Re: [spctools-discuss] XPRESS peak intensity value

[sudarshan kumar]

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 
> and area.  And if you just want the peak area for peptide IDs and your 
> sample isn't isotope labeled, run it in label-free mode where it will 
> simply pull out the peak area/intensity for each peptide/precursor. 
>
> On Tue, Nov 14, 2023 at 12:39 PM Iryna Abramchuk  
> wrote:
>
>> Thank you! Do you know if there is any way to extract the precursor peak 
>> intensity with XPRESS (or other TPP tools)? 
>>
>> On Tuesday, November 7, 2023 at 4:32:25 PM UTC-5 Jimmy Eng wrote:
>>
>>> "peak_intensity" is the maximum peak intensity of the ion chromatogram.
>>>
>>> On Tue, Nov 7, 2023 at 1:00 PM Iryna Abramchuk  
>>> wrote:
>>>
 Hello all!
 I am using XPRESS in label-free mode (TPPv6.1.0), and interested in the 
 "peak_intensity" output value. I was just looking to confirm whether 
 "peak_intensity" is the precursor peak intensity, or if it's the maximum 
 peak intensity of the ion chromatogram?
 Thank you

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Re: [spctools-discuss] XPRESS peak intensity value

[Iryna Abramchuk]

Yes, I do see both peak_intensity and peak_area as XPRESS outputs in the 
XML files, and can also view these columns in the PepXML viewer
On Tuesday, November 14, 2023 at 4:35:55 PM UTC-5 Jimmy Eng wrote:

> Hopefully you get what you need from David's response.  But just to 
> clarify, XPRESS writes out both peak_intensity and peak_area when it runs.  
> So if you do see the "peak_intensity" column in the pepXML Viewer, go to 
> the "Pick Columns" tab  and select "peak_area" as a column to display.  
> More than anything, I'm just curious if you are able to display the 
> precursor "peak_area" by selecting that column with your existing analysis.
>
> On Tue, Nov 14, 2023 at 1:17 PM Iryna Abramchuk  
> wrote:
>
>> I am using XPRESS in label-free mode and at the moment I am seeing 
>> peak_intensity (which I understand is the maximum peak intensity of the ion 
>> chromatogram) among other outputs. I am looking for the precursor intensity 
>> though, which I do not see.
>> I think David's answer is what I was looking for (adding the -PREC option 
>> to get the precursor_intensity). Thank you for your help! 
>>
>> On Tuesday, November 14, 2023 at 3:46:34 PM UTC-5 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 
>>> and area.  And if you just want the peak area for peptide IDs and your 
>>> sample isn't isotope labeled, run it in label-free mode where it will 
>>> simply pull out the peak area/intensity for each peptide/precursor. 
>>>
>>> On Tue, Nov 14, 2023 at 12:39 PM Iryna Abramchuk  
>>> wrote:
>>>
 Thank you! Do you know if there is any way to extract the precursor 
 peak intensity with XPRESS (or other TPP tools)? 

 On Tuesday, November 7, 2023 at 4:32:25 PM UTC-5 Jimmy Eng wrote:

> "peak_intensity" is the maximum peak intensity of the ion chromatogram.
>
> On Tue, Nov 7, 2023 at 1:00 PM Iryna Abramchuk  
> wrote:
>
>> Hello all!
>> I am using XPRESS in label-free mode (TPPv6.1.0), and interested in 
>> the "peak_intensity" output value. I was just looking to confirm whether 
>> "peak_intensity" is the precursor peak intensity, or if it's the maximum 
>> peak intensity of the ion chromatogram?
>> Thank you
>>
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>>  
>> 
>> .
>>
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Re: [spctools-discuss] XPRESS peak intensity value

[Jimmy Eng]

Hopefully you get what you need from David's response.  But just to
clarify, XPRESS writes out both peak_intensity and peak_area when it runs.
So if you do see the "peak_intensity" column in the pepXML Viewer, go to
the "Pick Columns" tab  and select "peak_area" as a column to display.
More than anything, I'm just curious if you are able to display the
precursor "peak_area" by selecting that column with your existing analysis.

On Tue, Nov 14, 2023 at 1:17 PM Iryna Abramchuk 
wrote:

> I am using XPRESS in label-free mode and at the moment I am seeing
> peak_intensity (which I understand is the maximum peak intensity of the ion
> chromatogram) among other outputs. I am looking for the precursor intensity
> though, which I do not see.
> I think David's answer is what I was looking for (adding the -PREC option
> to get the precursor_intensity). Thank you for your help!
>
> On Tuesday, November 14, 2023 at 3:46:34 PM UTC-5 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
>> and area.  And if you just want the peak area for peptide IDs and your
>> sample isn't isotope labeled, run it in label-free mode where it will
>> simply pull out the peak area/intensity for each peptide/precursor.
>>
>> On Tue, Nov 14, 2023 at 12:39 PM Iryna Abramchuk 
>> wrote:
>>
>>> Thank you! Do you know if there is any way to extract the precursor peak
>>> intensity with XPRESS (or other TPP tools)?
>>>
>>> On Tuesday, November 7, 2023 at 4:32:25 PM UTC-5 Jimmy Eng wrote:
>>>
 "peak_intensity" is the maximum peak intensity of the ion chromatogram.

 On Tue, Nov 7, 2023 at 1:00 PM Iryna Abramchuk 
 wrote:

> Hello all!
> I am using XPRESS in label-free mode (TPPv6.1.0), and interested in
> the "peak_intensity" output value. I was just looking to confirm whether
> "peak_intensity" is the precursor peak intensity, or if it's the maximum
> peak intensity of the ion chromatogram?
> Thank you
>
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> 
> .
>
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Re: [spctools-discuss] XPRESS peak intensity value

[Iryna Abramchuk]

Awesome, thank you so much! 

On Tuesday, November 14, 2023 at 3:47:45 PM UTC-5 David Shteynberg wrote:

> Hello Iryna,
>
> The xinteract tool in the TPP, accessed in Petunia interface in [TPP 
> Tools] -> [Analyze peptides]) , the option -PREC can be specified in the 
> [PeptideProphet Options] -> [Enter additional options to pass directly to 
> the command-line (expert use only!)].  This option will record 
> precursor_intensity for each PSM in the pepXML file.  You can then add this 
> column in PepXMLViewer and it should be populated with parent intensities 
> from the mzML file.
>
> Cheers!
> -David
>
> On Tue, Nov 14, 2023 at 12:39 PM Iryna Abramchuk  
> wrote:
>
>> Thank you! Do you know if there is any way to extract the precursor peak 
>> intensity with XPRESS (or other TPP tools)? 
>>
>> On Tuesday, November 7, 2023 at 4:32:25 PM UTC-5 Jimmy Eng wrote:
>>
>>> "peak_intensity" is the maximum peak intensity of the ion chromatogram.
>>>
>>> On Tue, Nov 7, 2023 at 1:00 PM Iryna Abramchuk  
>>> wrote:
>>>
 Hello all!
 I am using XPRESS in label-free mode (TPPv6.1.0), and interested in the 
 "peak_intensity" output value. I was just looking to confirm whether 
 "peak_intensity" is the precursor peak intensity, or if it's the maximum 
 peak intensity of the ion chromatogram?
 Thank you

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 .

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>>  
>> 
>> .
>>
>

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Re: [spctools-discuss] XPRESS peak intensity value

[Iryna Abramchuk]

I am using XPRESS in label-free mode and at the moment I am seeing 
peak_intensity (which I understand is the maximum peak intensity of the ion 
chromatogram) among other outputs. I am looking for the precursor intensity 
though, which I do not see.
I think David's answer is what I was looking for (adding the -PREC option 
to get the precursor_intensity). Thank you for your help! 

On Tuesday, November 14, 2023 at 3:46:34 PM UTC-5 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 
> and area.  And if you just want the peak area for peptide IDs and your 
> sample isn't isotope labeled, run it in label-free mode where it will 
> simply pull out the peak area/intensity for each peptide/precursor. 
>
> On Tue, Nov 14, 2023 at 12:39 PM Iryna Abramchuk  
> wrote:
>
>> Thank you! Do you know if there is any way to extract the precursor peak 
>> intensity with XPRESS (or other TPP tools)? 
>>
>> On Tuesday, November 7, 2023 at 4:32:25 PM UTC-5 Jimmy Eng wrote:
>>
>>> "peak_intensity" is the maximum peak intensity of the ion chromatogram.
>>>
>>> On Tue, Nov 7, 2023 at 1:00 PM Iryna Abramchuk  
>>> wrote:
>>>
 Hello all!
 I am using XPRESS in label-free mode (TPPv6.1.0), and interested in the 
 "peak_intensity" output value. I was just looking to confirm whether 
 "peak_intensity" is the precursor peak intensity, or if it's the maximum 
 peak intensity of the ion chromatogram?
 Thank you

 -- 
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 .

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>> https://groups.google.com/d/msgid/spctools-discuss/9c3553a8-a00d-4e0b-97f1-065b7171f0c6n%40googlegroups.com
>>  
>> 
>> .
>>
>

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Re: [spctools-discuss] XPRESS peak intensity value

['David Shteynberg' via spctools-discuss]

Hello Iryna,

The xinteract tool in the TPP, accessed in Petunia interface in [TPP Tools]
-> [Analyze peptides]) , the option -PREC can be specified in the
[PeptideProphet Options] -> [Enter additional options to pass directly to
the command-line (expert use only!)].  This option will record
precursor_intensity for each PSM in the pepXML file.  You can then add this
column in PepXMLViewer and it should be populated with parent intensities
from the mzML file.

Cheers!
-David

On Tue, Nov 14, 2023 at 12:39 PM Iryna Abramchuk 
wrote:

> Thank you! Do you know if there is any way to extract the precursor peak
> intensity with XPRESS (or other TPP tools)?
>
> On Tuesday, November 7, 2023 at 4:32:25 PM UTC-5 Jimmy Eng wrote:
>
>> "peak_intensity" is the maximum peak intensity of the ion chromatogram.
>>
>> On Tue, Nov 7, 2023 at 1:00 PM Iryna Abramchuk 
>> wrote:
>>
>>> Hello all!
>>> I am using XPRESS in label-free mode (TPPv6.1.0), and interested in the
>>> "peak_intensity" output value. I was just looking to confirm whether
>>> "peak_intensity" is the precursor peak intensity, or if it's the maximum
>>> peak intensity of the ion chromatogram?
>>> Thank you
>>>
>>> --
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>>> Groups "spctools-discuss" group.
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>>> 
>>> .
>>>
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Re: [spctools-discuss] XPRESS peak intensity value

[Jimmy Eng]

I might need some clarification on what you're asking as XPRESS (and
possibly the other quant tools) does extract the precursor peak intensity
and area.  And if you just want the peak area for peptide IDs and your
sample isn't isotope labeled, run it in label-free mode where it will
simply pull out the peak area/intensity for each peptide/precursor.

On Tue, Nov 14, 2023 at 12:39 PM Iryna Abramchuk 
wrote:

> Thank you! Do you know if there is any way to extract the precursor peak
> intensity with XPRESS (or other TPP tools)?
>
> On Tuesday, November 7, 2023 at 4:32:25 PM UTC-5 Jimmy Eng wrote:
>
>> "peak_intensity" is the maximum peak intensity of the ion chromatogram.
>>
>> On Tue, Nov 7, 2023 at 1:00 PM Iryna Abramchuk 
>> wrote:
>>
>>> Hello all!
>>> I am using XPRESS in label-free mode (TPPv6.1.0), and interested in the
>>> "peak_intensity" output value. I was just looking to confirm whether
>>> "peak_intensity" is the precursor peak intensity, or if it's the maximum
>>> peak intensity of the ion chromatogram?
>>> Thank you
>>>
>>> --
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>>> Groups "spctools-discuss" group.
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>>> 
>>> .
>>>
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> 
> .
>

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Re: [spctools-discuss] XPRESS peak intensity value

[Iryna Abramchuk]

Thank you! Do you know if there is any way to extract the precursor peak 
intensity with XPRESS (or other TPP tools)? 

On Tuesday, November 7, 2023 at 4:32:25 PM UTC-5 Jimmy Eng wrote:

> "peak_intensity" is the maximum peak intensity of the ion chromatogram.
>
> On Tue, Nov 7, 2023 at 1:00 PM Iryna Abramchuk  
> wrote:
>
>> Hello all!
>> I am using XPRESS in label-free mode (TPPv6.1.0), and interested in the 
>> "peak_intensity" output value. I was just looking to confirm whether 
>> "peak_intensity" is the precursor peak intensity, or if it's the maximum 
>> peak intensity of the ion chromatogram?
>> Thank you
>>
>> -- 
>> You received this message because you are subscribed to the Google Groups 
>> "spctools-discuss" group.
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>> email to spctools-discu...@googlegroups.com.
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>> https://groups.google.com/d/msgid/spctools-discuss/ea66065e-0b21-43cd-9f00-703ad9e8d3f7n%40googlegroups.com
>>  
>> 
>> .
>>
>

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Re: [spctools-discuss] XPRESS peak intensity value

[Jimmy Eng]

"peak_intensity" is the maximum peak intensity of the ion chromatogram.

On Tue, Nov 7, 2023 at 1:00 PM Iryna Abramchuk 
wrote:

> Hello all!
> I am using XPRESS in label-free mode (TPPv6.1.0), and interested in the
> "peak_intensity" output value. I was just looking to confirm whether
> "peak_intensity" is the precursor peak intensity, or if it's the maximum
> peak intensity of the ion chromatogram?
> Thank you
>
> --
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> "spctools-discuss" group.
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> 
> .
>

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[spctools-discuss] XPRESS peak intensity value

[Iryna Abramchuk]

Hello all!
I am using XPRESS in label-free mode (TPPv6.1.0), and interested in the 
"peak_intensity" output value. I was just looking to confirm whether 
"peak_intensity" is the precursor peak intensity, or if it's the maximum 
peak intensity of the ion chromatogram?
Thank you

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