Hi David,
I attempted a run with PTMProphet with MASSDIFFMODE (I wasn't not sure what
the usage is for this feature, I looked at the source code on sourceforge
and did a best guess: is there a file outlining the different usages of
optional features somewhere online?) and ran with the ipro.pep.xml file
that I generated from the wide tolerance comet search. I received several
warnings back but the .ptm.pep.xml file was written and I can see peptides
with assigned sites of modifcation. Just wondering if these warnings mean
that some mods were not written to the output file? Is there anything
missing in the MASSDIFFMODE command that I should include?
Best,
Adam
>PTMProphetParser MZTOL=0.2 MASSDIFFMODE
interact_widetol_minus_saha_2.ipro.pep.xml
interact_widetol_minus_saha_2.ptm.pep.xml
INFO: Reading file interact_widetol_minus_saha_2.ipro.pep.xml ...
INFO: processed 500/8911 spectrum_queries.
INFO: processed 1000/8911 spectrum_queries.
INFO: processed 1500/8911 spectrum_queries.
INFO: processed 2000/8911 spectrum_queries.
INFO: processed 2500/8911 spectrum_queries.
INFO: processed 3000/8911 spectrum_queries.
INFO: processed 3500/8911 spectrum_queries.
INFO: processed 4000/8911 spectrum_queries.
INFO: processed 4500/8911 spectrum_queries.
INFO: processed 5000/8911 spectrum_queries.
INFO: processed 5500/8911 spectrum_queries.
INFO: processed 6000/8911 spectrum_queries.
INFO: processed 6500/8911 spectrum_queries.
INFO: processed 7000/8911 spectrum_queries.
INFO: processed 7500/8911 spectrum_queries.
INFO: processed 8000/8911 spectrum_queries.
INFO: processed 8500/8911 spectrum_queries.
Iterating PTM Model: ....5.done
INFO: Writing file interact_widetol_minus_saha_2.ptm.pep.xml ...
INFO: Reading file interact_widetol_minus_saha_2.ipro.pep.xml ...
WARNING: Illegal PTM-shuffled peptide detected with non-matching mass:
L[113]IEKGLR
Neutral Mass (from pepXML) = 827.487
Neutral Computed Mass for Evaluation = 827.523
PPM difference = 43.9714
WARNING: Illegal PTM-shuffled peptide detected with non-matching mass:
I[113]EKGLR
Neutral Mass (from pepXML) = 827.487
Neutral Computed Mass for Evaluation = 827.523
PPM difference = 43.9714
WARNING: Illegal PTM-shuffled peptide detected with non-matching mass:
E[129]KGLR
Neutral Mass (from pepXML) = 827.487
Neutral Computed Mass for Evaluation = 827.523
PPM difference = 43.9714
WARNING: Illegal PTM-shuffled peptide detected with non-matching mass:
K[128]GLR
Neutral Mass (from pepXML) = 827.487
Neutral Computed Mass for Evaluation = 827.523
PPM difference = 43.9714
WARNING: Illegal PTM-shuffled peptide detected with non-matching mass:
L[113]R
Neutral Mass (from pepXML) = 827.487
Neutral Computed Mass for Evaluation = 827.523
PPM difference = 43.9714
WARNING: Illegal PTM-shuffled peptide detected with non-matching mass:
R[156]
Neutral Mass (from pepXML) = 827.487
Neutral Computed Mass for Evaluation = 827.523
PPM difference = 43.9714
WARNING: Illegal PTM-shuffled peptide detected with non-matching mass:
L[113]IEKGLR
Neutral Mass (from pepXML) = 827.487
Neutral Computed Mass for Evaluation = 827.523
PPM difference = 43.9714
WARNING: Illegal PTM-shuffled peptide detected with non-matching mass:
I[113]EKGLR
Neutral Mass (from pepXML) = 827.487
Neutral Computed Mass for Evaluation = 827.523
PPM difference = 43.9714
WARNING: Illegal PTM-shuffled peptide detected with non-matching mass:
E[129]KGLR
Neutral Mass (from pepXML) = 827.487
Neutral Computed Mass for Evaluation = 827.523
PPM difference = 43.9714
WARNING: Illegal PTM-shuffled peptide detected with non-matching mass:
K[128]GLR
Neutral Mass (from pepXML) = 827.487
Neutral Computed Mass for Evaluation = 827.523
PPM difference = 43.9714
WARNING: Illegal PTM-shuffled peptide detected with non-matching mass:
G[57]LR
Neutral Mass (from pepXML) = 827.487
Neutral Computed Mass for Evaluation = 827.523
PPM difference = 43.9714
On Tuesday, September 26, 2017 at 5:50:48 PM UTC-5, David Shteynberg wrote:
>
> MASSDIFFMODE should be compatible with most pepXML files from comet and
> beyond. The only issue I see with using SpectraST is that the DECOYS are
> going to be different, so you have to take that into consideration if you
> are combining SpectraST results with other search engines and have
> different sets DECOYS sequences then the result should probably not be
> combined with the NSS model on. I am working on something that will
> facilitate the combining of SpectraST results with other search engines.
> For now however, you can run iProphet on the SpectraST search results
> independently.
>
> Cheers,
> -David
>
> On Tue, Sep 26, 2017 at 2:24 PM, Adam R <[email protected] <javascript:>>
> wrote:
>
>> Thanks David for the tip! I will give MSFragger a try but unfortunately I
>> will have to wait for MTA authorization. In the meantime, would there be
>> any limitation to using a comet-generated pep.xml file using a wide-mass
>> window? Is the MASSDIFFMODE feature compatible with comet? Would there be
>> any compatibility issues when combining with SpectraST results in iProphet?
>>
>> Best,
>>
>> Adam
>>
>> On Tuesday, September 26, 2017 at 11:00:24 AM UTC-5, David Shteynberg
>> wrote:
>>>
>>> Hi Adam,
>>>
>>> Yes there is a mode in PTMProphet you can enable called MASSDIFFMODE, it
>>> will localize the mass difference like a PTM. I have tried this using
>>> MSFragger and tier-wise open mass searching using SpectraST.
>>>
>>> -David
>>>
>>> On Mon, Sep 25, 2017 at 11:09 AM, Adam R <[email protected]> wrote:
>>>
>>>> Hi David,
>>>>
>>>> Thank you for the prompt response! I will give it a try from the
>>>> command line. I also have a follow-up question to ask to this as I have
>>>> been wondering about other ways to tackle the data.
>>>>
>>>> Gygi's group published a paper in 2015 (
>>>> http://www.nature.com/nbt/journal/v33/n7/abs/nbt.3267.html) about
>>>> using wide mass tolerance windows for searching spectra (+/- 500 Da
>>>> windows) to identify modifications in unassigned spectra. They went on to
>>>> use the Ascore algorithm to identify the sites of modifcation. I'm
>>>> wondering whether this would be possible to perform with the current
>>>> iteration of TPP? (i.e. wide mass tolerant search with comet followed by
>>>> site analysis by PTM Prophet) PTM Prophet's input requires the amino acid
>>>> and the mass shifts for PTMs but I'm wondering whether it could be
>>>> utilized
>>>> to identify "un-specified" mods on any amino acid.
>>>>
>>>> Best,
>>>>
>>>> Adam
>>>>
>>>> On Monday, September 25, 2017 at 11:47:39 AM UTC-5, David Shteynberg
>>>> wrote:
>>>>>
>>>>> There are a couple things wrong here. Primarily there is a bug in
>>>>> current distributed version of PTMProphet that prevents it from being run
>>>>> through the web-interface. There is already a fix available, however,
>>>>> you
>>>>> will probably want to run this from the command line because of reasons
>>>>> that follow. Your command needs some adjustment. As is it will try to
>>>>> localize a different "PTM" on the amino acids you have specified for each
>>>>> set of amino acids, when what you want it to localize on any amino acid.
>>>>> You can try the following in a command terminal
>>>>>
>>>>> cd c:\TPP\data\[YOUR_DATA_DIRECTORY]
>>>>>
>>>>> PTMProphetParser MZTOL=0.2 ABCDEFGHIJKLMNOPQRSTUVXWYZ:639.3169
>>>>> [YOUR_INPUT_PEPXML] [YOUR_OUTPUT_PEPXML]
>>>>>
>>>>>
>>>>> Thank you for reporting the issue.
>>>>>
>>>>> -David
>>>>>
>>>>>
>>>>> On Sun, Sep 24, 2017 at 11:19 AM, wicher89 <[email protected]> wrote:
>>>>>
>>>>>> Hi Everyone,
>>>>>>
>>>>>> I am analyzing peptides from cells that have been treated with a UV
>>>>>> crosslinker attached to a small molecule (ABPP method). This results in
>>>>>> mono-linked peptides. Because the UV cross-linker is not residue
>>>>>> specific,
>>>>>> I am forced to search the data in comet with a modification of 639.3118
>>>>>> Da
>>>>>> on any amino acid other than those with fixed modifications. I am able
>>>>>> to
>>>>>> process the output files until the iProphet step, but am running into
>>>>>> command failure at PTM Prophet. Is there a maximum limit on the number
>>>>>> of
>>>>>> amino acids used at once in a single line entry for a modification? I
>>>>>> have
>>>>>> attached screenshots of the parameters used and the command failure
>>>>>> output.
>>>>>>
>>>>>> Thanks!
>>>>>>
>>>>>>
>>>>>> --
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>>>>>
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>>>
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