Re: [spctools-discuss] Can not download the tutorial.exe file

with your IT people. Brian On Sun, Nov 21, 2010 at 7:48 PM, 钟传奇 andy...@gmail.com wrote: Yes. In Getting the Tutorial Data part, you will find you need to download tutorial data from the website (http://www.insilicos.com/data/tutorial.exe) to proceed. On Mon, Nov 22, 2010 at 3:34 AM, Brian Pratt

Re: [spctools-discuss] Re: How to create a composite database containing forward and decoy sequences with contaminants and trypsin

lines between entries, otherwise entries will get deleted when you create your decoy database. On Jan 27, 8:36 pm, 钟传奇 andy...@gmail.com wrote: Hi guys, I want to implement a database search, but I do not know how to create a composite database containing forward and decoy sequences

[spctools-discuss] How to combine multiple analyses from the fractionation experiments?

Hi, everyone, I have 20 fractionation using HILIC. Data of each fractionation was searched using Mascot, resulting in 20 pepXML files. How to combine these fractionation result data using TPP? Thanks a lot. -- You received this message because you are subscribed to the Google Groups

[spctools-discuss] Why ASAPRatio results show N/A???

Hi,everyone, I used SILAC(lys+8, arg+10) to label my cell lines, and used TripleTOF 5600 to analyze my samples. After converting raw data to .mgf files, which were searched by Mascot, I used PeptideProphet to analyze pep.xml files. I checked the resulting interact.pep.xml files, which seemed

Re: [spctools-discuss] Databases used for searching

According to a paper named published and perished the influence of the searched protein database on the long-term storage of proteomics data published in MCP, UniProtKB seems the best database for applications that rely on the long-term storage of proteomics data. On Mon, Aug 22, 2011 at 10:16

Re: [spctools-discuss] ascore for phospho site localization

Hi,David, The link you provided for downloading PTMProphet not valid,could you offer any other way I can download PTMProphet? On Tue, Oct 18, 2011 at 7:29 AM, David Shteynberg david.shteynb...@systemsbiology.org wrote: Hi LW, Yes I have used ascore with some success, although it is not

Re: [spctools-discuss] Re: Announcing TPP release: 4.5.0 Rapture

Hi, I want to ask whether this new version can be directly installed not uninstalling the old version. On Sat, Nov 5, 2011 at 1:00 AM, naturofix shaungarn...@gmail.com wrote: I have the exactly the same problem, and did what you suggested. found that adding #include stdint.h to

[spctools-discuss] Problems when running ASAPRatio

Hi,guys. I use ASAPratio to analyze my SILAC data, and when running PeptideProphet, everything looks fine. But ramp Construct Input Path: file not found is shown in the command after runing ASAPRatio. I do not know what is going wrong. Thanks. -- You received this message because you are

Re: [spctools-discuss] mzWiff question: can't convert .wiff file to .mzXML

AB Sciex has released the software named AB SCIEX Data Converter that convert wiff files to MGF or mzML, and you can download this software at this http://www.absciex.com/downloads/software-downloads . Particularly, AB Sciex does not recommend that wiff files are directly converted to mzXML,

[spctools-discuss] About ptmprophet in TPP

Hi, everyone, I want to use ptmprophet to analyze the phosphorylation sites localization, but I do not know what type of file should be imported into PTMprophet. I have converted mascot dat files to pepXML, and analyzed pepXML using interact and iprophet. Thanks a lot. -- You received this

Re: [spctools-discuss] About ptmprophet in TPP

AM, 钟传奇 andy...@gmail.com wrote: Hi, everyone, I want to use ptmprophet to analyze the phosphorylation sites localization, but I do not know what type of file should be imported into PTMprophet. I have converted mascot dat files to pepXML, and analyzed pepXML using interact and iprophet

Re: [spctools-discuss] OMSSA help

You can download OMSSA searching engine at this link, http://www.chem.wisc.edu/~coon/software.php. On Fri, Dec 6, 2013 at 12:59 PM, srihari sharma sriharisharma...@gmail.comwrote: Hello, I am a very new student of OMSSA database search. I have my .mgf files with me. I am intending to do an

Re: [spctools-discuss] Re: A question about pepXML files.

- is this the case? Hannes On 13 February 2014 12:08, 钟传奇 andy...@gmail.com wrote: The zipped pepXML file is in the attachment. Chuan-Qi Zhong On Thu, Feb 13, 2014 at 7:05 PM, 钟传奇 andy...@gmail.com wrote: I used openMS to process my data, and the results, idXML files, are then converted

[spctools-discuss] A question about Mayu.

Hi, I have used Mayu integrated in TPP to analyze my data. The log file of Mayu showed that there is no decoy proteins found, and the log file is in the attachment. I generated my database for searching with other tools than the reverse_fasta.pl tool in the Mayu, and set the parameter Tag

Re: [spctools-discuss] A question about Mayu.

top decoy tools expect decoys to be labeled with prefix. David On May 20, 2014 11:19 PM, 钟传奇 andy...@gmail.com wrote: Hi, I have used Mayu integrated in TPP to analyze my data. The log file of Mayu showed that there is no decoy proteins found, and the log file is in the attachment. I

Re: [spctools-discuss] HOW to get the Specify Tandem Parameters File?~~~help~~~

The parameter files tandem_params.xml are in the the folder named parameters, which of path normally is C:\Inetpub\wwwroot\ISB\data\parameters. Before starting searching, you should modify the parameters in the file, such as precursor ion tolerance and modification if necessary. On Thu, Jul 3,

[spctools-discuss] How to set iprobility value cutoff input for proteinprophet?

Hi, I noticed that I can set a peptideprophet probability value cutoff for proteinprophet analysis, but if I want to use a iprophet probability value for proteinprophet analysis, how can I do? I can not find this option in proteinprophet. Thanks. Best, -- You received this message because you

Re: [spctools-discuss] Export to .xls from command line

I have the same question. Hope someone can help. On Tue, Aug 12, 2014 at 5:12 AM, Adam Oberstein adam.oberst...@gmail.com wrote: Dear TPP team, I'm trying to automate my data analysis workflow using the binaries included with tpp v4.7.1 on linux. I have database search -- peptide prophet

Re: [spctools-discuss] Export to .xls from command line

1 -I pepXMLfile Hope this helps, --Luis On Tue, Aug 12, 2014 at 4:49 AM, 钟传奇 andy...@gmail.com wrote: I have the same question. Hope someone can help. On Tue, Aug 12, 2014 at 5:12 AM, Adam Oberstein adam.oberst...@gmail.com wrote: Dear TPP team, I'm trying to automate my data

Re: [spctools-discuss] Export to .xls from command line

This command-line is used for exporting default information (peptide sequence and protein infromation, etc) of pepxml into a excel file, and how to export other infromation (such as Z, missed cleavage sites, etc) into a excel file? On Fri, Aug 15, 2014 at 5:19 PM, 钟传奇 andy...@gmail.com wrote

Re: [spctools-discuss] Wiff file conversion to mzML

Here is my way to process wiff files. First, wiff files were converted to mzML files using msconvert (AB Sciex). Second, mzML were converted to mzXML files using proteowizard MS convert. Finally, mzXML were searched using Xtandem. Hope this help. Best, On Wed, Sep 3, 2014 at 3:53 PM, Jana

Re: [spctools-discuss] Export to .xls from command line

Adam, thanks. It is useful for me. On Saturday, October 11, 2014, Adam Oberstein adam.oberst...@gmail.com wrote: Another tip: when using the -C option, the list of columns needs to include some sort of string formatting. For example, this is the full command I'm using to export:

[spctools-discuss] PTMProphet error

Hi, I run PTMProphet analysis for ipro.pep.xml, and error happened, multiple static mods with different masses found on aminoacid C, can not be processed together with PTMprophet. In fact, I just have variable mods on Oxidation (M) and phosphorylation (STY) , and fixed mod on Carbamidomethyl (C)

Re: [spctools-discuss] protxml and MAYU

As I know, MAYU can be applied to the iProphet output, not ProteinProphet output. On Tue, Mar 24, 2015 at 10:48 PM, hh1985 hh.earlyd...@gmail.com wrote: Hi, I am planning to do LFQ using ProteinQuantifier from OpenMS, which can take ProteinProphet results as the identification input.

Re: [spctools-discuss] how to continue or kill my jobs?

Hi, I came across this issue and solved it in the following way. Find the TPP username folder (normally should be C:\inetpub\tpp-bin\users\guest), and delete the file the name of which contains the date of task. Note: do not delete .jobs and .password files. Hope it helps. On Sun, Apr 12, 2015 at

Re: [spctools-discuss] Comet database search error

Hi Jimmy, I also want to ask how to update Comet in TPP in Ubuntu system. Does Comet work if I just replaced the Comet file like you mentioned in the email. Thanks. On Mon, Jun 13, 2016 at 2:24 PM, Jimmy Eng wrote: > Vijay, > > Update to the latest Comet and try again.

Re: [spctools-discuss] Tutorial for Decoy peptide and protein validation

I guess the developers of TPP are TOO busy to respond to you. Similarly, no one repond to my question concerning PTMprophet. Have you succeeded to run peptideprophet and iprophet? On Sun, Jun 19, 2016 at 2:47 AM, Vijay Kumar wrote: > Hi, > Where i will get the complete

Re: [spctools-discuss] Question About iprophet/Spectral library

I have never done the SpectraST search. When you create a consensus library using SpectraST, you actually removed redundant spectra. You can refer to Nature method paper about SpectraST. Here is the link: http://www.nature.com/nmeth/journal/v5/n10/full/nmeth.1254.html On Tue, Sep 20, 2016 at

Re: [spctools-discuss] Question About iprophet/Spectral library

1.You can refer to the MCP paper about iProphet. Here is the link: http://www.mcponline.org/content/10/12/M111.007690.long. 2. SpectraST can create a consensus library by removing the redundant spectra. SpectraST can handle more than 225,000 spectra, and I used SpectraST to process much more than