Re: [spctools-discuss] running ASAPratio for SILAC data

['David Shteynberg' via spctools-discuss]

Of course, I am glad to help.  The old and the new versions should run
faster on the centroided data.  There is no way to tell *a priori* with
ASAPRatio how long it will take, but since it ran to completion on my
machine and it generates one dot per ten PSMs it has processed; based on
the dots you can see how much of the ASAPRatio processing has completed.
Here are the dots from my run on your data:

[image: image.png]

On Mon, Dec 4, 2023 at 2:57 PM sudarshan kumar 
wrote:

> Thank you so much David for doing this for me. In fact I was running
> asapratio again on the centroid mzml file. But I see that though express
> completed easily but the asapratio is still running. Is there any way in
> tpp to see how much time will it take to complete.
>
> But I will try with the version you have shared the link with me. Should I
> use centroid mzml for this ?.
>
> Regards, Sudarshan
>
> On Mon, Dec 4, 2023, 2:29 PM 'David Shteynberg' via spctools-discuss <
> spctools-discuss@googlegroups.com> wrote:
>
>> Hello Sudarshan, again!
>>
>> I was able to update the ASAPRatioPeptideParser.exe tool for your testing
>> purposes to see if it runs a bit faster after some optimization I was able
>> to implement.  Please download the following version:
>> https://drive.google.com/file/d/1Pe1pBFZ9BOxrrYNY6O8rkrybKaGtDhZZ/view?usp=sharing
>>
>> And replace the copy you have in C:/TPP/bin/
>>
>> When I ran it on my not very powerful desktop computer it completed on
>> your data in about 42,000 seconds using the new code (less than 12 hours)
>>
>> [image: image.png]
>>
>>
>> Notice that the interface still says that "This command is still
>> running..." even though the log says "job completed"
>>
>> This is because for very long jobs the webserver times-out before the job
>> completes.  To solve this the user must click the link just above that is
>> next to the text: "If you commands have actually completed 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 query-
>>> I used same samples - for label free and SILAC express?
>>> Ideally I should get a similar conclusion from both the experiments.
>>> But the differentially expressed proteins are different in the two
>>> analyses.
>>>
>>> NOte: I have used only one run file of control and one run file of
>>> treatment for LFQ
>>> While for SILAC I have used 6 run files of same samples (technical
>>> replicates).
>>>
>>> Please let me know where I am wrong? In my point of view increasing the
>>> number of run files will improve PSM and hence quantification using
>>> express. What should i believe my SILAC express results or the same
>>> sample LFQ (st. peters results)?
>>>
>>>
>>> On Mon, Dec 4, 2023 at 10:58 AM sudarshan kumar <
>>> kumarsuders...@gmail.com> 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 kumar <
 kumarsuders...@gmail.com> wrote:

> can i select all the three options?
> Will it impact Express analysis?
> Centroid all scans (MS1 and MS2) -- meaningful only if data was
> acquired in profile mode
> Compress peak lists for smaller output file
> Write the output as a gzipped file (other TPP tools can read gzipped
> files directly)
>
> On Wed, Nov 29, 2023 at 1:37 PM David Shteynberg <
> dshteynb...@systemsbiology.org> wrote:
>
>> Dear Sud,
>>
>> I was able to process your dataset!  Although, I am still working on
>> getting a faster version of ASAPRatio compiled for your testing purposes.
>> Meanwhile you can help the process by filtering your files so that zero
>> intensity peaks in the MS1 data are removed and the MS1 data is
>> centroided.  You can accomplish both of these things using the msconvert
>> tool.  This will help 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 <
>> kumarsuders...@gmail.com> wrote:
>>
>> Hi David,
>> could you get time to see into my analysis? I need your advice.
>> Best regards,
>> Sud
>>
>> On Wed, Nov 22, 2023 at 3:51 PM 'David Shteynberg' via
>> spctools-discuss  wrote:
>>
>>> Hello Sudarshan,
>>>
>>> Please zip this directory on your system:
>>> c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param
>>>
>>> Then upload the zip file to your favorite cloud server and share the
>>> link with me.
>>>
>>> Thanks!
>>> -David
>>>
>>> On Wed, Nov 22, 2023 at 3:17 PM sudarshan kumar <
>>> 

Re: [spctools-discuss] running ASAPratio for SILAC data

[sudarshan kumar]

Thank you so much David for doing this for me. In fact I was running
asapratio again on the centroid mzml file. But I see that though express
completed easily but the asapratio is still running. Is there any way in
tpp to see how much time will it take to complete.

But I will try with the version you have shared the link with me. Should I
use centroid mzml for this ?.

Regards, Sudarshan

On Mon, Dec 4, 2023, 2:29 PM 'David Shteynberg' via spctools-discuss <
spctools-discuss@googlegroups.com> wrote:

> Hello Sudarshan, again!
>
> I was able to update the ASAPRatioPeptideParser.exe tool for your testing
> purposes to see if it runs a bit faster after some optimization I was able
> to implement.  Please download the following version:
> https://drive.google.com/file/d/1Pe1pBFZ9BOxrrYNY6O8rkrybKaGtDhZZ/view?usp=sharing
>
> And replace the copy you have in C:/TPP/bin/
>
> When I ran it on my not very powerful desktop computer it completed on
> your data in about 42,000 seconds using the new code (less than 12 hours)
>
> [image: image.png]
>
>
> Notice that the interface still says that "This command is still
> running..." even though the log says "job completed"
>
> This is because for very long jobs the webserver times-out before the job
> completes.  To solve this the user must click the link just above that is
> next to the text: "If you commands have actually completed 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 query-
>> I used same samples - for label free and SILAC express?
>> Ideally I should get a similar conclusion from both the experiments.
>> But the differentially expressed proteins are different in the two
>> analyses.
>>
>> NOte: I have used only one run file of control and one run file of
>> treatment for LFQ
>> While for SILAC I have used 6 run files of same samples (technical
>> replicates).
>>
>> Please let me know where I am wrong? In my point of view increasing the
>> number of run files will improve PSM and hence quantification using
>> express. What should i believe my SILAC express results or the same
>> 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 kumar <
>>> kumarsuders...@gmail.com> wrote:
>>>
 can i select all the three options?
 Will it impact Express analysis?
 Centroid all scans (MS1 and MS2) -- meaningful only if data was
 acquired in profile mode
 Compress peak lists for smaller output file
 Write the output as a gzipped file (other TPP tools can read gzipped
 files directly)

 On Wed, Nov 29, 2023 at 1:37 PM David Shteynberg <
 dshteynb...@systemsbiology.org> wrote:

> Dear Sud,
>
> I was able to process your dataset!  Although, I am still working on
> getting a faster version of ASAPRatio compiled for your testing purposes.
> Meanwhile you can help the process by filtering your files so that zero
> intensity peaks in the MS1 data are removed and the MS1 data is
> centroided.  You can accomplish both of these things using the msconvert
> tool.  This will help 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 <
> kumarsuders...@gmail.com> wrote:
>
> Hi David,
> could you get time to see into my analysis? I need your advice.
> Best regards,
> Sud
>
> On Wed, Nov 22, 2023 at 3:51 PM 'David Shteynberg' via
> spctools-discuss  wrote:
>
>> Hello Sudarshan,
>>
>> Please zip this directory on your system:
>> c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param
>>
>> Then upload the zip file to your favorite cloud server and share the
>> link with me.
>>
>> Thanks!
>> -David
>>
>> On Wed, Nov 22, 2023 at 3:17 PM sudarshan kumar <
>> kumarsuders...@gmail.com> wrote:
>>
>>> *EXECUTING: cd c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param && c:
>>> && C:/TPP/bin/xinteract -Ninteract_silaccomtwofiles.pep.xml -p0.0 -l6
>>> -THREADS=1 -PPM -OA -ipP -X-m0.1-c5-p1-L-nR,10.008269-nK,8.014199
>>> -A-lRK-F-C-Z-r0.05 110623_Silac_TEST_01.pep.xml
>>> 110623_Sud_LH_TEST_02.pep.xml*
>>>
>>> On Wed, Nov 22, 2023 at 3:07 PM sudarshan kumar <
>>> kumarsuders...@gmail.com> wrote:
>>>
 Thank you so much David,
 But can you tell me how can i compress? Do you mean this link?
 (6) ISB/SPC Trans Proteomic Pipeline :: jobs
 

Re: [spctools-discuss] running ASAPratio for SILAC data

['David Shteynberg' via spctools-discuss]

Hello Sudarshan, again!

I was able to update the ASAPRatioPeptideParser.exe tool for your testing
purposes to see if it runs a bit faster after some optimization I was able
to implement.  Please download the following version:
https://drive.google.com/file/d/1Pe1pBFZ9BOxrrYNY6O8rkrybKaGtDhZZ/view?usp=sharing

And replace the copy you have in C:/TPP/bin/

When I ran it on my not very powerful desktop computer it completed on your
data in about 42,000 seconds using the new code (less than 12 hours)

[image: image.png]


Notice that the interface still says that "This command is still
running..." even though the log says "job completed"

This is because for very long jobs the webserver times-out before the job
completes.  To solve this the user must click the link just above that is
next to the text: "If you commands have actually completed 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 query-
> I used same samples - for label free and SILAC express?
> Ideally I should get a similar conclusion from both the experiments.
> But the differentially expressed proteins are different in the two
> analyses.
>
> NOte: I have used only one run file of control and one run file of
> treatment for LFQ
> While for SILAC I have used 6 run files of same samples (technical
> replicates).
>
> Please let me know where I am wrong? In my point of view increasing the
> number of run files will improve PSM and hence quantification using
> express. What should i believe my SILAC express results or the same
> 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 kumar <
>> kumarsuders...@gmail.com> wrote:
>>
>>> can i select all the three options?
>>> Will it impact Express analysis?
>>> Centroid all scans (MS1 and MS2) -- meaningful only if data was acquired
>>> in profile mode
>>> Compress peak lists for smaller output file
>>> Write the output as a gzipped file (other TPP tools can read gzipped
>>> files directly)
>>>
>>> On Wed, Nov 29, 2023 at 1:37 PM David Shteynberg <
>>> dshteynb...@systemsbiology.org> wrote:
>>>
 Dear Sud,

 I was able to process your dataset!  Although, I am still working on
 getting a faster version of ASAPRatio compiled for your testing purposes.
 Meanwhile you can help the process by filtering your files so that zero
 intensity peaks in the MS1 data are removed and the MS1 data is
 centroided.  You can accomplish both of these things using the msconvert
 tool.  This will help 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? I need your advice.
 Best regards,
 Sud

 On Wed, Nov 22, 2023 at 3:51 PM 'David Shteynberg' via spctools-discuss
  wrote:

> Hello Sudarshan,
>
> Please zip this directory on your system:
> c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param
>
> Then upload the zip file to your favorite cloud server and share the
> link with me.
>
> Thanks!
> -David
>
> On Wed, Nov 22, 2023 at 3:17 PM sudarshan kumar <
> kumarsuders...@gmail.com> wrote:
>
>> *EXECUTING: cd c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param && c:
>> && C:/TPP/bin/xinteract -Ninteract_silaccomtwofiles.pep.xml -p0.0 -l6
>> -THREADS=1 -PPM -OA -ipP -X-m0.1-c5-p1-L-nR,10.008269-nK,8.014199
>> -A-lRK-F-C-Z-r0.05 110623_Silac_TEST_01.pep.xml
>> 110623_Sud_LH_TEST_02.pep.xml*
>>
>> On Wed, Nov 22, 2023 at 3:07 PM sudarshan kumar <
>> kumarsuders...@gmail.com> wrote:
>>
>>> Thank you so much David,
>>> But can you tell me how can i compress? Do you mean this link?
>>> (6) ISB/SPC Trans Proteomic Pipeline :: jobs
>>> 
>>>
>>> On Wed, Nov 22, 2023 at 2:31 PM 'David Shteynberg' via
>>> spctools-discuss  wrote:
>>>
 Dear Sudarshan,

 It is hard to say why this particular execution resulted in
 apparent failure, but if you are willing to compress the *whole
 directory *of this analysis and send me a download link, I would
 be happy to download this dataset and check why it failed.

 Cheers!
 -David

 On Wed, Nov 22, 2023 at 12:04 PM sudarshan kumar <
 kumarsuders...@gmail.com> wrote:

> Can 

Re: [spctools-discuss] running ASAPratio for SILAC data

['David Shteynberg' via spctools-discuss]

Hopefully, I am understanding your queries correctly, here goes.
Centroiding the data will reduce the number of peaks in the spectra and
reduce the running time of the analysis.  Compressing the files to make
them smaller will require that the tools reading the files uncompress the
data (usually internally) prior to using it which will increase the running
time.  As far as affecting the results, compressing the files should not
change the data while centroiding will. As far as how much this will affect
the final ratios probably depends on the quality of centroiding algorithm
and the quality of the data.  Run some tests yourself and get a feel on
some data you know well;  testing should help you refine your approach.
Hope that helps!

-David

On Mon, Dec 4, 2023, 10:59 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 kumar 
> wrote:
>
>> can i select all the three options?
>> Will it impact Express analysis?
>> Centroid all scans (MS1 and MS2) -- meaningful only if data was acquired
>> in profile mode
>> Compress peak lists for smaller output file
>> Write the output as a gzipped file (other TPP tools can read gzipped
>> files directly)
>>
>> On Wed, Nov 29, 2023 at 1:37 PM David Shteynberg <
>> dshteynb...@systemsbiology.org> wrote:
>>
>>> Dear Sud,
>>>
>>> I was able to process your dataset!  Although, I am still working on
>>> getting a faster version of ASAPRatio compiled for your testing purposes.
>>> Meanwhile you can help the process by filtering your files so that zero
>>> intensity peaks in the MS1 data are removed and the MS1 data is
>>> centroided.  You can accomplish both of these things using the msconvert
>>> tool.  This will help 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? I need your advice.
>>> Best regards,
>>> Sud
>>>
>>> On Wed, Nov 22, 2023 at 3:51 PM 'David Shteynberg' via spctools-discuss <
>>> spctools-discuss@googlegroups.com> wrote:
>>>
 Hello Sudarshan,

 Please zip this directory on your system:
 c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param

 Then upload the zip file to your favorite cloud server and share the
 link with me.

 Thanks!
 -David

 On Wed, Nov 22, 2023 at 3:17 PM sudarshan kumar <
 kumarsuders...@gmail.com> wrote:

> *EXECUTING: cd c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param && c:
> && C:/TPP/bin/xinteract -Ninteract_silaccomtwofiles.pep.xml -p0.0 -l6
> -THREADS=1 -PPM -OA -ipP -X-m0.1-c5-p1-L-nR,10.008269-nK,8.014199
> -A-lRK-F-C-Z-r0.05 110623_Silac_TEST_01.pep.xml
> 110623_Sud_LH_TEST_02.pep.xml*
>
> On Wed, Nov 22, 2023 at 3:07 PM sudarshan kumar <
> kumarsuders...@gmail.com> wrote:
>
>> Thank you so much David,
>> But can you tell me how can i compress? Do you mean this link?
>> (6) ISB/SPC Trans Proteomic Pipeline :: jobs
>> 
>>
>> On Wed, Nov 22, 2023 at 2:31 PM 'David Shteynberg' via
>> spctools-discuss  wrote:
>>
>>> Dear Sudarshan,
>>>
>>> It is hard to say why this particular execution resulted in apparent
>>> failure, but if you are willing to compress the *whole directory *of
>>> this analysis and send me a download link, I would be happy to download
>>> this dataset and check why it failed.
>>>
>>> Cheers!
>>> -David
>>>
>>> On Wed, Nov 22, 2023 at 12:04 PM sudarshan kumar <
>>> kumarsuders...@gmail.com> wrote:
>>>
 Can anyone please help me know, why when I am running express and
 ASAPratio it always takes more than two days time and though express is
 completed but after running for around 80% in asapratio it stucks and 
 shows
 only the running status but nothing moves ahead.  >>> 2023-11-22 120242.png>



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 Groups "spctools-discuss" group.
 To unsubscribe from this group and stop receiving emails from it,
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 https://groups.google.com/d/msgid/spctools-discuss/a1b10bac-e49a-429f-a255-500332721e7fn%40googlegroups.com
 
 .

>>>
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>>> You received this message because you are subscribed to the Google

Re: [spctools-discuss] running ASAPratio for SILAC data

[sudarshan kumar]

one more query-
I used same samples - for label free and SILAC express?
Ideally I should get a similar conclusion from both the experiments.
But the differentially expressed proteins are different in the two analyses.

NOte: I have used only one run file of control and one run file of
treatment for LFQ
While for SILAC I have used 6 run files of same samples (technical
replicates).

Please let me know where I am wrong? In my point of view increasing the
number of run files will improve PSM and hence quantification using
express. What should i believe my SILAC express results or the same
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 kumar 
> wrote:
>
>> can i select all the three options?
>> Will it impact Express analysis?
>> Centroid all scans (MS1 and MS2) -- meaningful only if data was acquired
>> in profile mode
>> Compress peak lists for smaller output file
>> Write the output as a gzipped file (other TPP tools can read gzipped
>> files directly)
>>
>> On Wed, Nov 29, 2023 at 1:37 PM David Shteynberg <
>> dshteynb...@systemsbiology.org> wrote:
>>
>>> Dear Sud,
>>>
>>> I was able to process your dataset!  Although, I am still working on
>>> getting a faster version of ASAPRatio compiled for your testing purposes.
>>> Meanwhile you can help the process by filtering your files so that zero
>>> intensity peaks in the MS1 data are removed and the MS1 data is
>>> centroided.  You can accomplish both of these things using the msconvert
>>> tool.  This will help 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? I need your advice.
>>> Best regards,
>>> Sud
>>>
>>> On Wed, Nov 22, 2023 at 3:51 PM 'David Shteynberg' via spctools-discuss <
>>> spctools-discuss@googlegroups.com> wrote:
>>>
 Hello Sudarshan,

 Please zip this directory on your system:
 c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param

 Then upload the zip file to your favorite cloud server and share the
 link with me.

 Thanks!
 -David

 On Wed, Nov 22, 2023 at 3:17 PM sudarshan kumar <
 kumarsuders...@gmail.com> wrote:

> *EXECUTING: cd c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param && c:
> && C:/TPP/bin/xinteract -Ninteract_silaccomtwofiles.pep.xml -p0.0 -l6
> -THREADS=1 -PPM -OA -ipP -X-m0.1-c5-p1-L-nR,10.008269-nK,8.014199
> -A-lRK-F-C-Z-r0.05 110623_Silac_TEST_01.pep.xml
> 110623_Sud_LH_TEST_02.pep.xml*
>
> On Wed, Nov 22, 2023 at 3:07 PM sudarshan kumar <
> kumarsuders...@gmail.com> wrote:
>
>> Thank you so much David,
>> But can you tell me how can i compress? Do you mean this link?
>> (6) ISB/SPC Trans Proteomic Pipeline :: jobs
>> 
>>
>> On Wed, Nov 22, 2023 at 2:31 PM 'David Shteynberg' via
>> spctools-discuss  wrote:
>>
>>> Dear Sudarshan,
>>>
>>> It is hard to say why this particular execution resulted in apparent
>>> failure, but if you are willing to compress the *whole directory *of
>>> this analysis and send me a download link, I would be happy to download
>>> this dataset and check why it failed.
>>>
>>> Cheers!
>>> -David
>>>
>>> On Wed, Nov 22, 2023 at 12:04 PM sudarshan kumar <
>>> kumarsuders...@gmail.com> wrote:
>>>
 Can anyone please help me know, why when I am running express and
 ASAPratio it always takes more than two days time and though express is
 completed but after running for around 80% in asapratio it stucks and 
 shows
 only the running status but nothing moves ahead.  >>> 2023-11-22 120242.png>



 --
 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,
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 To view this discussion on the web visit
 https://groups.google.com/d/msgid/spctools-discuss/a1b10bac-e49a-429f-a255-500332721e7fn%40googlegroups.com
 
 .

>>>
>>> --
>>> 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,

Re: [spctools-discuss] running ASAPratio for SILAC data

[sudarshan kumar]

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 (MS1 and MS2) -- meaningful only if data was acquired
> in profile mode
> Compress peak lists for smaller output file
> Write the output as a gzipped file (other TPP tools can read gzipped files
> directly)
>
> On Wed, Nov 29, 2023 at 1:37 PM David Shteynberg <
> dshteynb...@systemsbiology.org> wrote:
>
>> Dear Sud,
>>
>> I was able to process your dataset!  Although, I am still working on
>> getting a faster version of ASAPRatio compiled for your testing purposes.
>> Meanwhile you can help the process by filtering your files so that zero
>> intensity peaks in the MS1 data are removed and the MS1 data is
>> centroided.  You can accomplish both of these things using the msconvert
>> tool.  This will help 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? I need your advice.
>> Best regards,
>> Sud
>>
>> On Wed, Nov 22, 2023 at 3:51 PM 'David Shteynberg' via spctools-discuss <
>> spctools-discuss@googlegroups.com> wrote:
>>
>>> Hello Sudarshan,
>>>
>>> Please zip this directory on your system:
>>> c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param
>>>
>>> Then upload the zip file to your favorite cloud server and share the
>>> link with me.
>>>
>>> Thanks!
>>> -David
>>>
>>> On Wed, Nov 22, 2023 at 3:17 PM sudarshan kumar <
>>> kumarsuders...@gmail.com> wrote:
>>>
 *EXECUTING: cd c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param && c: &&
 C:/TPP/bin/xinteract -Ninteract_silaccomtwofiles.pep.xml -p0.0 -l6
 -THREADS=1 -PPM -OA -ipP -X-m0.1-c5-p1-L-nR,10.008269-nK,8.014199
 -A-lRK-F-C-Z-r0.05 110623_Silac_TEST_01.pep.xml
 110623_Sud_LH_TEST_02.pep.xml*

 On Wed, Nov 22, 2023 at 3:07 PM sudarshan kumar <
 kumarsuders...@gmail.com> wrote:

> Thank you so much David,
> But can you tell me how can i compress? Do you mean this link?
> (6) ISB/SPC Trans Proteomic Pipeline :: jobs
> 
>
> On Wed, Nov 22, 2023 at 2:31 PM 'David Shteynberg' via
> spctools-discuss  wrote:
>
>> Dear Sudarshan,
>>
>> It is hard to say why this particular execution resulted in apparent
>> failure, but if you are willing to compress the *whole directory *of
>> this analysis and send me a download link, I would be happy to download
>> this dataset and check why it failed.
>>
>> Cheers!
>> -David
>>
>> On Wed, Nov 22, 2023 at 12:04 PM sudarshan kumar <
>> kumarsuders...@gmail.com> wrote:
>>
>>> Can anyone please help me know, why when I am running express and
>>> ASAPratio it always takes more than two days time and though express is
>>> completed but after running for around 80% in asapratio it stucks and 
>>> shows
>>> only the running status but nothing moves ahead.  >> 2023-11-22 120242.png>
>>>
>>>
>>>
>>> --
>>> 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/a1b10bac-e49a-429f-a255-500332721e7fn%40googlegroups.com
>>> 
>>> .
>>>
>>
>> --
>> 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/CAGJJY%3D8LhUKQ0CgKHSA55wddG9HwYASJNYKwXfvRYLCEXr0y2w%40mail.gmail.com
>> 
>> .
>>
>
>
> --
> ---
> 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

Re: [spctools-discuss] running ASAPratio for SILAC data

[sudarshan kumar]

can i select all the three options?
Will it impact Express analysis?
Centroid all scans (MS1 and MS2) -- meaningful only if data was acquired in
profile mode
Compress peak lists for smaller output file
Write the output as a gzipped file (other TPP tools can read gzipped files
directly)

On Wed, Nov 29, 2023 at 1:37 PM David Shteynberg <
dshteynb...@systemsbiology.org> wrote:

> Dear Sud,
>
> I was able to process your dataset!  Although, I am still working on
> getting a faster version of ASAPRatio compiled for your testing purposes.
> Meanwhile you can help the process by filtering your files so that zero
> intensity peaks in the MS1 data are removed and the MS1 data is
> centroided.  You can accomplish both of these things using the msconvert
> tool.  This will help 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? I need your advice.
> Best regards,
> Sud
>
> On Wed, Nov 22, 2023 at 3:51 PM 'David Shteynberg' via spctools-discuss <
> spctools-discuss@googlegroups.com> wrote:
>
>> Hello Sudarshan,
>>
>> Please zip this directory on your system:
>> c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param
>>
>> Then upload the zip file to your favorite cloud server and share the link
>> with me.
>>
>> Thanks!
>> -David
>>
>> On Wed, Nov 22, 2023 at 3:17 PM sudarshan kumar 
>> wrote:
>>
>>> *EXECUTING: cd c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param && c: &&
>>> C:/TPP/bin/xinteract -Ninteract_silaccomtwofiles.pep.xml -p0.0 -l6
>>> -THREADS=1 -PPM -OA -ipP -X-m0.1-c5-p1-L-nR,10.008269-nK,8.014199
>>> -A-lRK-F-C-Z-r0.05 110623_Silac_TEST_01.pep.xml
>>> 110623_Sud_LH_TEST_02.pep.xml*
>>>
>>> On Wed, Nov 22, 2023 at 3:07 PM sudarshan kumar <
>>> kumarsuders...@gmail.com> wrote:
>>>
 Thank you so much David,
 But can you tell me how can i compress? Do you mean this link?
 (6) ISB/SPC Trans Proteomic Pipeline :: jobs
 

 On Wed, Nov 22, 2023 at 2:31 PM 'David Shteynberg' via spctools-discuss
  wrote:

> Dear Sudarshan,
>
> It is hard to say why this particular execution resulted in apparent
> failure, but if you are willing to compress the *whole directory *of
> this analysis and send me a download link, I would be happy to download
> this dataset and check why it failed.
>
> Cheers!
> -David
>
> On Wed, Nov 22, 2023 at 12:04 PM sudarshan kumar <
> kumarsuders...@gmail.com> wrote:
>
>> Can anyone please help me know, why when I am running express and
>> ASAPratio it always takes more than two days time and though express is
>> completed but after running for around 80% in asapratio it stucks and 
>> shows
>> only the running status but nothing moves ahead.  > 2023-11-22 120242.png>
>>
>>
>>
>> --
>> 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/a1b10bac-e49a-429f-a255-500332721e7fn%40googlegroups.com
>> 
>> .
>>
>
> --
> 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/CAGJJY%3D8LhUKQ0CgKHSA55wddG9HwYASJNYKwXfvRYLCEXr0y2w%40mail.gmail.com
> 
> .
>


 --
 ---
 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


>>>
>>> --
>>> ---
>>> The real voyage of discovery 

Re: [spctools-discuss] running ASAPratio for SILAC data

[sudarshan kumar]

Thank you so much . I will try the way have suggested.
Best regards
Sud

On Wed, Nov 29, 2023, 1:37 PM David Shteynberg <
dshteynb...@systemsbiology.org> wrote:

> Dear Sud,
>
> I was able to process your dataset!  Although, I am still working on
> getting a faster version of ASAPRatio compiled for your testing purposes.
> Meanwhile you can help the process by filtering your files so that zero
> intensity peaks in the MS1 data are removed and the MS1 data is
> centroided.  You can accomplish both of these things using the msconvert
> tool.  This will help 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? I need your advice.
> Best regards,
> Sud
>
> On Wed, Nov 22, 2023 at 3:51 PM 'David Shteynberg' via spctools-discuss <
> spctools-discuss@googlegroups.com> wrote:
>
>> Hello Sudarshan,
>>
>> Please zip this directory on your system:
>> c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param
>>
>> Then upload the zip file to your favorite cloud server and share the link
>> with me.
>>
>> Thanks!
>> -David
>>
>> On Wed, Nov 22, 2023 at 3:17 PM sudarshan kumar 
>> wrote:
>>
>>> *EXECUTING: cd c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param && c: &&
>>> C:/TPP/bin/xinteract -Ninteract_silaccomtwofiles.pep.xml -p0.0 -l6
>>> -THREADS=1 -PPM -OA -ipP -X-m0.1-c5-p1-L-nR,10.008269-nK,8.014199
>>> -A-lRK-F-C-Z-r0.05 110623_Silac_TEST_01.pep.xml
>>> 110623_Sud_LH_TEST_02.pep.xml*
>>>
>>> On Wed, Nov 22, 2023 at 3:07 PM sudarshan kumar <
>>> kumarsuders...@gmail.com> wrote:
>>>
 Thank you so much David,
 But can you tell me how can i compress? Do you mean this link?
 (6) ISB/SPC Trans Proteomic Pipeline :: jobs
 

 On Wed, Nov 22, 2023 at 2:31 PM 'David Shteynberg' via spctools-discuss
  wrote:

> Dear Sudarshan,
>
> It is hard to say why this particular execution resulted in apparent
> failure, but if you are willing to compress the *whole directory *of
> this analysis and send me a download link, I would be happy to download
> this dataset and check why it failed.
>
> Cheers!
> -David
>
> On Wed, Nov 22, 2023 at 12:04 PM sudarshan kumar <
> kumarsuders...@gmail.com> wrote:
>
>> Can anyone please help me know, why when I am running express and
>> ASAPratio it always takes more than two days time and though express is
>> completed but after running for around 80% in asapratio it stucks and 
>> shows
>> only the running status but nothing moves ahead.  > 2023-11-22 120242.png>
>>
>>
>>
>> --
>> 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/a1b10bac-e49a-429f-a255-500332721e7fn%40googlegroups.com
>> 
>> .
>>
>
> --
> 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/CAGJJY%3D8LhUKQ0CgKHSA55wddG9HwYASJNYKwXfvRYLCEXr0y2w%40mail.gmail.com
> 
> .
>


 --
 ---
 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


>>>
>>> --
>>> ---
>>> 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 

Re: [spctools-discuss] running ASAPratio for SILAC data

[David Shteynberg]

Dear Sud,

I was able to process your dataset!  Although, I am still working on getting a 
faster version of ASAPRatio compiled for your testing purposes.  Meanwhile you 
can help the process by filtering your files so that zero intensity peaks in 
the MS1 data are removed and the MS1 data is centroided.  You can accomplish 
both of these things using the msconvert tool.  This will help 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? I need your advice.
> Best regards,
> Sud
> 
> On Wed, Nov 22, 2023 at 3:51 PM 'David Shteynberg' via spctools-discuss 
>  > wrote:
>> Hello Sudarshan,
>> 
>> Please zip this directory on your system: 
>> c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param
>> 
>> Then upload the zip file to your favorite cloud server and share the link 
>> with me.
>> 
>> Thanks!
>> -David
>> 
>> On Wed, Nov 22, 2023 at 3:17 PM sudarshan kumar > > wrote:
>>> EXECUTING: cd c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param && c: && 
>>> C:/TPP/bin/xinteract -Ninteract_silaccomtwofiles.pep.xml -p0.0 -l6 
>>> -THREADS=1 -PPM -OA -ipP -X-m0.1-c5-p1-L-nR,10.008269-nK,8.014199 
>>> -A-lRK-F-C-Z-r0.05 110623_Silac_TEST_01.pep.xml 
>>> 110623_Sud_LH_TEST_02.pep.xml
>>> 
>>> On Wed, Nov 22, 2023 at 3:07 PM sudarshan kumar >> > wrote:
 Thank you so much David,
 But can you tell me how can i compress? Do you mean this link?
 (6) ISB/SPC Trans Proteomic Pipeline :: jobs 
 
 
 On Wed, Nov 22, 2023 at 2:31 PM 'David Shteynberg' via spctools-discuss 
 >>> > wrote:
> Dear Sudarshan,
> 
> It is hard to say why this particular execution resulted in apparent 
> failure, but if you are willing to compress the whole directory of this 
> analysis and send me a download link, I would be happy to download this 
> dataset and check why it failed.
> 
> Cheers!
> -David
> 
> On Wed, Nov 22, 2023 at 12:04 PM sudarshan kumar 
> mailto:kumarsuders...@gmail.com>> wrote:
>> Can anyone please help me know, why when I am running express and 
>> ASAPratio it always takes more than two days time and though express is 
>> completed but after running for around 80% in asapratio it stucks and 
>> shows only the running status but nothing moves ahead.  > 2023-11-22 120242.png>
>> 
>> 
>> 
>> -- 
>> 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/a1b10bac-e49a-429f-a255-500332721e7fn%40googlegroups.com
>>  
>> .
> 
> 
> -- 
> 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/CAGJJY%3D8LhUKQ0CgKHSA55wddG9HwYASJNYKwXfvRYLCEXr0y2w%40mail.gmail.com
>  
> .
 
 
 --
 ---
 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
 
>>> 
>>> 
>>> --
>>> ---
>>> The real voyage of discovery consists not in seeking new lands but seeing 
>>> with new eyes. — Marcel Proust
>>> 
>>> Dr. Sudarshan Kumar
>>> (Fulbright-Nehru