[spctools-discuss] Re: The link to the script seems outdated
Thanks for the link, Jimmy. I'm not a programmer myself. It seems like sed is a unix text manipulator app? I'm not sure if it's easier to modify the lines in protxml2html.pl such that it can retrieve the protein descriptions properly from the ipi fasta file,? Have you any idea who I can consult regarding the code in protxml2html? Really appreciate your help on this. Bernard On Jun 6, 1:06 am, Jimmy Eng j...@systemsbiology.org wrote: Bernard, Here's the updated location for the getdb.ipi script:http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteom... I personally don't know the circumstances under which the protein names do or do not display in ProteinProphet. Maybe another developer on the list knows. Possibly when certain non alpha-numeric characters are part of an accession number??? - Jimmy Bernt wrote: Hi Jimmy, I'm facing the same problem as Cynthia, but the link to the getdb.ipi script seems to be outdated. Can you point me to any other links to enable protein names to be displayed in ProteinProphet? I'm using Petunia in windows. Are there any scripts which have been written for such a config? Many thanks! Bernard --~--~-~--~~~---~--~~ 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] No peptide passing MPT filter
Hi, I am using TPP version 4.2.1 on windows. My raw file is from Orbitrap. The process until peptide prophet works smoothly. I am searching with Mascot against a database that includes decoy entries and no enzyme. I use the following run options for peptide prophet: MINPROB=0.05 ACCMASS The peptide prophet command ends successfully, but in the result pepXML file all the peptides has a negative probability and when looking in the plotmodel it is written that Estimated total number of correct peptide assignments in dataset: 0.0 . Do I use the correct run options? Should I choose other options? Thanks, Keren --~--~-~--~~~---~--~~ 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: fasta file length and match precision
Hi Kris, So is this a question about SEQUEST performance and behavior? You might be better off asking Thermo about that. On the other hand there are lots of SEQUEST users on this list so you might get an answer here too... Brian -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of Kris Sent: Monday, June 15, 2009 7:31 AM To: spctools-discuss Subject: [spctools-discuss] fasta file length and match precision Sorry if this is covered somewhere else, I was unable to find the answer to this question. I am using TPP with SEQUEST to search for peptides in mass spectra. I had an original fastafile (specified in the parameters file by database_name=) that I have been using for all my database_search runs. I just generated a new fasta file that included the possibility of amino acids being cut off the N-terminus of the protein fragments. E.G. If the original fasta file contained MVMNDANQAQITATFKTK The new fasta file contains MVMNDANQAQITATFKTK VMNDANQAQITATFKTK MNDANQAQITATFKTK NDANQAQITATFKTK DANQAQITATFKTK ANQAQITATFKTK NQAQITATFKTK QAQITATFKTK AQITATFKTK These sequences were included because I was concerned that the database_search would not find proteins where the N-terminus was modified. (My work mainly concerns the N-termini of proteins). I ran some preliminary tests to see how this would affect the run speed and results. Using the original fasta file, a run took 3.5 hours. Using the new longer fasta file (which has all the sequences of the original file and more), the same run took 2 hours. There were about 6000 peptides found when run with the original fasta file and only about 2500 peptides found when run with the new longer fasta file. Using the new fasta file, I found some peptide matches with probability of 1 that had slightly lower probability (around 0.9) when using the original fasta file. MY QUESTIONS: Does using a longer fasta file somehow cause a lose of precision when searching for peptide matches in mass spec data? How does the fasta file length (and specifically adding the same sequences with a shortened N-terminus) affect the database_searches and more importantly the peptide matches output? Thank, Kris --~--~-~--~~~---~--~~ 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] fasta file length and match precision
Sorry if this is covered somewhere else, I was unable to find the answer to this question. I am using TPP with SEQUEST to search for peptides in mass spectra. I had an original fastafile (specified in the parameters file by database_name=) that I have been using for all my database_search runs. I just generated a new fasta file that included the possibility of amino acids being cut off the N-terminus of the protein fragments. E.G. If the original fasta file contained MVMNDANQAQITATFKTK The new fasta file contains MVMNDANQAQITATFKTK VMNDANQAQITATFKTK MNDANQAQITATFKTK NDANQAQITATFKTK DANQAQITATFKTK ANQAQITATFKTK NQAQITATFKTK QAQITATFKTK AQITATFKTK These sequences were included because I was concerned that the database_search would not find proteins where the N-terminus was modified. (My work mainly concerns the N-termini of proteins). I ran some preliminary tests to see how this would affect the run speed and results. Using the original fasta file, a run took 3.5 hours. Using the new longer fasta file (which has all the sequences of the original file and more), the same run took 2 hours. There were about 6000 peptides found when run with the original fasta file and only about 2500 peptides found when run with the new longer fasta file. Using the new fasta file, I found some peptide matches with probability of 1 that had slightly lower probability (around 0.9) when using the original fasta file. MY QUESTIONS: Does using a longer fasta file somehow cause a lose of precision when searching for peptide matches in mass spec data? How does the fasta file length (and specifically adding the same sequences with a shortened N-terminus) affect the database_searches and more importantly the peptide matches output? Thank, Kris --~--~-~--~~~---~--~~ 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: fasta file length and match precision
I actually found out that I left some data out of one of the fasta files. So, you can disregard the descriptions of my runs I posted before. My question is probably more about SEQUEST behavior. But it also includes the behavior of PeptideProphet. My question is basically: Will using a large database_file (in fasta format) affect the SEQUEST output or Peptide Prophet output in a positive or negative way? In other words, will a large database of sequences give more or less valid peptide matches? -Kris On Jun 15, 11:13 am, Brian Pratt brian.pr...@insilicos.com wrote: Hi Kris, So is this a question about SEQUEST performance and behavior? You might be better off asking Thermo about that. On the other hand there are lots of SEQUEST users on this list so you might get an answer here too... Brian -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of Kris Sent: Monday, June 15, 2009 7:31 AM To: spctools-discuss Subject: [spctools-discuss] fasta file length and match precision Sorry if this is covered somewhere else, I was unable to find the answer to this question. I am using TPP with SEQUEST to search for peptides in mass spectra. I had an original fastafile (specified in the parameters file by database_name=) that I have been using for all my database_search runs. I just generated a new fasta file that included the possibility of amino acids being cut off the N-terminus of the protein fragments. E.G. If the original fasta file contained MVMNDANQAQITATFKTK The new fasta file contains MVMNDANQAQITATFKTK VMNDANQAQITATFKTK MNDANQAQITATFKTK NDANQAQITATFKTK DANQAQITATFKTK ANQAQITATFKTK NQAQITATFKTK QAQITATFKTK AQITATFKTK These sequences were included because I was concerned that the database_search would not find proteins where the N-terminus was modified. (My work mainly concerns the N-termini of proteins). I ran some preliminary tests to see how this would affect the run speed and results. Using the original fasta file, a run took 3.5 hours. Using the new longer fasta file (which has all the sequences of the original file and more), the same run took 2 hours. There were about 6000 peptides found when run with the original fasta file and only about 2500 peptides found when run with the new longer fasta file. Using the new fasta file, I found some peptide matches with probability of 1 that had slightly lower probability (around 0.9) when using the original fasta file. MY QUESTIONS: Does using a longer fasta file somehow cause a lose of precision when searching for peptide matches in mass spec data? How does the fasta file length (and specifically adding the same sequences with a shortened N-terminus) affect the database_searches and more importantly the peptide matches output? Thank, Kris --~--~-~--~~~---~--~~ 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: quantification in ASAPRatio n-term labeled samples
Dear David, Thank you for the answer, Ok, so please tell me if i'm correct. In case of double labelling with light and heavy acetyl, should I only click on proper change labeled residues (selecting standard modifications and doubly select n) and then specify those two labels (light and heavy acetyl) in window: specified label mass? should I also use static modification quantification option? It's pitty there is no detailed manual for operations like this, and I have to disturb you guys. Thanks in advance, Filip --~--~-~--~~~---~--~~ 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: X!Tandem Parameters File
Hi James, I'm sure that what I do is the best way but it work for me pretty well: I make one X!tandem input for every search conditions I use and usually save them with the relevant data in the relevant data folder. You can start with X!tandem sample input file (downloaded form http://www.thegpm.org/TANDEM/api/eg.xml) add to it the k-score plugin settings: (http://tools.proteomecenter.org/wiki/index.php?title=TPP:X! Tandem_and_the_TPP) and your specific changes (Lys C etc). And when you will be asked for the parameter file specify this xml file. It will overrule the default parameter file of the TPP when specified. Good luck, Oded On Jun 14, 2:10 am, James Dowell jadow...@hotmail.com wrote: Hi, I am trying to set-up the TPP to run an X!Tandem search. I've read Jimmy Eng's tutorial on using X!Tandem within the TPP. The problem I'm having is editing the X!Tandem parameters file. Should I be editing the default parameters file (tandem_params) in the parameters folder? Or should I be creating a new parameters file in the data folder? I'm trying to search data that needs the enzyme set to Lys-C and I can't seem to find the protein cleavage input in the default params file. Thanks, James --~--~-~--~~~---~--~~ 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] tpp building
Hi, I have Windows XP with latest SP and MVC++ 8 (or 2005). I installed active perl ver 5.8.8. I downloaded tpp ver 4.2.0 and exported the head version of win-lib from SVN and put them into ***\tpp\win_lib ***\tpp\trans_proteomic_pipeline 1. When I tried to build TPP_XML_ONLY solution I got a error 1..\..\win_lib\UnxUtils\usr\local\wbin\tar.exe: Error opening archive: Failed to open '..\trans_proteomic_pipeline\extern \boost_1_39_0.tar.bz2': No such file or directory I see that I have tar.exe and boost_1_39_0.tar.bz2 files. ***\tpp\win_lib\UnxUtils\tpp\tar.exe ***\tpp\trans_proteomic_pipeline\extern\boost_1_39_0.tar.bz2 When I checked this in cmd I also have error == C:\Development\tpp\trans_proteomic_pipeline\srcdir ..\..\win_lib \UnxUtils\usr\l ocal\wbin\tar.exe Volume in drive C has no label. Volume Serial Number is 6CBD-8DFF Directory of C:\Development\tpp\win_lib\UnxUtils\usr\local\wbin 06/12/2009 04:38 PM93,184 tar.exe 1 File(s) 93,184 bytes 0 Dir(s) 124,038,029,312 bytes free C:\Development\tpp\trans_proteomic_pipeline\srcdir .. \trans_proteomic_pipeline\ extern\boost_1_39_0.tar.bz2 The system cannot find the path specified. == 2. README_WIN.txt file has == - win_lib (rename not allowed) you must extract the boost libary files from the zip file in win_lib == I manually extracted boost_1_39_0.tar.bz2 into \win_lib \boost_1_39_0\*** but it didn't help 3. I extracted boost_1_39_0.tar.bz2 into ***\tpp \trans_proteomic_pipeline\extern\boost_1_39_0\*** 4. I still have a lot of errors with boost headears files, like = fatal error C1083: Cannot open include file: 'boost/shared_ptr.hpp': No such file or directory = Where and how boost library should be placed? Like, ***\tpp\trans_proteomic_pipeline\extern\boost_1_39_0\boost ***\tpp\trans_proteomic_pipeline\extern\boost_1_39_0\doc and so on ... Any help? Thanks, Andrei. --~--~-~--~~~---~--~~ 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: tpp building
The fundamental problem is that you're trying to mix and match versions of different parts of the source tree. If you'll get the win_lib revision that's the same era as the rest of the tree it should be fine. Brian -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of Vasilich Sent: Monday, June 15, 2009 5:02 PM To: spctools-discuss Subject: [spctools-discuss] tpp building Hi, I have Windows XP with latest SP and MVC++ 8 (or 2005). I installed active perl ver 5.8.8. I downloaded tpp ver 4.2.0 and exported the head version of win-lib from SVN and put them into ***\tpp\win_lib ***\tpp\trans_proteomic_pipeline 1. When I tried to build TPP_XML_ONLY solution I got a error 1..\..\win_lib\UnxUtils\usr\local\wbin\tar.exe: Error opening archive: Failed to open '..\trans_proteomic_pipeline\extern \boost_1_39_0.tar.bz2': No such file or directory I see that I have tar.exe and boost_1_39_0.tar.bz2 files. ***\tpp\win_lib\UnxUtils\tpp\tar.exe ***\tpp\trans_proteomic_pipeline\extern\boost_1_39_0.tar.bz2 When I checked this in cmd I also have error == C:\Development\tpp\trans_proteomic_pipeline\srcdir ..\..\win_lib \UnxUtils\usr\l ocal\wbin\tar.exe Volume in drive C has no label. Volume Serial Number is 6CBD-8DFF Directory of C:\Development\tpp\win_lib\UnxUtils\usr\local\wbin 06/12/2009 04:38 PM93,184 tar.exe 1 File(s) 93,184 bytes 0 Dir(s) 124,038,029,312 bytes free C:\Development\tpp\trans_proteomic_pipeline\srcdir .. \trans_proteomic_pipeline\ extern\boost_1_39_0.tar.bz2 The system cannot find the path specified. == 2. README_WIN.txt file has == - win_lib (rename not allowed) you must extract the boost libary files from the zip file in win_lib == I manually extracted boost_1_39_0.tar.bz2 into \win_lib \boost_1_39_0\*** but it didn't help 3. I extracted boost_1_39_0.tar.bz2 into ***\tpp \trans_proteomic_pipeline\extern\boost_1_39_0\*** 4. I still have a lot of errors with boost headears files, like = fatal error C1083: Cannot open include file: 'boost/shared_ptr.hpp': No such file or directory = Where and how boost library should be placed? Like, ***\tpp\trans_proteomic_pipeline\extern\boost_1_39_0\boost ***\tpp\trans_proteomic_pipeline\extern\boost_1_39_0\doc and so on ... Any help? Thanks, Andrei. --~--~-~--~~~---~--~~ 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 -~--~~~~--~~--~--~---
