Re: [spctools-discuss] Problem with ReAdW
Is there no way to convert RAW files without using XCalibur SDK ? Regards, Amit Kumar Yadav Senior Research Fellow (SRF-CSIR) IGIB, New Delhi (India) http://masswiz.igib.res.in On Sat, Feb 27, 2010 at 4:22 AM, Omoruyi Osula wrote: > It worked. Thank you. > On 2/25/, Jimmy Eng wrote: > > You're calling it wrong (old style). Type 'ReAdW' without any other > > arguments to find the current usage statement. Assuming you want to > > centroid, compress (which you should), invoke it as > > > >ReAdW --centroid --compress --mzXML filename.RAW > > > > > > On Thu, Feb 25, 2010 at 8:54 AM, oosula wrote: > >> I'm having difficulty converting my .RAW file to mzXML using the ReAdW > >> program. After downloading the program along with all the necessary > >> files ( zlib.dll, .RAW file, etc), I then went to the command prompt, > >> found my directory which contained the ReAdW and the file of interest, > >> and from there tried to do the conversion. I basically typed "ReAdW > >> filename.RAW c after the path name based on some online directions I > >> found, and it just keeps taking me back to instructions that can be > >> found in the README text that comes with the program. In other words, > >> it won't convert the file at all. Can anyone help me?? > >> > >> -- > >> You received this message because you are subscribed to the Google > Groups > >> "spctools-discuss" group. > >> To post to this group, send email to spctools-disc...@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-disc...@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-disc...@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-disc...@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] how to analyze the big file size date with TPP
Hi Eileen, Perhaps you could start by posting the output from a failed TPP run (just copy and paste from the TPP GUI). "Will not work" doesn't provide enough information for anyone to make a helpful observation. Brian On Mon, Mar 8, 2010 at 3:59 PM, Eileen Yue wrote: > Dear All: > Last time, I send this message to this mail list and want to get some > advice. I still do not solve the problem. Here I would like describe this > problem in detail and hope someone may give me some advice and help me solve > this problem. > > Basically, I use SCX-HPLC/MS to separate the SILAC sample, which is labeled > with isotope. I did off-line SCX-HPLC/MS and collected 30 fractions for the > LC/MS. The mass spectrometry is the new version from Thermo and called Velo. > After the sequest search with database, the results are very big file. All > the 30 fractions search files are almost 14G even after I zipped them. That > means each fraction is almost 1G. I tried to analyze one fraction with TPP > software and it works. When I load 5 or more fractions, TPP will not work > anymore. > > Does anyone have any advice how to analyze such big file size data with > TPP? Is there any other way to help me to analyze all the data. The major > things that I need combine all the fraction and get protein ASAP ratio. > > Thank you for your kind help > > Eileen > > -Original Message- > From: spctools-discuss@googlegroups.com [mailto: > spctools-disc...@googlegroups.com] On Behalf Of Eileen Yue > Sent: 04 March 2010 16:44 > To: spctools-discuss@googlegroups.com > Subject: [spctools-discuss] problem to analyze the VELO data with TPP > > Dear All: > I tried to use TPP to analyze the SILAC data produced from Velo under > Xcaliber 2.1. The sequest results for each fraction is very big and I have > total 30 fraction. I tried ONE fraction with TPP and it is fine to convert > the raw data into mzxml and sequest results to pepxml. When I try to analyze > more fraction together such as only 5 fraction, TPP does not work. Can > anyone tell me how to analyze my data and any advice for this situation? > > Thank you so much for your help > Eileen > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-disc...@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-disc...@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-disc...@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] how to analyze the big file size date with TPP
Dear All: Last time, I send this message to this mail list and want to get some advice. I still do not solve the problem. Here I would like describe this problem in detail and hope someone may give me some advice and help me solve this problem. Basically, I use SCX-HPLC/MS to separate the SILAC sample, which is labeled with isotope. I did off-line SCX-HPLC/MS and collected 30 fractions for the LC/MS. The mass spectrometry is the new version from Thermo and called Velo. After the sequest search with database, the results are very big file. All the 30 fractions search files are almost 14G even after I zipped them. That means each fraction is almost 1G. I tried to analyze one fraction with TPP software and it works. When I load 5 or more fractions, TPP will not work anymore. Does anyone have any advice how to analyze such big file size data with TPP? Is there any other way to help me to analyze all the data. The major things that I need combine all the fraction and get protein ASAP ratio. Thank you for your kind help Eileen -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of Eileen Yue Sent: 04 March 2010 16:44 To: spctools-discuss@googlegroups.com Subject: [spctools-discuss] problem to analyze the VELO data with TPP Dear All: I tried to use TPP to analyze the SILAC data produced from Velo under Xcaliber 2.1. The sequest results for each fraction is very big and I have total 30 fraction. I tried ONE fraction with TPP and it is fine to convert the raw data into mzxml and sequest results to pepxml. When I try to analyze more fraction together such as only 5 fraction, TPP does not work. Can anyone tell me how to analyze my data and any advice for this situation? Thank you so much for your help Eileen -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-disc...@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-disc...@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 writing files to MAPPED windows network drive
Hi, I am trying to configure TPP to mapped windows network drive. Please suggest fighting with it for days Here is testing scenario : a) I have created test directory "C:\Proteomics\dev\Inetpub\wwwroot \ISB." b) Then mapped Y: on my machine to "C:\Proteomics\dev" c) I have provided full permission to "C:\Proteomics\dev" directory Issue : e) When I try to change httpd.conf file to mapped drive location, apache server does not start, but as soon as I change Y to C it starts properly. There is no error message in the log. f) If I try to use UNC path, on running X-Interact from GUI, I get message as "UNC paths not supported" g) If I start apache from command prompt and try to run X-Interact from GUI, on every click blank command window appears and TPP gets stuck on PepXMLViewer.cgi "running: "Y:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I y:/ Inetpub/wwwroot/ISB/data/SAN/aTPPiclData/server-123/Test_Executer/ iTRAQ_Carbamidomethyl_PQD_research/Test_Y_interact.xml"" Here is my httpd.conf --- # # Begin settings for the Trans Proteomic Pipeline # # Add 5-hour timeout Timeout 18000 AddType text/html .shtml AddHandler server-parsed .shtml SetEnv WEBSERVER_ROOT Y:/Inetpub/wwwroot SetEnv WEBSERVER_URL http://123.15.26.52:1441 Alias /ISB "Y:/Inetpub/wwwroot/ISB" #BrowserMatch "MSIE" AuthDigestEnableQueryStringHack=On AllowOverride None Options Includes Indexes FollowSymLinks MultiViews Order allow,deny Allow from all Alias /tpp-bin "C:/Inetpub/tpp-bin" Options ExecCGI Includes Indexes MultiViews AllowOverride AuthConfig Limit Order allow,deny Allow from all AddHandler cgi-script .cgi .pl #ScriptInterpreterSource Registry PassEnv WEBSERVER_ROOT PassEnv WEBSERVER_TMP Alias /schema "Y:/Inetpub/wwwroot/schema" Options Indexes MultiViews Includes AllowOverride None Order allow,deny Allow from all AddType text/html .shtml AddHandler server-parsed .shtml PassEnv WEBSERVER_ROOT PassEnv WEBSERVER_TMP # # End settings for the Trans Proteomic Pipeline # -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-disc...@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.
