[spctools-discuss] Re: Stpeter comet vs Xtandem?
Hi Jason, Thanks a lot for the information. I would very much like to attend one of your courses, if you guys are having one in Europe. We plan on doing some protein sequencing in our lab in the next few months, so I'm sure the course will be worth it. Thanks again for your time, Panos On Tuesday, 5 June 2018 19:08:20 UTC+3, Jason Winget wrote: > > Hi Panos, > From your questions it seems like you would get a lot of benefit from the > TPP 5-day course. I suggest keeping an eye on this group for announcements > of when one might be available that you can attend. > > Here are some brief answers in the meantime. Each search engine is > attempting to assign as many spectra to peptides as possible, however each > takes its own approach to solving this problem. Therefore some engines > perform better in certain circumstances, while others might prevail in > alternate circumstances. The speed of the search engine is not correlated > with the quality of its output. There are a number of good papers on mass > spec search engines that you can easily explore via pubmed or google > scholar. > > Generally analysts will just use a single search engine because it's the > common one used in their lab. An example of this would be the Andromeda > search engine built into the popular MaxQuant software, or Mascot which has > a long history in the field. The TPP is agnostic and allows the analyst to > use the search engine of their choice, although it comes with some bundled > in for convenience. I would suggest trying a few on your data to get an > empirical idea of which perform the best for your platform. > > Combining results from multiple search engines does generally boost total > peptide-spectrum matches, but I wouldn't say it's a common practice. The > trade off in computational time may not be worth the gains. > > Again, I strongly suggest you attend the TPP course or chat with some of > the team at a conference booth, because I am leaving out a lot of nuance > here. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
[spctools-discuss] Re: Stpeter comet vs Xtandem?
I have recently started playing with proteomics data and I have pretty much the same question as Volkix (although I haven't reached the StPeter step yet)! So what is the main difference between Comet and Xtandem? For example, is one better-suited for particular data than the other? As Volkix also mentioned, perhaps their most obvious difference is that Comet is much faster than Xtandem. How is this explained? Does it have a consequence on the quality of the results? I read in a tutorial TPP paper (Deutsch et al. 2010; Proteomics) that the pepXML results from multiple search engines can be combined together. So is combining different search engines something people usually do? If it is, what other search engines are usually used? The paper refers to SpectraST, but since 8 years have passed since it was published, I'm wondering if there have been any changes lately... Thanks, Panos On Sunday, 25 March 2018 19:00:39 UTC+3, Jason Winget wrote: > > Any search engine should work, as long as you can generate a valid ProtXML > file as input to StPeter -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
[spctools-discuss] Re: Convert mgf to mzML/mzXML
Thanks Antonio! I will give it a try. On Sunday, 3 June 2018 16:36:35 UTC+3, Antonio Ortega wrote: > > Hi Panos > > You can give it a try with > https://github.com/compomics/ThermoRawFileParser . It supports raw -> > mgf conversion in Linux, and a raw -> mzML conversion is on the making. I > have successfully been able to extract mgf files from RAW files in Linux > with this tool. > The instructions for how to set it up are given in the README.md file. If > you experience difficulties, have a look at the issues (open and closed), > or open a new one ;) > > Best > > Antonio > > lørdag den 2. juni 2018 kl. 21.40.08 UTC+2 skrev Panos Ioannidis: >> >> Yes, I did think of setting up a Windows VM for such conversions, and >> maybe it's unavoidable after all... >> >> Thanks a lot for your time! >> >> P >> >> On Saturday, 2 June 2018 19:06:48 UTC+3, Michael Hoopmann wrote: >>> >>> No, there isn't a native tool for Linux that reads vendor formats. >>> Unfortunately, vendor formats are proprietary and requires the vendor >>> drivers to access those files and convert them. All of those drivers are >>> Windows only, as the vendors have decided that is their platform of choice. >>> Thermo will eventually release a Linux compatible driver set for Mono, >>> maybe you can even get your hands on the development version - but it will >>> only read the file. Converting it to another format will require additional >>> coding or interfacing with ProteoWizard. >>> >>> One possible solution would be to create a Windows virtual machine for >>> converting vendor formats. It can be fired up inside Linux, then convert >>> the vendor files to mzML using msconvert from ProteoWizard, copy the mzML >>> files back to your Linux filesystem, and wind down the VM. >>> >>> Cheers, >>> Mike >>> >>> -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
[spctools-discuss] Re: TPP 5.1.0 installation fails
Hi again Mike, I did try "make clean" and recompiling from the beginning but without luck. I even set up an Ubuntu VM (my machine runs Debian) and used the step by step installation guide for Ubuntu that you have in the wiki. I also tried different g++/gcc versions (4.8, 4.9, 6.0, 7.0, 8.0) because I saw in the wiki that TPP needs a particular g++ version sometimes. However, every single time "mzIMLDemo" couldn't compile successfully... What I eventually decided to do is just skip compiling mzIMLDemo! What does it do in the pipeline? From its name I understand that maybe it's not really necessary. Of course I'm still in the first steps of the pipeline (I have only used tandem with my mgf files), so maybe that's why I haven't needed mzIMLDemo yet... P On Saturday, 2 June 2018 01:06:52 UTC+3, Michael Hoopmann wrote: > > Hi Panos, > Sorry for the slow reply - getting ready for ASMS... > > It seems there might be an order of operations issue with the make file. > This might have occurred as a result of your previous partial builds. You > can try to build the particular toolset that is giving you the problem by > typing: make libmzimltools > > Otherwise, perhaps a make clean and then rebuild will work. > > Cheers, > Mike > > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
[spctools-discuss] Re: Convert mgf to mzML/mzXML
Yes, I did think of setting up a Windows VM for such conversions, and maybe it's unavoidable after all... Thanks a lot for your time! P On Saturday, 2 June 2018 19:06:48 UTC+3, Michael Hoopmann wrote: > > No, there isn't a native tool for Linux that reads vendor formats. > Unfortunately, vendor formats are proprietary and requires the vendor > drivers to access those files and convert them. All of those drivers are > Windows only, as the vendors have decided that is their platform of choice. > Thermo will eventually release a Linux compatible driver set for Mono, > maybe you can even get your hands on the development version - but it will > only read the file. Converting it to another format will require additional > coding or interfacing with ProteoWizard. > > One possible solution would be to create a Windows virtual machine for > converting vendor formats. It can be fired up inside Linux, then convert > the vendor files to mzML using msconvert from ProteoWizard, copy the mzML > files back to your Linux filesystem, and wind down the VM. > > Cheers, > Mike > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
[spctools-discuss] Re: Convert mgf to mzML/mzXML
Thanks a lot Mike! And what if I want to convert RAW files to mzML in Linux? The Linux version of ProteoWizard tools says that they cannot process vendor files (such as RAW). Is there an alternative? I have already tried using msconvert with wine but didn't work? Is there a conversion tool running natively in Linux? Panos On Saturday, 2 June 2018 01:15:26 UTC+3, Michael Hoopmann wrote: > > I would use msconvert from proteoWizard, It's part of the TPP. The command > line would look like this: > > >msconvert yourFile.mgf --mzML > > you can also simply type "msconvert" for examples of the many conversion > options available to you. > > Cheers, > Mike > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
[spctools-discuss] Convert mgf to mzML/mzXML
Hello, Does anyone know how to convert mgf files to mzML/mzXML? Thanks, Panos -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
[spctools-discuss] Re: Running database search from commandline
Hello Florian, I know it's been quite a time since you posted, but is there any chance you still have this small program? I'm also interested in running TPP from the commandline... Thanks! Panos On Monday, 19 December 2011 19:29:39 UTC+2, Florian wrote: > > Thanks so much, actually, I found a former post where it was > explained. Sorry for that. Just if someone should be interested: I > have a small program that build the taxonomy and the parameter files > so that the whole analysis process can be automated. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
[spctools-discuss] TPP 5.1.0 installation fails
Hello again, Please disregard my last message; I found that you have already posted a solution, which I followed. Unfortunately, however, the installation fails again, although at another point. I'm pasting the failing command below. g++ -L/home/panos/Programs/TPP_5.1.0_src/build/gnu-x86_64/lib / home/panos/Programs/TPP_5.1.0_src/build/gnu-x86_64/artifacts/Parsers/ mzIMLTools/mzIMLDemo/CPepXMLAnalysis.o /home/panos/Programs/TPP_5.1.0_src/ build/gnu-x86_64/artifacts/Parsers/mzIMLTools/mzIMLDemo/CPepXMLPeptide.o / home/panos/Programs/TPP_5.1.0_src/build/gnu-x86_64/artifacts/Parsers/ mzIMLTools/mzIMLDemo/CPepXMLPSM.o /home/panos/Programs/TPP_5.1.0_src/build/ gnu-x86_64/artifacts/Parsers/mzIMLTools/mzIMLDemo/CPepXMLSearch.o /home/ panos/Programs/TPP_5.1.0_src/build/gnu-x86_64/artifacts/Parsers/mzIMLTools/ mzIMLDemo/CPepXMLSpectrum.o /home/panos/Programs/TPP_5.1.0_src/build/gnu- x86_64/artifacts/Parsers/mzIMLTools/mzIMLDemo/cpxIndPeptide.o /home/panos/ Programs/TPP_5.1.0_src/build/gnu-x86_64/artifacts/Parsers/mzIMLTools/ mzIMLDemo/cpxModInfo.o /home/panos/Programs/TPP_5.1.0_src/build/gnu-x86_64/ artifacts/Parsers/mzIMLTools/mzIMLDemo/cpxPeptide.o /home/panos/Programs/ TPP_5.1.0_src/build/gnu-x86_64/artifacts/Parsers/mzIMLTools/mzIMLDemo/ cpxProtein.o /home/panos/Programs/TPP_5.1.0_src/build/gnu-x86_64/artifacts/ Parsers/mzIMLTools/mzIMLDemo/cpxProteinGroup.o /home/panos/Programs/TPP_5. 1.0_src/build/gnu-x86_64/artifacts/Parsers/mzIMLTools/mzIMLDemo/ PepXMLParser3.o /home/panos/Programs/TPP_5.1.0_src/build/gnu-x86_64/ artifacts/Parsers/mzIMLTools/mzIMLDemo/ProtXMLParser2.o /home/panos/Programs /TPP_5.1.0_src/build/gnu-x86_64/artifacts/Parsers/mzIMLTools/mzIMLDemo/ mzIMLDemo.o /home/panos/Programs/TPP_5.1.0_src/build/gnu-x86_64/lib/libtpp.a /home/panos/Programs/TPP_5.1.0_src/build/gnu-x86_64/lib/libmzparser.a -lexpat -lz /home/panos/Programs/TPP_5.1.0_src/build/gnu-x86_64/lib/libmzimltools.a -lexpat -lz -o /home/panos/Programs/TPP_5.1.0_src/build/gnu-x86_64/bin/ MzIMLDemo /home/panos/Programs/TPP_5.1.0_src/build/gnu-x86_64/artifacts/Parsers/ mzIMLTools/mzIMLDemo/mzIMLDemo.o: In function `convertProt(CMzIdentML&, char*)': mzIMLDemo.cpp:(.text+0x45f7): undefined reference to `CProteinAmbiguityGroup ::addParamValue(std::string, std::string, double)' mzIMLDemo.cpp:(.text+0x4697): undefined reference to `CProteinAmbiguityGroup::addParamValue(std::string, std::string, std::string)' mzIMLDemo.cpp:(.text+0x47d2): undefined reference to `CProteinAmbiguityGroup::addProteinDetectionHypothesis(std::string, std::string, bool)' collect2: error: ld returned 1 exit status /home/panos/Programs/TPP_5.1.0_src/src/Parsers/Makefile:219: recipe for target '/home/panos/Programs/TPP_5.1.0_src/build/gnu-x86_64/bin/MzIMLDemo' failed make: *** [/home/panos/Programs/TPP_5.1.0_src/build/gnu-x86_64/bin/MzIMLDemo] Error 1 I must say here that the installation failed at a previous command as well, which I was able to overcome by manually compiling with g++-6 (and then running "make all" which resumes from where it left off). g++-6 -O2 -Wno-deprecated -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DTPPLIB -I/home/panos/Programs/TPP_5.1.0_src/src -I/home/panos/Programs/TPP_5.1.0 _src/build/gnu-x86_64/include -D__LINUX__ -fPIC -MMD -c -o /home/panos/ Programs/TPP_5.1.0_src/build/gnu-x86_64/artifacts/Parsers/mzIMLTools/ CProteinAmbiguityGroup.o /home/panos/Programs/TPP_5.1.0_src/src/Parsers/ mzIMLTools/CProteinAmbiguityGroup.cpp Unfortunately I couldn't do the same with "MzIMLDemo"... Any help is appreciated, Panos -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
