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.
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,
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
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
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,
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
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:
>
>
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
, 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
?
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
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.
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:
ill 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 tool for Lin
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
*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. 01.05.15 UTC+2 skrev Michael Hoopman
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.
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
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
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
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:
. 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,
It looks
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
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,
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());
Here is the
publication: https://pubs.acs.org/doi/10.1021/acs.jproteome.7b00786
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To: 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
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
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,
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
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]
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
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
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,
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
Hi OK,
In the tandem params, you need to change:
note type=input label=scoring, algorithmk-score/note
to
note type=input label=scoring, algorithmhrk-score/note
Then I would recommend lowering the spectrum, fragment monoisotopic
mass error values to something small and appropriate for
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 need to access the
latest methods
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
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
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:
note type=input label=spectrum, threads2/note
Cheers,
Mike
On 7/5/2011 5:45 PM, Qinzhe Wang wrote:
Hi
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