably be best to go wiff-mzML-mgf. We could then use either format to load onto our mascot server. Our goal is to get our raw data out and be able to analyze it however we want, beyond protein pilot. Bottomline: - It is super slow using a 32-bit machine running XP to convert wiffs to mgfs with the mascot.dll script. What's my best choice/tool? - Is the only way to download msconvert with the TPP package? Any direct download links? - I can get a version of ProteinPilot3 and install without a lic, or is Skyline a better alternative? Sorry for the remedial questions, but reading through other posts I figured it might be best to ask
[spctools-discuss] Re: AB-Sciex TripleTOF wiff files to MGFs
I haven't played around with compression, but that would be simply adding a -z [ --zlib ] correct? I am using this page more so than the help on sourceforge for command arguments. http://groups.google.com/group/xcms/msg/53e2a2b462a5448c Thanks for the help, and I will let you know if something better comes from this. As an aside, my goal for this specific issue (as opposed to my initial issue of converting wiffs to load MS/MS data elsewhere) is I would like some LC-MS data to visualize for peptide extractions. Everything else works fine for protein ID of tryptic samples with the mgfs. - Ben On Mar 3, 10:30 am, Brian Pratt brian.pr...@insilicos.com wrote: A well constructed mzXML file would normally be somewhat smaller than its mzML equivalent - make sure you've got peaklist compression turned on (IIRC the msconvert default is no compression, which seems like a Bad Thing to me but there you have it). On Wed, Mar 2, 2011 at 10:37 PM, ben benane...@gmail.com wrote: I wanted to provide an update. First, it appears that the export mgf function from within peak view isn't very good and talking to AB folks it seems more like a left over beta function. Second, the AB folks have unanimously confirmed that the mascot.dlll script shouldn't be used in this case (Analyst TF 1.5 with TripleTOF data), and based on the resulting mgfs and mascot results, I agree. Lastly, I was able to join the beta and the converter has the ability to easily generate an mgf which is exactly what proteinpilot then sends to the Mascot server, albeit without any profile data. It also has an option to make an mzML which works great, only takes about 30 minutes, and results in a ~2 GB file. I am still struggling with how to get this mzML file to mzXML since certain programs (Progenesis LC-MS, VIPER, MAVEN, etc.) take mzXML not mzML. When I convert the mzML file with msconvert, so far it simply stalls out though the file appears to be about 6GB large. If anyone has any clue about this or would like an example mzML to play with, please let me know. Thanks again for all the helpful feedback, especially about the beta. On Feb 22, 5:59 pm, ben benane...@gmail.com wrote: I didn't realize that about PeakView. So I am generating mgfs from a single wiff 4 ways right now: dll script within Analyst, dll script within Daemon, through PeakView (which took about two seconds), and using Distiller (going on 3 hours right now). Then I will compare them. Thanks for all the ideas, and for the updates about msconvert. Am bugging our AB-Sciex guy about the purported standalone converter. - Ben On Feb 22, 1:55 pm, lgillet gil...@imsb.biol.ethz.ch wrote: Hi Ben, I do not know how you look at your runs, but the PeakView software (I use Version 1.1) that open the raw data wiff files can actually export mgf format. You need to open the IDA runs with the IDA explorer, select filtering criteria you want (rt, spectra quality) and then right click on the map and export to mgf. You can even get consensus spectra during the mgf export (the software pre-compiles MSMS spectra of close m/z and rt from parameters you can set yourself). Hope that helps. Ludovic On Feb 22, 4:17 pm, Matt Chambers matt.chamber...@gmail.com wrote: ProteinPilot 3 doesn't support the 5200 or 5600 afaik so neither can msconvert. We're helping to test a new api that will add that support but it won't be available until the testing is over (probably another month or so). In the meantime, try to get a copy of the AB's new beta standalone converter that Eric mentioned. -Matt On Feb 22, 2011 2:55 AM, Eric Deutsch edeut...@systemsbiology.org wrote: Hi Ben, we have had some trouble with msconvert and TripleTOF. It seems that the ProteinPilot dll calls that msconvert uses does not get the precursor m/zs right. At least this happened at one time, I'm not certain this is still a problem. However, AB is beta testing a converter tool that will convert a TripleTOF file to an MGF. I don't know about it speed. But you might ask them if you can be a beta tester. Regards, Eric -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools- disc...@googlegroups.com] On Behalf Of ben Sent: Monday, February 21, 2011 11:04 AM To: spctools-discuss Subject: [spctools-discuss] AB-Sciex TripleTOF wiff files to MGFs Just wanted to get an idea about what other people get for processing time when converting wiff files to other formats. Presently I am using the mascot.dll script within AnalystTF as well as within Mascot Daemon (the latter taking roughly 4 hours for a single wiff). I am wondering if using msconvert is the route I should go. Matt seems to recommend this based
Re: [spctools-discuss] Re: AB-Sciex TripleTOF wiff files to MGFs
If you want to post some samples to the list, use msconvert with an index filter. Try: msconvert original.mzML -o subset --filter index 0-100 -z msconvert original.mzML -o subset --filter index 0-100 -z --mzXML And attach both the subset mzML and mzXML for comparison. Thanks, -Matt On 3/3/2011 10:19 AM, ben wrote: I haven't played around with compression, but that would be simply adding a -z [ --zlib ] correct? I am using this page more so than the help on sourceforge for command arguments. http://groups.google.com/group/xcms/msg/53e2a2b462a5448c Thanks for the help, and I will let you know if something better comes from this. As an aside, my goal for this specific issue (as opposed to my initial issue of converting wiffs to load MS/MS data elsewhere) is I would like some LC-MS data to visualize for peptide extractions. Everything else works fine for protein ID of tryptic samples with the mgfs. - Ben On Mar 3, 10:30 am, Brian Prattbrian.pr...@insilicos.com wrote: A well constructed mzXML file would normally be somewhat smaller than its mzML equivalent - make sure you've got peaklist compression turned on (IIRC the msconvert default is no compression, which seems like a Bad Thing to me but there you have it). On Wed, Mar 2, 2011 at 10:37 PM, benbenane...@gmail.com wrote: I wanted to provide an update. First, it appears that the export mgf function from within peak view isn't very good and talking to AB folks it seems more like a left over beta function. Second, the AB folks have unanimously confirmed that the mascot.dlll script shouldn't be used in this case (Analyst TF 1.5 with TripleTOF data), and based on the resulting mgfs and mascot results, I agree. Lastly, I was able to join the beta and the converter has the ability to easily generate an mgf which is exactly what proteinpilot then sends to the Mascot server, albeit without any profile data. It also has an option to make an mzML which works great, only takes about 30 minutes, and results in a ~2 GB file. I am still struggling with how to get this mzML file to mzXML since certain programs (Progenesis LC-MS, VIPER, MAVEN, etc.) take mzXML not mzML. When I convert the mzML file with msconvert, so far it simply stalls out though the file appears to be about 6GB large. If anyone has any clue about this or would like an example mzML to play with, please let me know. Thanks again for all the helpful feedback, especially about the beta. -- 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.
[spctools-discuss] Re: AB-Sciex TripleTOF wiff files to MGFs
I wanted to provide an update. First, it appears that the export mgf function from within peak view isn't very good and talking to AB folks it seems more like a left over beta function. Second, the AB folks have unanimously confirmed that the mascot.dlll script shouldn't be used in this case (Analyst TF 1.5 with TripleTOF data), and based on the resulting mgfs and mascot results, I agree. Lastly, I was able to join the beta and the converter has the ability to easily generate an mgf which is exactly what proteinpilot then sends to the Mascot server, albeit without any profile data. It also has an option to make an mzML which works great, only takes about 30 minutes, and results in a ~2 GB file. I am still struggling with how to get this mzML file to mzXML since certain programs (Progenesis LC-MS, VIPER, MAVEN, etc.) take mzXML not mzML. When I convert the mzML file with msconvert, so far it simply stalls out though the file appears to be about 6GB large. If anyone has any clue about this or would like an example mzML to play with, please let me know. Thanks again for all the helpful feedback, especially about the beta. On Feb 22, 5:59 pm, ben benane...@gmail.com wrote: I didn't realize that about PeakView. So I am generating mgfs from a single wiff 4 ways right now: dll script within Analyst, dll script within Daemon, through PeakView (which took about two seconds), and using Distiller (going on 3 hours right now). Then I will compare them. Thanks for all the ideas, and for the updates about msconvert. Am bugging our AB-Sciex guy about the purported standalone converter. - Ben On Feb 22, 1:55 pm, lgillet gil...@imsb.biol.ethz.ch wrote: Hi Ben, I do not know how you look at your runs, but the PeakView software (I use Version 1.1) that open the raw data wiff files can actually export mgf format. You need to open the IDA runs with the IDA explorer, select filtering criteria you want (rt, spectra quality) and then right click on the map and export to mgf. You can even get consensus spectra during the mgf export (the software pre-compiles MSMS spectra of close m/z and rt from parameters you can set yourself). Hope that helps. Ludovic On Feb 22, 4:17 pm, Matt Chambers matt.chamber...@gmail.com wrote: ProteinPilot 3 doesn't support the 5200 or 5600 afaik so neither can msconvert. We're helping to test a new api that will add that support but it won't be available until the testing is over (probably another month or so). In the meantime, try to get a copy of the AB's new beta standalone converter that Eric mentioned. -Matt On Feb 22, 2011 2:55 AM, Eric Deutsch edeut...@systemsbiology.org wrote: Hi Ben, we have had some trouble with msconvert and TripleTOF. It seems that the ProteinPilot dll calls that msconvert uses does not get the precursor m/zs right. At least this happened at one time, I'm not certain this is still a problem. However, AB is beta testing a converter tool that will convert a TripleTOF file to an MGF. I don't know about it speed. But you might ask them if you can be a beta tester. Regards, Eric -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools- disc...@googlegroups.com] On Behalf Of ben Sent: Monday, February 21, 2011 11:04 AM To: spctools-discuss Subject: [spctools-discuss] AB-Sciex TripleTOF wiff files to MGFs Just wanted to get an idea about what other people get for processing time when converting wiff files to other formats. Presently I am using the mascot.dll script within AnalystTF as well as within Mascot Daemon (the latter taking roughly 4 hours for a single wiff). I am wondering if using msconvert is the route I should go. Matt seems to recommend this based on some threads in this group I saw from January, and it would probably be best to go wiff-mzML-mgf. We could then use either format to load onto our mascot server. Our goal is to get our raw data out and be able to analyze it however we want, beyond protein pilot. Bottomline: - It is super slow using a 32-bit machine running XP to convert wiffs to mgfs with the mascot.dll script. What's my best choice/tool? - Is the only way to download msconvert with the TPP package? Any direct download links? - I can get a version of ProteinPilot3 and install without a lic, or is Skyline a better alternative? Sorry for the remedial questions, but reading through other posts I figured it might be best to ask before I start. Thanks for any help I can get. - Ben -- 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
[spctools-discuss] Re: AB-Sciex TripleTOF wiff files to MGFs
Hi Ben, I do not know how you look at your runs, but the PeakView software (I use Version 1.1) that open the raw data wiff files can actually export mgf format. You need to open the IDA runs with the IDA explorer, select filtering criteria you want (rt, spectra quality) and then right click on the map and export to mgf. You can even get consensus spectra during the mgf export (the software pre-compiles MSMS spectra of close m/z and rt from parameters you can set yourself). Hope that helps. Ludovic On Feb 22, 4:17 pm, Matt Chambers matt.chamber...@gmail.com wrote: ProteinPilot 3 doesn't support the 5200 or 5600 afaik so neither can msconvert. We're helping to test a new api that will add that support but it won't be available until the testing is over (probably another month or so). In the meantime, try to get a copy of the AB's new beta standalone converter that Eric mentioned. -Matt On Feb 22, 2011 2:55 AM, Eric Deutsch edeut...@systemsbiology.org wrote: Hi Ben, we have had some trouble with msconvert and TripleTOF. It seems that the ProteinPilot dll calls that msconvert uses does not get the precursor m/zs right. At least this happened at one time, I'm not certain this is still a problem. However, AB is beta testing a converter tool that will convert a TripleTOF file to an MGF. I don't know about it speed. But you might ask them if you can be a beta tester. Regards, Eric -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools- disc...@googlegroups.com] On Behalf Of ben Sent: Monday, February 21, 2011 11:04 AM To: spctools-discuss Subject: [spctools-discuss] AB-Sciex TripleTOF wiff files to MGFs Just wanted to get an idea about what other people get for processing time when converting wiff files to other formats. Presently I am using the mascot.dll script within AnalystTF as well as within Mascot Daemon (the latter taking roughly 4 hours for a single wiff). I am wondering if using msconvert is the route I should go. Matt seems to recommend this based on some threads in this group I saw from January, and it would probably be best to go wiff-mzML-mgf. We could then use either format to load onto our mascot server. Our goal is to get our raw data out and be able to analyze it however we want, beyond protein pilot. Bottomline: - It is super slow using a 32-bit machine running XP to convert wiffs to mgfs with the mascot.dll script. What's my best choice/tool? - Is the only way to download msconvert with the TPP package? Any direct download links? - I can get a version of ProteinPilot3 and install without a lic, or is Skyline a better alternative? Sorry for the remedial questions, but reading through other posts I figured it might be best to ask before I start. Thanks for any help I can get. - Ben -- 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.
[spctools-discuss] Re: AB-Sciex TripleTOF wiff files to MGFs
I didn't realize that about PeakView. So I am generating mgfs from a single wiff 4 ways right now: dll script within Analyst, dll script within Daemon, through PeakView (which took about two seconds), and using Distiller (going on 3 hours right now). Then I will compare them. Thanks for all the ideas, and for the updates about msconvert. Am bugging our AB-Sciex guy about the purported standalone converter. - Ben On Feb 22, 1:55 pm, lgillet gil...@imsb.biol.ethz.ch wrote: Hi Ben, I do not know how you look at your runs, but the PeakView software (I use Version 1.1) that open the raw data wiff files can actually export mgf format. You need to open the IDA runs with the IDA explorer, select filtering criteria you want (rt, spectra quality) and then right click on the map and export to mgf. You can even get consensus spectra during the mgf export (the software pre-compiles MSMS spectra of close m/z and rt from parameters you can set yourself). Hope that helps. Ludovic On Feb 22, 4:17 pm, Matt Chambers matt.chamber...@gmail.com wrote: ProteinPilot 3 doesn't support the 5200 or 5600 afaik so neither can msconvert. We're helping to test a new api that will add that support but it won't be available until the testing is over (probably another month or so). In the meantime, try to get a copy of the AB's new beta standalone converter that Eric mentioned. -Matt On Feb 22, 2011 2:55 AM, Eric Deutsch edeut...@systemsbiology.org wrote: Hi Ben, we have had some trouble with msconvert and TripleTOF. It seems that the ProteinPilot dll calls that msconvert uses does not get the precursor m/zs right. At least this happened at one time, I'm not certain this is still a problem. However, AB is beta testing a converter tool that will convert a TripleTOF file to an MGF. I don't know about it speed. But you might ask them if you can be a beta tester. Regards, Eric -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools- disc...@googlegroups.com] On Behalf Of ben Sent: Monday, February 21, 2011 11:04 AM To: spctools-discuss Subject: [spctools-discuss] AB-Sciex TripleTOF wiff files to MGFs Just wanted to get an idea about what other people get for processing time when converting wiff files to other formats. Presently I am using the mascot.dll script within AnalystTF as well as within Mascot Daemon (the latter taking roughly 4 hours for a single wiff). I am wondering if using msconvert is the route I should go. Matt seems to recommend this based on some threads in this group I saw from January, and it would probably be best to go wiff-mzML-mgf. We could then use either format to load onto our mascot server. Our goal is to get our raw data out and be able to analyze it however we want, beyond protein pilot. Bottomline: - It is super slow using a 32-bit machine running XP to convert wiffs to mgfs with the mascot.dll script. What's my best choice/tool? - Is the only way to download msconvert with the TPP package? Any direct download links? - I can get a version of ProteinPilot3 and install without a lic, or is Skyline a better alternative? Sorry for the remedial questions, but reading through other posts I figured it might be best to ask before I start. Thanks for any help I can get. - Ben -- 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.
