Hi,
I am countinously getting this error LibraPeptideParser, and getting any(*file
not found:* not created or deleted?), while if running the same files without
Libra it is working fine.
how can I be able to correct the issue?
Error msg
running: "C:/TPP/bin/LibraPeptideParser
*How can I perceive the phospho residue identified protein? *
I have performed the complete analysis, up to PTMProphet, I am able to
identify the 10,000 phospho sites for the peptides. My question is how can
I link these phospho sites to identify them in the protein information and
see only
I have ran these files in tandem (labelled with iTRAQ 4plex channels)
previously, it completed comfortably, but now when I am running these files
again the below indicated error is getting repeated. Any, clue how I can
get rid of this error, to complete the process.
Note: This error occurs in
Hi, TPP,
I am working in TPP using *Bruker Maxis HD q-TOF machine *which generates
.d file. I have analysed the data using COMET search engine it works very
good and my 7 run analysis got completed in 18 hours (generation of pepXML)
using 10 treads in the system (defalut parameters). Further I
a place where the RT model is explained.
Thank you very much.
Ali
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/processed-pepXML for comparison with the new hits that I run PepPro
on them?
Many Thanks,
Ali
On Thursday, January 5, 2017 at 2:42:14 PM UTC-5, David Shteynberg wrote:
>
> Hello Ali,
>
> The RT model in PeptideProphet can be used to boost the probabilities of
> peptides close to
it look like? How
can I create it?
Thank you very much.
Sincerely,
Ali
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to
investigate more carefully.
I have another unrelated question which I am going to ask in another topic.
Sincerely,
Ali
On Wednesday, January 4, 2017 at 6:28:24 PM UTC-5, Eric Deutsch wrote:
>
> Hi Ali, my thoughts are that for this dataset and analysis,
> PeptideProphet+iProph
ntent.com/-jmsbfmBfbXA/WG1hNLP8e1I/BBI/SBnRc5-naTw09vjKk0K4m9xcCBgS-1Z8QCLcB/s1600/Picture2.png>
Do you have any thoughts on this?
Thank you very much,
Ali
On Wednesday, January 4, 2017 at 3:08:14 PM UTC-5, Ali wrote:
>
> Dear David and Eric
>
> Thanks for your replies an
Dear David and Eric
Thanks for your replies and suggestions. I thought that I might be able to
increase identification by accepting hits with lower thresholds. I do
understand what you mentioned here.
Thanks again,
Ali
On Tuesday, January 3, 2017 at 1:57:38 PM UTC-5, Eric Deutsch wrote
ch engine results including SpectraST (Except for X!
Tandem GPM).
Thank you very much,
Ali
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PepPro/iPro probability? Is
there a way that I allow a higher FDR without changing the probability
threshold?
Thank you very much in advance.
Ali
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Dear Jean Christophe
He has done those steps. This was what he was getting afterwards. Thanks
again for your help!
Sincerely,
Ali
On Wednesday, October 19, 2016 at 3:35:37 PM UTC-4, Jean-Christophe Ducom
wrote:
>
> I do not see the step where VERSION file has to be modified (replace
nux-x86_64*
*cp: omitting directory `/root/TPP_5.0.0-src/extern/ProteoWizard/pwiz-msi/'*
*make: *** [/root/TPP_5.0.0-src/build/linux-x86_64] Error 1*
*[root@nkr-rc-neu TPP_5.0.0-src]#*
Do you know what should we do now?
Many Thanks.
Sincerely,
Ali
On Wednesday, October 19, 2016 at 2:38:56 AM
Thank you so much Jean Christophe!
I will forward your instructions to him.
Sincerely,
Ali
On Wednesday, October 19, 2016 at 2:38:56 AM UTC-4, Jean-Christophe Ducom
wrote:
>
> I had same issues few days ago. I went thru scripts and saw some issues
> with pwiz-msi.
> Here is m
inside
the TPP's GUI? and why do I usually get Internal Server Error when I select
Tandem as the pipeline?
Many Thanks,
Ali
On Wednesday, October 12, 2016 at 6:41:55 PM UTC-4, David Shteynberg wrote:
>
> The TPP is not tested to work with ProteomeDiscoverer pepXML. Sure you
> ca
with comet. I have to figure
out how it works first.
I will upload the ProteomeDiscoverer pep.xml in the folder that you have
it's link, if you had a few minutes just take a look at it. May be it
needed a few tweaks to work with PeptideProphet.
Thanks so much,
Ali
On Wednesday, October 12, 2016 at 6:41
post just now, I am having problem with processing them with PeptideProphet
and InteractParser. Do you have experience with these files? I can send you
a sample of the pepxml files for you.
Sincerely,
Ali
On Wednesday, October 12, 2016 at 6:12:57 PM UTC-4, David Shteynberg wrote:
>
>
Dear Waovoo
This is an old post but I thought may be you could help me. I have Proteome
Discoverer v2.0 exported pep.xml and it is not working with PeptideProphet.
How did you analyze your results with PeptideProphet?
Thank you very much,
Ali
On Wednesday, August 19, 2015 at 1:54:13 PM UTC-4
analysis
> contain 4+?
>
> -David
>
> On Wed, Oct 5, 2016 at 6:16 PM, Ali <sma.ban...@gmail.com >
> wrote:
>
>> Hi David
>>
>> We are only collecting 2+, 3+ and 4+ data. I am working on the cluster,
>> so I am using the GPM version and we were unable to
= -0.2
WARNING: Mixture model quality test failed for charge (2+).
WARNING: Mixture model quality test failed for charge (3+).
WARNING: Mixture model quality test failed for charge (4+).
Thanks,
Ali
On Wednesday, October 5, 2016 at 9:21:04 PM UTC-4, David Shteynberg wrote:
>
> I canno
and then
using PeptideProphet (as you instructed), I have not yet done so because I
wanted to make sure that we are getting results from the individual
searches. Is there an issue in my search parameters which is responsible
for the problem?
Many Thanks,
Ali
On Wednesday, October 5, 2016 at 7:06
vid
>
> On Tue, Oct 4, 2016 at 2:12 PM, Ali <sma.ban...@gmail.com >
> wrote:
>
>> It appears that PeptideProphet fails, I am getting this message:
>>
>> using Accurate Mass Bins
>> using PPM mass difference
>> (X! Tandem) (minprob 0)
>> adding
wer. I suggest you combine the results
> from all your runs and filter by the spectrum names later. Try this:
>
> InteractParser ./ALL.interact.xml ./*.tandem.pep.xml -S -Etrypsin
> PeptideProphetParser ./ALL.interact.xml ACCMASS PPM NOICAT MINPROB=0
>
>
> -David
>
> On
cause the issue? I am using Trypsin
enzyme and TMT 10 plex of K and TMT 10plex of N term fixed residue
modification.
Sincerely,
*Ali*
On Monday, October 3, 2016 at 5:57:39 PM UTC-4, David Shteynberg wrote:
>
> I highly recommend you start employing decoys in your search databas
-PeptideProphetParser ./100.interact.xml ACCMASS PPM NOICAT MINPROB=0
Thank you very much,
*Ali*
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ld to create on consensus library spectrum
> for that peptide. The SpectraST wiki page has all the details:
> http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST#SpectraST_Create_Mode
>
> -David
>
> On Tue, Sep 20, 2016 at 2:42 PM, Ali <sma.ban...@gmail.com &
) with
SpectraST?
Thank you very much.
On Tuesday, September 20, 2016 at 3:35:34 PM UTC-4, David Shteynberg wrote:
>
> Ali,
>
> iProphet will compute a probability of each unique spectrum separately.
> It only combines PSM if they represent repeated searches of the same
> spec
Sorry I made a mistake here! I am getting similar *peptides*! Not *spectra*!
On Monday, September 19, 2016 at 3:26:20 PM UTC-4, Ali wrote:
>
> Hello
>
> I am combining multiple search results (all from X!Tandem) using iprophet
> to then make a spectral library of them with Spectra
my library larger than
it should be.
Many Thanks,
Ali
On Tuesday, September 20, 2016 at 3:15:13 AM UTC-4, Eric Deutsch wrote:
>
> I suspect the problem is that an old 32-bit version of SpectraST will
> create a corrupt index for any library larger than 2 GB. The library splib
>
ut SpectraST.
> Here is the link:
> http://www.nature.com/nmeth/journal/v5/n10/full/nmeth.1254.html
>
> On Tue, Sep 20, 2016 at 10:44 AM, Ali <sma.ban...@gmail.com >
> wrote:
>
>> Hi
>>
>> Thanks so much for your answers!
>>
>> I created a lib
for your time,
Ali
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Many thanks for your response David!
I've read the page you mentioned, I wanted to make sure.
Sincerely,
Ali
On Monday, September 5, 2016 at 12:24:47 PM UTC-4, David Shteynberg wrote:
>
> Hello Ali,
>
> For more information on SpectraST please see the follow
Hi
Does any body know whether SpectraST uses retention time in analyzing a
shotgun data (a spectrast search) or not? Can I get some details about it?
Thank you very much,
*Ali*
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t;
> I suspect that is what is causing the mods that SpectraST doesn’t
> understand..
>
>
>
>
>
> *From:* Ali [mailto:sma.ban...@gmail.com ]
> *Sent:* Wednesday, August 31, 2016 8:23 PM
> *To:* spctools-discuss <spctools...@googlegroups.com >
> *Cc:*
I went through these steps again and I am still getting the same error and
everything in spectrast.
On Wednesday, August 31, 2016 at 11:04:39 PM UTC-4, Ali wrote:
>
> Thank you so much Eric for helping me. Let me tell you what I have done
> before this:
>
>
>- I ha
,TMT6plex should be about half of n,TMT6plex and it’s not. And a scenario
> where E,Glu->pyro-Glu is greater than K,TMT6plex is hard to fathom. These
> relative counts don’t make sense.
>
>
>
> I suggest checking your mass mods for the original search very carefully
> and
Q,Gln->pyro-Glu: 101
n,TMT6plex: 2879
On Wednesday, August 31, 2016 at 8:48:09 PM UTC-4, Ali wrote:
>
> Hi
>
> I want to create a library from a pep.xml file which is the result of X!
> Tandem search (I converted the X!Tandem to pep.xml using
Hi
I want to create a library from a pep.xml file which is the result of X!
Tandem search (I converted the X!Tandem to pep.xml using Tandem2XML) using
spectrast with the following simple command:
spectrast -cN1607011A_NC20A_10ul_180min.splib -cP0.9
1607011A_NC20A_10ul_180min.tandem.pep.xml
I
they are the same.
I will be giving all the search algorithms a try soon...
Ali
On Jul 17, 6:18 pm, Natalie Tasman natalie.tas...@insilicos.com
wrote:
Ah, ok, I see that mspire takes Thermo .srf files, which I believe are
the newer Sequest search result files
(http://mspire.rubyforge.org
Hi Natalie
I used sequest. I've sort of given up on that. I now convert my .raw
files directly to .pep.xml files using mspire. Its not much of a
pipeline anymore but it does the job.
Regards
Ali
On Jul 15, 9:19 pm, Natalie Tasman natalie.tas...@insilicos.com
wrote:
Hi Ali,
Greg made
Hi
I am unable to open pepxml viewer. I get the following error:
error:
can't open html templatec:/Inetpub/wwwroot;c:/Inetpub/wwwroot//ISB/
html/PepXMLViewer_noFile.html
Any advice will be appreciated.
Ali
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Hi Natalie
I have fixed the problem. The GUI was looking for the the
trans_proteomic_pipeline folder but cannot find it. I have unzipped
it in my C drive.
Regards
Ali
On Jul 7, 6:02 pm, Natalie Tasman natalie.tas...@insilicos.com
wrote:
Hello Ali,
It sounds like you're using the command
Hi
I'm new to TPP. I downloaded the software and attempted to convert
XCalibur .RAW to mzXML files as the first step of the pipeline. This
however failed as it complains of '--mzXML unknown option'. I checked
in my tpp-bin file that I have the ReAdW file. I used the ReAdW in
dos and it
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