Re: [spctools-discuss] sud silac asapratio

[sudarshan kumar]

 110623_Silac_TEST_01.mzML

 110623_Sud_LH_TEST_01.raw

 110623_Sud_LH_TEST_02.mzML

 110623_Sud_LH_TEST_02.raw

 UP00625.fasta



On Wed, Nov 22, 2023 at 4:10 PM 'David Shteynberg' via spctools-discuss <
spctools-discuss@googlegroups.com> wrote:

> You will also need to shared the mzML file containing the data.
>
> Thanks!
>
>
> On Wed, Nov 22, 2023 at 4:07 PM sudarshan kumar 
> wrote:
>
>>  interact_silaccomtwofiles.pep.zip
>> 
>>
>>
>> --
>> ---
>> The real voyage of discovery consists not in seeking new lands but seeing
>> with new eyes. — Marcel Proust
>>
>> Dr. Sudarshan Kumar
>> (Fulbright-Nehru Fellow)
>> (B.V.Sc.& A.H., M.V.Sc., PhD.)
>> Sr. Scientist
>> Animal Biotechnology Center
>> (Proteomics and Cell Biology Lab.)
>> National Dairy Research Institute Karnal, 132001
>> Haryana, India
>> Contact No 09254912456
>> URL www.ndri.res.in
>> Orcid Id: https://orcid.org/-0002-9816-4307
>>
>> --
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>> 
>> .
>>
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> 
> .
>


-- 
---
The real voyage of discovery consists not in seeking new lands but seeing
with new eyes. — Marcel Proust

Dr. Sudarshan Kumar
(Fulbright-Nehru Fellow)
(B.V.Sc.& A.H., M.V.Sc., PhD.)
Sr. Scientist
Animal Biotechnology Center
(Proteomics and Cell Biology Lab.)
National Dairy Research Institute Karnal, 132001
Haryana, India
Contact No 09254912456
URL www.ndri.res.in
Orcid Id: https://orcid.org/-0002-9816-4307

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Re: [spctools-discuss] sud silac asapratio

['David Shteynberg' via spctools-discuss]

You will also need to shared the mzML file containing the data.

Thanks!


On Wed, Nov 22, 2023 at 4:07 PM sudarshan kumar 
wrote:

>  interact_silaccomtwofiles.pep.zip
> 
>
>
> --
> ---
> The real voyage of discovery consists not in seeking new lands but seeing
> with new eyes. — Marcel Proust
>
> Dr. Sudarshan Kumar
> (Fulbright-Nehru Fellow)
> (B.V.Sc.& A.H., M.V.Sc., PhD.)
> Sr. Scientist
> Animal Biotechnology Center
> (Proteomics and Cell Biology Lab.)
> National Dairy Research Institute Karnal, 132001
> Haryana, India
> Contact No 09254912456
> URL www.ndri.res.in
> Orcid Id: https://orcid.org/-0002-9816-4307
>
> --
> 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-discuss+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/spctools-discuss/CALZrgHTc_iCrRsyveZmtaG%2B%2B9W5mMS7kQF%2Bj5Hd-7PPp0ghfAA%40mail.gmail.com
> 
> .
>

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[spctools-discuss] sud silac asapratio

[sudarshan kumar]

 interact_silaccomtwofiles.pep.zip



-- 
---
The real voyage of discovery consists not in seeking new lands but seeing
with new eyes. — Marcel Proust

Dr. Sudarshan Kumar
(Fulbright-Nehru Fellow)
(B.V.Sc.& A.H., M.V.Sc., PhD.)
Sr. Scientist
Animal Biotechnology Center
(Proteomics and Cell Biology Lab.)
National Dairy Research Institute Karnal, 132001
Haryana, India
Contact No 09254912456
URL www.ndri.res.in
Orcid Id: https://orcid.org/-0002-9816-4307

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Re: [spctools-discuss] Re: EXpress in SILAC

[sudarshan kumar]

Oh ! thank you
Let me explain-
I have mixed two samples light and heavy labelled proteins (at cell level)
But if the cell count was not equal in the two groups, it will result in
unequal contribution of proteins to the mixture. In this case the ratio L/H
for individual protein will not be correct.
The solution is normalization (as we do in St. Peter)

so I wanted to know if such normalization is done in Express before
calculating the light to heavy ratio.


On Wed, Nov 22, 2023 at 3:07 PM Jimmy Eng  wrote:

> I don't know what "normalized intensity/peak area" of each peptide means
> in this context but I can say that XPRESS doesn't do any normalization.  It
> simply reports light area to heavy area ratios.  You'll have to do
> adjustments after the fact i.e. centering the mean ratio to 1:1 if you
> expect the bulk of your samples to be 1:1.
> On Wednesday, November 22, 2023 at 1:12:35 PM UTC-8 sudarshan kumar wrote:
>
>> How do we know that the express ratio is calculated from the normalized
>> intensity /peak area of each peptide?
>>
>> I ask this question because when we mix the light and heavy samples,
>> there may be difference in the initial quantity of protein taken from the
>> two groups.
>>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
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> 
> .
>


-- 
---
The real voyage of discovery consists not in seeking new lands but seeing
with new eyes. — Marcel Proust

Dr. Sudarshan Kumar
(Fulbright-Nehru Fellow)
(B.V.Sc.& A.H., M.V.Sc., PhD.)
Sr. Scientist
Animal Biotechnology Center
(Proteomics and Cell Biology Lab.)
National Dairy Research Institute Karnal, 132001
Haryana, India
Contact No 09254912456
URL www.ndri.res.in
Orcid Id: https://orcid.org/-0002-9816-4307

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[spctools-discuss] Re: EXpress in SILAC

[Jimmy Eng]

I don't know what "normalized intensity/peak area" of each peptide means in 
this context but I can say that XPRESS doesn't do any normalization.  It 
simply reports light area to heavy area ratios.  You'll have to do 
adjustments after the fact i.e. centering the mean ratio to 1:1 if you 
expect the bulk of your samples to be 1:1.
On Wednesday, November 22, 2023 at 1:12:35 PM UTC-8 sudarshan kumar wrote:

> How do we know that the express ratio is calculated from the normalized 
> intensity /peak area of each peptide?
>
> I ask this question because when we mix the light and heavy samples, there 
> may be difference in the initial quantity of protein taken from the two 
> groups.
>

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[spctools-discuss] EXpress in SILAC

[sudarshan kumar]

How do we know that the express ratio is calculated from the normalized 
intensity /peak area of each peptide?

I ask this question because when we mix the light and heavy samples, there 
may be difference in the initial quantity of protein taken from the two 
groups.

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