One more question. I am using COMET prior to the peptide prophet steps.
COMET is already generating decoy database (concatenated search), do I need
to turn the decoy search off in COMET?
On Tuesday, May 14, 2024 at 2:38:00 PM UTC+5:30 Debojyoti Pal wrote:
> Thank you Dr David! That is rea
del known' ones (if any)
> as follows:
> [image: image.png]
>
> Hopefully this helps you process your dataset. Let us know if you have
> additional questions.
>
> Cheers!
> -David
>
>
>
> On Sun, May 12, 2024 at 2:38 AM Debojyoti Pal wrote:
>
>>
ood workflow would be to compute the raw TMT
> values with Libra and then export to MSstatsTMT and do all your
> normalization and comparisons there.
>
>
>
> Regards,
>
> Eric
>
>
>
>
>
>
>
> *From:* spctools...@googlegroups.com *On
> Beh
Dear TPP team
I would like to point out that one of the most important aspects of
iTRAQ/TMT quantification is proper normalization. Many studies have
demonstrated the crucial importance of global spectrum level normalization
i.e. normalization of the whole data by the respective total
And should I tick the "input is from iProphet" if I am using the PTM
Prophet file generated on the iProphet xml (as input in Protein Prophet)?
On Saturday, August 5, 2023 at 8:32:20 AM UTC+5:30 Debojyoti Pal wrote:
> Hi
>
> I can either input peptide prophet file as input
Hi
I can either input peptide prophet file as input or PTM prophet file as
input. What difference will it make?
Regards
Debojyoti
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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
Can anyone help me with this, please?
On Monday, July 31, 2023 at 11:39:47 PM UTC+5:30 Debojyoti Pal wrote:
> Dear all
>
> I am quantifying an iTRAQ run, where one of the channel seems to be having
> lower intensity across the board (around 20%). I am thinking of the TIC
>
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:
Dear all
I am quantifying an iTRAQ run, where one of the channel seems to be having
lower intensity across the board (around 20%). I am thinking of the TIC
normalization (total intensity), but it is mentioned as "not recommended"
in LIBRA settings.
Why is it so? If I am mixing equal
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
prophet results itself,
rather that needing to go back it peptide prophet and check individual
peptides. Also, please have an option to display absolute/normalized
values in addition to ratio.
Thank you so much and my apologies if this is the wrong platform to post
this.
Regards
Debojyoti Pal
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