First, I would try changing the "spectrum, threads" parameter to 8 to
get the full use of your cpu. I'm assuming that the quad core is
hyperthreaded, so that it appears to behave like an 8-core computer.
That should put your usage up to 100%.
Cheers,
Mike
On 1/25/2011 6:49 AM, Zac wrote:
I a
Hi Qinzhe,
I am assuming you are using X!Tandem to do the database searches. In
that case, set the threads parameter in the X!Tandem params file to the
number of cores you want to use:
2
Cheers,
Mike
On 7/5/2011 5:45 PM, Qinzhe Wang wrote:
Hi everyone,
I have installed TPP to perform datab
Hi Bo,
You could try using the msconvert tool from proteoWizard:
http://proteowizard.sourceforge.net/downloads.shtml
Cheers,
Mike
On 10/7/2011 5:23 AM, Bo Ek wrote:
Hi!
I'm collecting ms data (not ms/ms) from an Agilent MSD TOF instrument
and get my rusult files in the format .wiff. Usually t
Hello,
It appears you have a missing/bogus index in your .mzXML files. Try
running indexmzXML on your .mzXML files, then repeat tandem2xml.
Cheers,
Mike
On 1/17/2012 6:55 AM, Gabriel Gray wrote:
Hi,
We're getting the following error when running tandem2xml from the
command line using TPP v4.1
Hi Josh,
Not all the methods are in the old interface. You need to access the
latest methods from IXRawfile5. A good example of how to use this
interface is in
https://proteowizard.svn.sourceforge.net/svnroot/proteowizard/trunk/pwiz/pwiz_aux/msrc/utility/vendor_api/thermo/RawFile.cpp
check the
garding this
issue, but I have not heard back
yet. I have very little programming experience, so any
troubleshooting suggestions are welcome.
Thanks!
Josh
On Monday, August 27, 2012 5:01:48 PM UTC-5, Michael Hoopmann wrote:
Hi Josh,
Not all the methods are in the old interface. You
Hi OK,
In the tandem params, you need to change:
k-score
to
hrk-score
Then I would recommend lowering the "spectrum, fragment monoisotopic
mass error" values to something small and appropriate for hi-res data.
Cheers,
Mike
On 5/12/2013 11:45 PM, 2kl...@gmail.com wrote:
Hi All,
Is the hi
Hi Avinash,
Are you building from the TPP source or from the GPM source? The GPM
support for the mzXML format is poorly (or hardly) implemented. It does
not accept files that make use of some very basic features of the
format. For the TPP version, we made several improvements to accept all
mzX
Hi Peter,
No, what happens is that multiple true peptides will map to the same
protein, but practically all false peptides will map singly to unique
proteins. As a result, the protein FDR will likely be greater than 1%.
Typically, if you do not perform some sort of protein level statistics,
yo
Hi Peter,
ProteinProphet uses the PeptideProphet results, so if many peptides in
ProteinProphet show no phosphorylation, these peptides were identified
this way in PeptideProphet. I am not sure how to answer your first
question, as I know nothing about your actual data, and it is unlikely
to b
Hi Zeyu,
On a windows system, use the "type" command. For example:
type file1.fasta file2.fasta > combined.fasta
Cheers,
Mike
On 2/19/2014 9:14 AM, Joseph Slagel wrote:
Zeyu,
If your on a Linux system, there's the "cat" command:
http://en.wikipedia.org/wiki/Cat_%28Unix%29
http://www.thegeeks
Hi Sebastian,
It seems despite limiting the number of spectra, you still are running
low on memory when running Comet. I am guessing that the spectra are
high resolution and require a really small fragment_bin_tol? If this is
not the case, let me know. Otherwise, try setting spectrum_batch_size
Hi Bob,
Brian mentioned something that brought stalled applications to mind. Sometimes
a virus scanner can halt the application at its start without warning you,
leaving it in limbo indefinitely. If you are using a virus scanner, you can try
disabling it to see if it solves the problem. If so,
I don’t require them in my software that reads pepXML because I don’t find
these tags reliable, specifically in cases where they are missing. Like
SpectraST, Kojak doesn’t export these either.
Cheers,
Mike
From: spctools-discuss@googlegroups.com
[mailto:spctools-discuss@googlegroups.com] O
Hi Connor,
In the example file you provided, I see that your
761801 points to the middle of the intensity
array of scan 100 and not to the start of the indexList.
Your actual indexListOffset looks to be 769983. The error message is because
the indexListOffset needs to be set to the correct
Manuscript is in review, but documentation is already under construction:
http://tools.proteomecenter.org/wiki/index.php?title=Software:StPeter
Cheers,
Mike
From: spctools-discuss@googlegroups.com
[mailto:spctools-discuss@googlegroups.com] On Behalf Of Filippo GENOVESE
Sent: Monday, Decembe
The current release of Kojak doesn’t allow for this. However, I just uploaded
these changes to the Kojak source tree:
1. Addition of selenocysteine to the amino acid canon (with mass
150.9536303).
2. Ability to add or change the mass of any alphabetical character with
the new aa_ma
: spctools-discuss@googlegroups.com
Subject: RE: [spctools-discuss] Selenocysteine in Kojak
Thanks, Mike. For a stupid GUI user, how can this be done?
_
From: Michael Hoopmann <mailto:michael.hoopm...@systemsbiology.org>
Sent: 28.12.2017 23:29
To: spctools-discuss@googlegrou
Here is the
publication: https://pubs.acs.org/doi/10.1021/acs.jproteome.7b00786
--
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to spctools-discuss+unsubscr...
Hi Monica,
Thanks for reporting the bug. I have a fix for the source tree, but sourceforge
is having problems right now. You can add the fix manually, though, by going
into CProteinAmbiguityGroup.cpp and changing:
sprintf(dbid, "%s_%d", baseRef, proteinDetectionHypothesis->size());
to
Hi Alexander,
It looks like the blanks belong to proteins in a group, possibly where there
are no non-degenerate peptides for those proteins. It might be possible to
perform the quantification if you allow degenerate peptides in the analysis
with the –d option when you run StPeter.
Cheers,
Mi
Hi Antonio,
To use StPeter, you must perform peptide validation and protein inference
first. These are done, minimally, with the PeptideProphet and
ProteinProphet tools, respectively. They are needed because StPeter
quantifies proteins, not peptides, and thus you need to first perform
protein i
work. The
entire SIn column appears as blank for all values (including the ones which
were previously shown). I'm not sure if this is the intended output for the
software or not. Thank you for your help!
On Wednesday, May 16, 2018 at 5:36:33 PM UTC-4, Michael Hoopmann wrote:
Hi Alexander,
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: mak
You can find the StPeter version by typing StPeter from a command line or
looking back through your logs in the TPP interface. In any case, it might
be that this latest feature of StPeter wasn't implemented at the time of
release for version 5.1.0. I think it missed by six or eight weeks.
That
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 su
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 wi
Hi Panos,
mzIMLDemo is a demonstration application of the mzIdentML support tools in
TPP. It is non-essential and still in development, so you're right, it
isn't necessary. That being said, it shouldn't be allowed to halt the build
process. I suspect this will be fixed in TPP release 5.1.1.
Chee
ed as
> coming from peptide *k,* and then for all *pn* peptides coming from
> protein *K.* This total sum whould make protein's K SI.
>
>
> Thanks for your help and time!! :)
>
>
> Best
>
>
> Antonio
>
>
> onsdag den 23. maj 2018 kl.
Hi Antonio,
You are correct and you will need access to the MS2 spectra. Indeed, that
is the incentive argued by Griffin, that MS2 fragment intensity gives some
advantage to quantification in MS2-based methods for overlapping signals.
However, there is a lot more literature out there (and far mo
t; still only possible through mono or a windows vm? How does your group at
> ISB handle this and which VM setup do you recommend?
>
> Best,
>
> Adam
>
> On Saturday, June 2, 2018 at 11:06:48 AM UTC-5, Michael Hoopmann wrote:
>>
>> No, there isn't a native to
Hi Kamal,
Yes, you can use PeptideProphet to validate Kojak results. Select “Kojak” from
your pipeline in the upper right of the TPP page, and it will default
PeptideProphet parameters for Kojak. Input is the PepXML output from Kojak.
The windows version of Percolator can be found here:
htt
Hi Gabriella,
I’m not an expert on Percolator (or machine learning) but I think the problem
is simply that the dataset is too small. There are only 128 results, which need
to be split into training and cross-validation test sets, and thus there isn’t
much data to train or test the models. Manua
?
Thanks a lot,
Gabriella
On Monday, November 12, 2018 at 9:39:01 PM UTC+1, Michael Hoopmann wrote:
Hi Gabriella,
I’m not an expert on Percolator (or machine learning) but I think the problem
is simply that the dataset is too small. There are only 128 results, which need
to be split into
, Jason Winget, Michael Hoopmann, Institute for Systems
Biology
Version 1.2.0 October 11 2017
** BEGIN StPeter ANALYSIS **
Time at start of analysis: Thu Feb 21 14:23:02 2019
Parameters:
degenerate peptides = no
fdr = 0.01
sample load = 0
tolerance = 0.4
intensities = no
Hi Zsuzsi,
Could you try renaming your enzyme, "trypsin_gluc" ? I think that is the
secret enzyme name that PeptideProphet recognizes for that enzyme
combination. Sorry for the trouble, I'll have dig through the code to see
who is at fault (Kojak or PeptideProphet) for not properly interpreting th
I think you found a bug. There is some rare property of a particular
precursor scan in that file that Kojak isn't handling correctly. I'll
probably need access to that particular mzML file to identify the bug. I'll
reach out to you by email.
On Monday, April 6, 2020 at 12:39:33 PM UTC-7, Lindse
Thanks for sending me the file, I was able to replicate the bug. It has
been fixed in the newest version of Kojak. For those with similar problems,
the newest Kojak can be found here: http://www.kojak-ms.org/download.html
Instructions for manually upgrading your Kojak before the next TPP release
Hi Thomas,
Sorry for the slow response, but HUPO is over now. I'll help take a look
and find the problem.
Cheers,
Mike
On Sun, Sep 15, 2019 at 11:56 PM Thomas Gossenreiter <
thomas.gossenrei...@gmail.com> wrote:
> Please find the links to the files below:
>
> https://drive.google.com/open?id=1bO2
Hi,
I can shed some light on the mzIdentML support. Regarding the fragmentation
information, it isn’t in the mzID file because it isn’t in the pepXML file.
tpp2mzid can only convert values it is given as input.
The dimethylated peptide error messages might be only a minor concern
indicat
Hi Alastair,
There is a much newer version of tpp2mzid in our current release candidates of
TPP version 6. I’m hoping that the error messages have been resolved in this
new version. However, I also need the fasta search database file to run the
conversion with the newer tpp2mzid. Could you also
Hi Alastair,
I can definitely reproduce the error, which is caused by the presence of two
identical fasta databases in your search space. I’ll need some time to fix the
bug and report back to you.
Cheers,
Mike
From: 'Alastair Skeffington' via spctools-discuss
Sent: Monday, June 21, 2021
Hi Alastair,
Yes, you can try this workaround and it should convert:
1. Open up your ipro.pep.xml file in a text editor
2. Find and replace all instances of
“../../../../Databases/EhuxAllproteins_MCC_decoy.fasta” with
“../../Databases/EhuxAllproteins_MCC_decoy.fasta”
3. S
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