ools-discuss" group.
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> <h
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> .
>
>
> I recommend this data is searched without strict tryptic-end requirements
> on the peptides.
>
> Cheers!
> -David
>
>
> On Jul 26, 2024, at 10:18 AM, sudarshan kumar
> wrote:
>
> Thank you so muc
Please share notepad version of comet.param version 2024.
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When I used comet param 2023 in TPP 7.1.0. It aborts the search saying that
your comet is of 2023 version.
On Thu, Jul 25, 2024 at 4:40 PM sudarshan kumar
wrote:
> Hi, David,
> Can you please also share the comet param version 2024. Or please let me
> know where i can downloa
Hi, David,
Can you please also share the comet param version 2024. Or please let me
know where i can download it from.
Regards
Sud
On Thu, Jul 25, 2024 at 12:00 PM sudarshan kumar
wrote:
> Hi David,
> I tried 7.1.0 also. and I see that the problem is still the same (0
> probabilit
; together and reshare? I will need at least those file to try to reproduce
> your process.
>
> Cheers!
>
> On Wed, Jul 24, 2024, 2:19 AM sudarshan kumar
> wrote:
>
>>
>> 20240417_AN_171_POS_LCMSMS_00.mzML
>> <https://drive.google.com/file/d/1qNf8C08bcg0K
rote:
>
> Can you compress the mzML file, the search database and your search
> together and reshare? I will need at least those file to try to reproduce
> your process.
>
> Cheers!
>
> On Wed, Jul 24, 2024, 2:19 AM sudarshan kumar
> wrote:
>
&g
20240417_AN_171_POS_LCMSMS_00.mzML
<https://drive.google.com/file/d/1qNf8C08bcg0KwF56HmonihILxh3uVqyU/view?usp=drive_web>
please find the mzml file shared through drive
On Wed, Jul 24, 2024 at 12:40 AM sudarshan kumar
wrote:
> Thank you so much David,
> Please find the screenshot
Hi,
Can you please explain why?
When I searched with tandem, IT shows all good hits as I expected from the
sample.
But when I used peptide prophet, The result is all 0 probability?
I tried merging 4 files and individually also. But in all cases the
probability comes to 0.
where is the problem>
d but the server
> timed out, click here"
>
> I hope this helps you process your data given your current computational
> resources in less than 1 day.
>
> Cheers!
> -David
>
> On Mon, Dec 4, 2023 at 11:05 AM sudarshan kumar
> wrote:
>
>> one more
sample LFQ (st. peters results)?
On Mon, Dec 4, 2023 at 10:58 AM sudarshan kumar
wrote:
> Hi David,
> I am using this tutorial for Expressan dASAPratio . can yuo please
> comment on if I am using the right one.?
> Regards,
> Sud
>
> On Thu, Nov 30, 2023 at 10:53 AM sudarshan kum
Hi David,
I am using this tutorial for Expressan dASAPratio . can yuo please
comment on if I am using the right one.?
Regards,
Sud
On Thu, Nov 30, 2023 at 10:53 AM sudarshan kumar
wrote:
> can i select all the three options?
> Will it impact Express analysis?
> Centroid all scans (MS
Hi Jimmy,
Can you please explain my query.
Regards,
Sud
On Wed, Nov 22, 2023 at 3:13 PM sudarshan kumar
wrote:
> 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
this particular case in the next few days.
>
> Cheers!
> -David
>
> On Nov 29, 2023, at 10:17 AM, sudarshan kumar
> wrote:
>
> Hi David,
> could you get time to see into my analysis? I need your advice.
> Best regards,
> Sud
>
> On Wed, Nov 22, 2023
reduce the time requirement to process this dataset.
> I should have more to say about this particular case in the next few days.
>
> Cheers!
> -David
>
> On Nov 29, 2023, at 10:17 AM, sudarshan kumar
> wrote:
>
> Hi David,
> could you get time to see into my analysis?
n 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:
>
&
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://orci
gt; 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,
&g
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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Do we have any dedicated discussion group for SILAC using aspartio and
express?
On Tuesday, November 14, 2023 at 12:46:34 PM UTC-8 Jimmy Eng wrote:
> I might need some clarification on what you're asking as XPRESS (and
> possibly the other quant tools) does extract the precursor peak intensity
*
*It says Lysine cannot be both in variable modification and static
modification.*
*Please suggest. though I am running the files without static modification.*
On Wednesday, November 15, 2023 at 12:03:12 PM UTC-8 sudarshan kumar wrote:
> Can anyone please extend help to me in SILAC run a
Can anyone please extend help to me in SILAC run analysis using ASAPratio
and express
I am facing problem at
1. Xtandem search with two files. It is taking too much time and doestnt
move ahead after a few hours.
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Hi,
Can anyone please share with me the simple step by step workflow of SILAC
data analysis.
I have a run of bacterial proteome with mixture of light and heavy labelled
lysine peptides. K8 Da.
Best
Sud
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Hi
can anyone please share or refer to me the aquisition settings and search
settings/script for running silac labelled samples in Thermo Lumos.
I shall highly appreciate your quick reply.
Best,
Sud
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"spctools-disc
ntified in each sample goes down drastically in few
>> of the samples although all the files had similar number of displayed
>> spectra upto iprophet.
>> CAn you please explain th reason?
>> thanks
>> sud
>>
>>
>>
>> On Thu, Aug 17, 2023, 10:15 sudarsha
ss 6 samples. But the total
number of proteins identified in each sample goes down drastically in few
of the samples although all the files had similar number of displayed
spectra upto iprophet.
CAn you please explain th reason?
thanks
sud
On Thu, Aug 17, 2023, 10:15 sudarshan kumar
wrote:
> O
#x27;t identify), but it still puts all values in an easy
> to conceptualize, and positive, scale.
>
> These standardized numbers are comparable across samples (to obtain
> ratios) so long as the samples were acquired with the same instrument
> method and chromatography conditions.
>
and
in StPeter what does negative SIn scor emean? I see all of them being
negative
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Anyone can please explain-
1. Does Stpeter SIn value represent a ratio between control and treated
files?
2. I understand that all the files /MS runs are integrated to make one
.prot file after the protein prophet analysis.
3. So in StPeter how do we know the SIn score for a particular protein is
Dear friends,
I am trying to kill a job which was taking too much time. I even
uninstalled the program and reinstalled TPP. But it is still showing the
command is still running and in the "job list" there are jobs running which
is not finishing by kill job command. Can anyone please help me what
-ae09-589b37ecd6fcn%40googlegroups.com
> <https://groups.google.com/d/msgid/spctools-discuss/af6d08ea-6eb3-475a-ae09-589b37ecd6fcn%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
>
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d08ea-6eb3-475a-ae09-589b37ecd6fcn%40googlegroups.com
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Can anyone please hare with me The *"comet search parameters for TMT 6plex
labeled tryptic peptides*???
It will be a great help.
Regards,
Sud
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I have analyzed a data file using peptide prophet. I got results.
But when I am analyzing by iprophet i see a blank page . can anyone tell me
what does it mean.
Where is the problem?
Regards,
Sudarshan
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Dear members,
I want to use peptide sequences from the result after the peptide prophet
search. But the sequences also contains modification mass in it.
P.GSM[147.04]GLPGPKGSSGDPGKPGEAGNA.G
How can we remove it. so that the column of sequences can be converted into
fasta files.
Reg,
--
Yo
I feel like there is a problem in your conversion.
Better, validate the search parameters (which you are using at present)
with some *known (may be in you lab old data file) *correct file (raw or
mzml). See, to confirm if the search parameters you are using are working.
If the problem still persist
t;
> This tends to be a very computationally expensive search, so limiting your
> sequence database to a modest size would be beneficial.
>
>
>
> Eric
>
>
>
>
>
>
>
> *From:* spctools-discuss@googlegroups.com <
> spctools-discuss@googlegroups.com> *On
Dear members,
I am new to this group. Can anyone help me get a standard refined search
parameters either in comet or tandem or in any other search engine to
identify endogenous peptides.
1. These peptides have not been cleaved by any enzyme
2. Modification are typically not as those which happe
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