Re: [spctools-discuss] Variable mod query in COMET

[Debojyoti Pal]

I meant that they would come up with something to get it done with only
variable modifications. By updating the code. Not by the static + variable
workaround we are doing.

Thanks
Debojyoti

On Tue, Aug 1, 2023 at 10:14 AM 'Luis Mendoza' via spctools-discuss <
spctools-discuss@googlegroups.com> wrote:

> This should already be possible with, e.g.
>
> variable_mod02 = 40.000 C 0 3 -1 0 0 0.0
> add_C_cysteine = 50.000
>
> (Of course using whatever masses are appropriate.)
>
> Or does this not work?
>
>
> On Mon, Jul 31, 2023 at 9:31 PM Debojyoti Pal 
> wrote:
>
>> Thanks Luis. I have asked this on the COMET group as well. They will
>> probably come up with an update or something to enable it.
>> On Tuesday, August 1, 2023 at 8:47:46 AM UTC+5:30 Luis Mendoza wrote:
>>
>>> Hi Debojyoti,
>>> Yes, I would say this is the most straightforward way of conducting this
>>> search.
>>> Note that you may need to make further adjustments to the variable mod
>>> string settings if, say, a given peptide must have *all* of its Cysteines
>>> in one state (+50) or the other (+90).  The default is to allow for mixed
>>> Cysteines in the peptide, e.g. PEPC[50]TIDEC[90]R.
>>> Hope this helps,
>>> --Luis
>>>
>>>
>>> On Mon, Jul 31, 2023 at 11:04 AM Debojyoti Pal 
>>> wrote:
>>>
 Hello everyone

 I have a specific scenario where I want to search for peptide in which
 cysteine must either have +50 or +90 mod. Basically:
 1) Cys can only have one of +50 or +90
 2) Cys much have one of +50 or +90 (ie It cannot be unmodified)

 Only way I can achieve this is to put a static mod of +50 and variable
 mod of +40 (40+50 = +90). Is there any better way to do this.

 Regards
 Debojyoti

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Re: [spctools-discuss] Variable mod query in COMET

['Luis Mendoza' via spctools-discuss]

This should already be possible with, e.g.

variable_mod02 = 40.000 C 0 3 -1 0 0 0.0
add_C_cysteine = 50.000

(Of course using whatever masses are appropriate.)

Or does this not work?


On Mon, Jul 31, 2023 at 9:31 PM Debojyoti Pal 
wrote:

> Thanks Luis. I have asked this on the COMET group as well. They will
> probably come up with an update or something to enable it.
> On Tuesday, August 1, 2023 at 8:47:46 AM UTC+5:30 Luis Mendoza wrote:
>
>> Hi Debojyoti,
>> Yes, I would say this is the most straightforward way of conducting this
>> search.
>> Note that you may need to make further adjustments to the variable mod
>> string settings if, say, a given peptide must have *all* of its Cysteines
>> in one state (+50) or the other (+90).  The default is to allow for mixed
>> Cysteines in the peptide, e.g. PEPC[50]TIDEC[90]R.
>> Hope this helps,
>> --Luis
>>
>>
>> On Mon, Jul 31, 2023 at 11:04 AM Debojyoti Pal 
>> wrote:
>>
>>> Hello everyone
>>>
>>> I have a specific scenario where I want to search for peptide in which
>>> cysteine must either have +50 or +90 mod. Basically:
>>> 1) Cys can only have one of +50 or +90
>>> 2) Cys much have one of +50 or +90 (ie It cannot be unmodified)
>>>
>>> Only way I can achieve this is to put a static mod of +50 and variable
>>> mod of +40 (40+50 = +90). Is there any better way to do this.
>>>
>>> Regards
>>> Debojyoti
>>>
>>> --
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>>> Groups "spctools-discuss" group.
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>>> https://groups.google.com/d/msgid/spctools-discuss/e4fc0662-b880-4a69-863f-4261444ba547n%40googlegroups.com
>>> 
>>> .
>>>
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>

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Re: [spctools-discuss] Variable mod query in COMET

[Debojyoti Pal]

Thanks Luis. I have asked this on the COMET group as well. They will 
probably come up with an update or something to enable it.
On Tuesday, August 1, 2023 at 8:47:46 AM UTC+5:30 Luis Mendoza wrote:

> Hi Debojyoti,
> Yes, I would say this is the most straightforward way of conducting this 
> search.
> Note that you may need to make further adjustments to the variable mod 
> string settings if, say, a given peptide must have *all* of its Cysteines 
> in one state (+50) or the other (+90).  The default is to allow for mixed 
> Cysteines in the peptide, e.g. PEPC[50]TIDEC[90]R.
> Hope this helps,
> --Luis
>
>
> On Mon, Jul 31, 2023 at 11:04 AM Debojyoti Pal  
> wrote:
>
>> Hello everyone
>>
>> I have a specific scenario where I want to search for peptide in which 
>> cysteine must either have +50 or +90 mod. Basically:
>> 1) Cys can only have one of +50 or +90
>> 2) Cys much have one of +50 or +90 (ie It cannot be unmodified)
>>
>> Only way I can achieve this is to put a static mod of +50 and variable 
>> mod of +40 (40+50 = +90). Is there any better way to do this.
>>
>> Regards
>> Debojyoti
>>
>> -- 
>> You received this message because you are subscribed to the Google Groups 
>> "spctools-discuss" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to spctools-discu...@googlegroups.com.
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/spctools-discuss/e4fc0662-b880-4a69-863f-4261444ba547n%40googlegroups.com
>>  
>> 
>> .
>>
>

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Re: [spctools-discuss] Variable mod query in COMET

['Luis Mendoza' via spctools-discuss]

Hi Debojyoti,
Yes, I would say this is the most straightforward way of conducting this
search.
Note that you may need to make further adjustments to the variable mod
string settings if, say, a given peptide must have *all* of its Cysteines
in one state (+50) or the other (+90).  The default is to allow for mixed
Cysteines in the peptide, e.g. PEPC[50]TIDEC[90]R.
Hope this helps,
--Luis


On Mon, Jul 31, 2023 at 11:04 AM Debojyoti Pal 
wrote:

> Hello everyone
>
> I have a specific scenario where I want to search for peptide in which
> cysteine must either have +50 or +90 mod. Basically:
> 1) Cys can only have one of +50 or +90
> 2) Cys much have one of +50 or +90 (ie It cannot be unmodified)
>
> Only way I can achieve this is to put a static mod of +50 and variable mod
> of +40 (40+50 = +90). Is there any better way to do this.
>
> Regards
> Debojyoti
>
> --
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> "spctools-discuss" group.
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> 
> .
>

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