proteowizard-support Mailing List for ProteoWizard

Thank you Matt for your time and support, I really appreciate it!

Andreas, I use the ChemStation from Agilent for open the signals
chromatograms. But for the 2D plots I use the GC Image software.

I don’t know how to use the other that you mentioned before. Maybe if you
have some advice I’ll try to use it and get the cuts.xml

Il giorno mar 12 nov 2024 alle 17:49 Chambers, Matthew <
mat...@gm...> ha scritto:

> I do see the modulation time in the acq.txt and acq.macml files. But I
> don't see a way to actually connect the RAW file with the pump's .D
> directory because they're not named the same nor is one a subset of the
> other:
>
> 001-P1-B1-CipN_AA25_ByphXPor_MS_NEG_01.D
> CipN_2D_BYPxPOR_CH3COOH_NEG_01.raw
>
> Those are just too different to connect automatically and I don't see any
> reference to the .D in the .RAW file.
>
> I think you'll have to follow Andreas's lead and make some script that
> converts the 1D scan times into LCxLC times by applying the modulation time
> as a modulus.
>
>
>
> On 11/8/2024 4:55 AM, Giovanna AQUINO wrote:
>
> Dear Matthew and Andreas,
>
> Apologies for the delayed response, I was out of the lab recently. I now
> have answers to your questions:
>
>    - Regarding the "non-MS detector," it results from using an Agilent
>    HPLC system alongside a Thermo MS detector. To support the external
>    metadata requirements, I’ll attach the relevant .D folder from the
>    Agilent analysis corresponding to each Thermo RAW file.
>    - The modulation time, which I set in the Agilent pump method, is 0.64
>    seconds.
>    - I didn’t find the curts.xml file in the .D folder. Do you have any
>    suggestions on where I might find it?
>
>
> My main objective is to identify the m/z precursor based on the retention
> times in the peak list from the RAW files and explore any possibility to
> correlate these retention times with those from the Agilent system.
> Ideally, this will allow me to pinpoint the corresponding spots on the
> LCxLC plot.
> Please let me know if you need further clarification or additional data.
>  001-P1-B1-CipN_AA25_ByphXPor_MS_NEG_01.D.zip
> <https://drive.google.com/file/d/19cbCvuFKXg048cfnmvs3nYUQy5utvbo_/view?usp=drive_web>
>  003-P1-B1-CipN_AA25_ByphXPor_MS_POS_02.D.zip
> <https://drive.google.com/file/d/1t7JIWFtMi5a4C3wKqSC8hJ587cNkvMsl/view?usp=drive_web>
>
>
> Il giorno gio 7 nov 2024 alle ore 17:31 Chambers, Matthew <
> mat...@gm...> ha scritto:
>
>> Hi Andreas, thanks for your insight! I'm curious why you think it
>> shouldn't be done by msconvert? (Inserting cvParams for the LCxLC
>> coordinates, I mean, not generating 2d chromatograms.) Looking at the time
>> vs. m/z heatmap for the whole RAW, I can definitely see the periodicity. Do
>> your 2d chromatograms collapse the m/z dimension (possibly filtered for
>> some m/z range of interest) and then plot the first column RT vs second
>> column RT with the summed intensity as color?
>>
>>
>> On 11/7/2024 3:32 AM, BREIDBACH Andreas wrote:
>>
>> Hi, I use here a pretty similar setup for LCxLC-MS. The Agilent software
>> creates a XML file in the respective acquisition directory (cuts.xml)
>>  which contains the transfer times. That combined with the RAW file can
>> then be used to construct the 2D-chromatogram. I personally do not think
>> this is something that should belong in msconvert.
>>
>>
>>
>> Andreas Breidbach
>>
>>
>>
>> *From:* Chambers, Matthew <mat...@gm...>
>> <mat...@gm...>
>> *Sent:* Wednesday, November 6, 2024 8:09 PM
>> *To:* Giovanna AQUINO <ga...@un...> <ga...@un...>
>> *Cc:* su...@pr...
>> *Subject:* Re: [proteowizard-support] Conversion orbitrap file
>>
>>
>>
>> Unfortunately I don't see any metadata in the file about LCxLC
>> coordinates. I don't see any non-MS detector which would provide something
>> like pump pressure or other QC traces like that. I'm pretty surprised about
>> that actually as those are pretty common in modern RAW files. Does this set
>> of RAW files have some external metadata file from the Agilent system that
>> could allow mapping 1d scan time to LCxLC coordinates? This single RAW file
>> is the output of an entire LCxLC gradient, right? Is the modulation time
>> something you set in the Agilent pump's method? Hypothetically if I had the
>> modulation time I might be able to derive the LCxLC coordinates from that
>> and the 1d scan time, but I'm not sure how accurate that would be. LCxLC is
>> definitely not something I'm experienced with.
>>
>> On 11/6/2024 11:04 AM, Giovanna AQUINO wrote:
>>
>>
>>
>> Il giorno mer 6 nov 2024 alle ore 16:55 Chambers, Matthew <
>> mat...@gm...> ha scritto:
>>
>> Can you share an example RAW file and I'll see if I can extract those
>> times from the metadata?
>>
>>
>> On 11/6/2024 2:08 AM, Giovanna AQUINO via proteowizard-support wrote:
>> > Dear Proteowizard support,
>> >
>> > I’m a PhD student from University of Salerno (Italy) and I’m writing
>> for any suggestion on how to convert 2D LCxLC data acquired on an
>> > Orbitrap Exploris 120 (Thermo).
>> >
>> > Our experiments were performed using an Agilent Infinity II 1290 LCxLC
>> system coupled online to an Exploris120 Mass Spectrometer (Thermo
>> > Scientific) in positive and negative ionization mode.
>> >
>> > Specifically, we would like to characterize a plant extract, and we
>> would like to use MZmine and Sirius for a detailed annotation of the
>> > metabolites.
>> >
>> > There are 3 CV parameters we would need:
>> >
>> > “MS:1002082“ -> First column elution time
>> >
>> > “MS:1002083“ -> Second column elution time
>> >
>> > “MS:1002042“ -> modulation time
>> >
>> >
>> > Until now I only got the possibility to download the mass list and the
>> related retention time, but they are refereed as a mono dimensional
>> > run.
>> >
>> > There is a possibility to convert an Orbitrap .raw file to obtain these
>> 3 CV parameters?
>> >
>> >
>> > Kind regards,
>> >
>> > Giovanna
>> >
>>
>>
>>
>>
>>
>

I do see the modulation time in the acq.txt and acq.macml files. But I don't see a way to actually connect the RAW file with the pump's .D 
directory because they're not named the same nor is one a subset of the other:

001-P1-B1-CipN_AA25_ByphXPor_MS_NEG_01.D
CipN_2D_BYPxPOR_CH3COOH_NEG_01.raw

Those are just too different to connect automatically and I don't see any reference to the .D in the .RAW file.

I think you'll have to follow Andreas's lead and make some script that converts the 1D scan times into LCxLC times by applying the 
modulation time as a modulus.


On 11/8/2024 4:55 AM, Giovanna AQUINO wrote:
>
> Dear Matthew and Andreas,
>
> Apologies for the delayed response, I was out of the lab recently. I now have answers to your questions:
>
>   * Regarding the "non-MS detector," it results from using an Agilent HPLC system alongside a Thermo MS detector. To support the external
>     metadata requirements, I’ll attach the relevant |.D| folder from the Agilent analysis corresponding to each Thermo RAW file.
>   * The modulation time, which I set in the Agilent pump method, is 0.64 seconds.
>   * I didn’t find the curts.xml file in the .D folder. Do you have any suggestions on where I might find it?
>
>
> My main objective is to identify the m/z precursor based on the retention times in the peak list from the RAW files and explore any 
> possibility to correlate these retention times with those from the Agilent system. Ideally, this will allow me to pinpoint the 
> corresponding spots on the LCxLC plot.
> Please let me know if you need further clarification or additional data.
> 001-P1-B1-CipN_AA25_ByphXPor_MS_NEG_01.D.zip <https://drive.google.com/file/d/19cbCvuFKXg048cfnmvs3nYUQy5utvbo_/view?usp=drive_web>
> 003-P1-B1-CipN_AA25_ByphXPor_MS_POS_02.D.zip <https://drive.google.com/file/d/1t7JIWFtMi5a4C3wKqSC8hJ587cNkvMsl/view?usp=drive_web>
>
>
> Il giorno gio 7 nov 2024 alle ore 17:31 Chambers, Matthew <mat...@gm...> ha scritto:
>
>     Hi Andreas, thanks for your insight! I'm curious why you think it shouldn't be done by msconvert? (Inserting cvParams for the LCxLC
>     coordinates, I mean, not generating 2d chromatograms.) Looking at the time vs. m/z heatmap for the whole RAW, I can definitely see the
>     periodicity. Do your 2d chromatograms collapse the m/z dimension (possibly filtered for some m/z range of interest) and then plot the
>     first column RT vs second column RT with the summed intensity as color?
>
>
>     On 11/7/2024 3:32 AM, BREIDBACH Andreas wrote:
>>
>>     Hi, I use here a pretty similar setup for LCxLC-MS. The Agilent software creates a XML file in the respective acquisition directory
>>     (cuts.xml)  which contains the transfer times. That combined with the RAW file can then be used to construct the 2D-chromatogram. I
>>     personally do not think this is something that should belong in msconvert.
>>
>>     Andreas Breidbach
>>
>>     *From:*Chambers, Matthew <mat...@gm...> <mailto:mat...@gm...>
>>     *Sent:* Wednesday, November 6, 2024 8:09 PM
>>     *To:* Giovanna AQUINO <ga...@un...> <mailto:ga...@un...>
>>     *Cc:* su...@pr...
>>     *Subject:* Re: [proteowizard-support] Conversion orbitrap file
>>
>>     Unfortunately I don't see any metadata in the file about LCxLC coordinates. I don't see any non-MS detector which would provide
>>     something like pump pressure or other QC traces like that. I'm pretty surprised about that actually as those are pretty common in
>>     modern RAW files. Does this set of RAW files have some external metadata file from the Agilent system that could allow mapping 1d
>>     scan time to LCxLC coordinates? This single RAW file is the output of an entire LCxLC gradient, right? Is the modulation time
>>     something you set in the Agilent pump's method? Hypothetically if I had the modulation time I might be able to derive the LCxLC
>>     coordinates from that and the 1d scan time, but I'm not sure how accurate that would be. LCxLC is definitely not something I'm
>>     experienced with.
>>
>>     On 11/6/2024 11:04 AM, Giovanna AQUINO wrote:
>>
>>
>>         Il giorno mer 6 nov 2024 alle ore 16:55 Chambers, Matthew <mat...@gm...> ha scritto:
>>
>>             Can you share an example RAW file and I'll see if I can extract those times from the metadata?
>>
>>
>>             On 11/6/2024 2:08 AM, Giovanna AQUINO via proteowizard-support wrote:
>>             > Dear Proteowizard support,
>>             >
>>             > I’m a PhD student from University of Salerno (Italy) and I’m writing for any suggestion on how to convert 2D LCxLC data
>>             acquired on an
>>             > Orbitrap Exploris 120 (Thermo).
>>             >
>>             > Our experiments were performed using an Agilent Infinity II 1290 LCxLC system coupled online to an Exploris120 Mass
>>             Spectrometer (Thermo
>>             > Scientific) in positive and negative ionization mode.
>>             >
>>             > Specifically, we would like to characterize a plant extract, and we would like to use MZmine and Sirius for a detailed
>>             annotation of the
>>             > metabolites.
>>             >
>>             > There are 3 CV parameters we would need:
>>             >
>>             > “MS:1002082“ -> First column elution time
>>             >
>>             > “MS:1002083“ -> Second column elution time
>>             >
>>             > “MS:1002042“ -> modulation time
>>             >
>>             >
>>             > Until now I only got the possibility to download the mass list and the related retention time, but they are refereed as a
>>             mono dimensional
>>             > run.
>>             >
>>             > There is a possibility to convert an Orbitrap .raw file to obtain these 3 CV parameters?
>>             >
>>             >
>>             > Kind regards,
>>             >
>>             > Giovanna
>>             >
>>
>

Hi Mat,

I do not know of any instrument software that would write the modulation time into the MS acquisition file. And as long as you have the run time of the MS and the modulation time of the 2D-LC it is very easy for the user to reconstruct first and second dimension run time. So why add another layer of complexity to msconvert.

@Giovanna: if the cuts.xml file is not in the acquisition directory then our setups are more different than I thought. I was doing the LC acquisitions with Agilent’s OpenLab 2D software, and the MS acquisitions with Xcalibur.

Cheers
Andreas

Andreas Breidbach
------------------
European Commission
Joint Research Centre
Reference Materials
https://ec.europa.eu/jrc/
Retieseweg 111, B-2440 Geel (Belgium)
Tel +32 (0)14 571 -205

The views expressed are purely those of the writer and may not in any circumstances be regarded as stating an official position of the European Commission.

From: Chambers, Matthew <mat...@gm...>
Sent: Thursday, November 7, 2024 5:31 PM
To: BREIDBACH Andreas (JRC-GEEL) <And...@ec...>; Giovanna AQUINO <ga...@un...>
Cc: su...@pr...
Subject: Re: [proteowizard-support] Conversion orbitrap file

Hi Andreas, thanks for your insight! I'm curious why you think it shouldn't be done by msconvert? (Inserting cvParams for the LCxLC coordinates, I mean, not generating 2d chromatograms.) Looking at the time vs. m/z heatmap for the whole RAW, I can definitely see the periodicity. Do your 2d chromatograms collapse the m/z dimension (possibly filtered for some m/z range of interest) and then plot the first column RT vs second column RT with the summed intensity as color?

On 11/7/2024 3:32 AM, BREIDBACH Andreas wrote:
Hi, I use here a pretty similar setup for LCxLC-MS. The Agilent software creates a XML file in the respective acquisition directory (cuts.xml)  which contains the transfer times. That combined with the RAW file can then be used to construct the 2D-chromatogram. I personally do not think this is something that should belong in msconvert.

Andreas Breidbach

From: Chambers, Matthew <mat...@gm...><mailto:mat...@gm...>
Sent: Wednesday, November 6, 2024 8:09 PM
To: Giovanna AQUINO <ga...@un...><mailto:ga...@un...>
Cc: su...@pr...<mailto:su...@pr...>
Subject: Re: [proteowizard-support] Conversion orbitrap file

Unfortunately I don't see any metadata in the file about LCxLC coordinates. I don't see any non-MS detector which would provide something like pump pressure or other QC traces like that. I'm pretty surprised about that actually as those are pretty common in modern RAW files. Does this set of RAW files have some external metadata file from the Agilent system that could allow mapping 1d scan time to LCxLC coordinates? This single RAW file is the output of an entire LCxLC gradient, right? Is the modulation time something you set in the Agilent pump's method? Hypothetically if I had the modulation time I might be able to derive the LCxLC coordinates from that and the 1d scan time, but I'm not sure how accurate that would be. LCxLC is definitely not something I'm experienced with.


On 11/6/2024 11:04 AM, Giovanna AQUINO wrote:


Il giorno mer 6 nov 2024 alle ore 16:55 Chambers, Matthew <mat...@gm...<mailto:mat...@gm...>> ha scritto:
Can you share an example RAW file and I'll see if I can extract those times from the metadata?


On 11/6/2024 2:08 AM, Giovanna AQUINO via proteowizard-support wrote:
> Dear Proteowizard support,
>
> I’m a PhD student from University of Salerno (Italy) and I’m writing for any suggestion on how to convert 2D LCxLC data acquired on an
> Orbitrap Exploris 120 (Thermo).
>
> Our experiments were performed using an Agilent Infinity II 1290 LCxLC system coupled online to an Exploris120 Mass Spectrometer (Thermo
> Scientific) in positive and negative ionization mode.
>
> Specifically, we would like to characterize a plant extract, and we would like to use MZmine and Sirius for a detailed annotation of the
> metabolites.
>
> There are 3 CV parameters we would need:
>
> “MS:1002082“ -> First column elution time
>
> “MS:1002083“ -> Second column elution time
>
> “MS:1002042“ -> modulation time
>
>
> Until now I only got the possibility to download the mass list and the related retention time, but they are refereed as a mono dimensional
> run.
>
> There is a possibility to convert an Orbitrap .raw file to obtain these 3 CV parameters?
>
>
> Kind regards,
>
> Giovanna
>

Motonao Nakao,

I think the one option which will make the most difference in the size of
the .mzML file is "Use numpress linear compression".

The following options gave me a .mzML file that was 178MB:
[image: image.png]

I do not know of any documentation for MSConvertGUI.

The documentation for the command-line program "msconvert.exe" is here:
https://proteowizard.sourceforge.io/tools/msconvert.html
-- Nick


On Sat, Nov 9, 2024 at 8:12 PM Brian Pratt <bs...@pr...> wrote:

> It would be useful to know what settings you have already tried. I don’t
> think you can change the precision in the human readable attributes but
> there are several options that change the size of the spectra
> representation.
>
>
>
> Sent from my phone, with apologies for brevity and strange autocorrections
>
> > On Nov 9, 2024, at 7:21 PM, motonao nakao <na...@be...> wrote:
> >
> > Dear Brian
> >
> > Thanks for your reply.
> > For example, the following wiff file is about 10 times larger than the
> > original file size.
> > Data can be picked up from the following Japanese metabobank
> > https://ddbj.nig.ac.jp/public/metabobank/study/MTBKS221/raw/
> > The file size of 180913_Top16_70_WT_Adr_G_1_Pos.wiff.scan is 40M
> > 460M when converted to .mzML
> > So, looking at the data, there is notation to 8 decimal places, but if
> > we reduce this to about 2 decimal places, the amount of file size will
> > be reduced considerably, and we would like to perform this.
> > I am having trouble understanding how to do this and is there a
> > MSconvertGUI manual?
> >
> > Sincerely
> >
> > 2024年11月10日(日) 8:12 Brian Pratt <bs...@pr...>:
> >>
> >> What settings are you currently using? In particular, what format are
> you converting from and to?
> >>
> >>>> On Nov 9, 2024, at 12:23 AM, motonao nakao <na...@be...>
> wrote:
> >>>
> >>> Dear temas
> >>>
> >>> When converting MS data using MSconverterGUI, what settings can I use
> >>> to remove the decimal points?
> >>> I want to reduce the file size.
> >>>
> >>> Sincerely
> >>> --
> >>> ++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-+
> >>> Motonao Nakao
> >>>   E-mail：na...@be...
> >>>   URL : https://be-force.co.jp
> >>> ++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-+
> >>>
> >>>
> >>> _______________________________________________
> >>> proteowizard-support mailing list
> >>> pro...@li...
> >>> https://lists.sourceforge.net/lists/listinfo/proteowizard-support
> >
> >
> >
> > --
> > ++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-+
> >    株式会社 ビーフォース
> >        中尾素直（Motonao Nakao)
> >    E-mail：na...@be...
> >    TEL : 092-982-2566 FAX : 092-982-2677
> >    URL : https://be-force.co.jp
> > ++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-+
>
>
> _______________________________________________
> proteowizard-support mailing list
> pro...@li...
> https://lists.sourceforge.net/lists/listinfo/proteowizard-support
>

It would be useful to know what settings you have already tried. I don’t think you can change the precision in the human readable attributes but there are several options that change the size of the spectra representation.



Sent from my phone, with apologies for brevity and strange autocorrections

> On Nov 9, 2024, at 7:21 PM, motonao nakao <na...@be...> wrote:
> 
> Dear Brian
> 
> Thanks for your reply.
> For example, the following wiff file is about 10 times larger than the
> original file size.
> Data can be picked up from the following Japanese metabobank
> https://ddbj.nig.ac.jp/public/metabobank/study/MTBKS221/raw/
> The file size of 180913_Top16_70_WT_Adr_G_1_Pos.wiff.scan is 40M
> 460M when converted to .mzML
> So, looking at the data, there is notation to 8 decimal places, but if
> we reduce this to about 2 decimal places, the amount of file size will
> be reduced considerably, and we would like to perform this.
> I am having trouble understanding how to do this and is there a
> MSconvertGUI manual?
> 
> Sincerely
> 
> 2024年11月10日(日) 8:12 Brian Pratt <bs...@pr...>:
>> 
>> What settings are you currently using? In particular, what format are you converting from and to?
>> 
>>>> On Nov 9, 2024, at 12:23 AM, motonao nakao <na...@be...> wrote:
>>> 
>>> Dear temas
>>> 
>>> When converting MS data using MSconverterGUI, what settings can I use
>>> to remove the decimal points?
>>> I want to reduce the file size.
>>> 
>>> Sincerely
>>> --
>>> ++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-+
>>> Motonao Nakao
>>>   E-mail：na...@be...
>>>   URL : https://be-force.co.jp
>>> ++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-+
>>> 
>>> 
>>> _______________________________________________
>>> proteowizard-support mailing list
>>> pro...@li...
>>> https://lists.sourceforge.net/lists/listinfo/proteowizard-support
> 
> 
> 
> --
> ++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-+
>    株式会社 ビーフォース
>        中尾素直（Motonao Nakao)
>    E-mail：na...@be...
>    TEL : 092-982-2566 FAX : 092-982-2677
>    URL : https://be-force.co.jp
> ++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-+

Dear Brian

Thanks for your reply.
For example, the following wiff file is about 10 times larger than the
original file size.
Data can be picked up from the following Japanese metabobank
https://ddbj.nig.ac.jp/public/metabobank/study/MTBKS221/raw/
The file size of 180913_Top16_70_WT_Adr_G_1_Pos.wiff.scan is 40M
460M when converted to .mzML
So, looking at the data, there is notation to 8 decimal places, but if
we reduce this to about 2 decimal places, the amount of file size will
be reduced considerably, and we would like to perform this.
I am having trouble understanding how to do this and is there a
MSconvertGUI manual?

Sincerely

2024年11月10日(日) 8:12 Brian Pratt <bs...@pr...>:
>
> What settings are you currently using? In particular, what format are you converting from and to?
>
> > On Nov 9, 2024, at 12:23 AM, motonao nakao <na...@be...> wrote:
> >
> > Dear temas
> >
> > When converting MS data using MSconverterGUI, what settings can I use
> > to remove the decimal points?
> > I want to reduce the file size.
> >
> > Sincerely
> > --
> > ++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-+
> > Motonao Nakao
> >    E-mail：na...@be...
> >    URL : https://be-force.co.jp
> > ++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-+
> >
> >
> > _______________________________________________
> > proteowizard-support mailing list
> > pro...@li...
> > https://lists.sourceforge.net/lists/listinfo/proteowizard-support



-- 
++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-+
    株式会社 ビーフォース
        中尾素直（Motonao Nakao)
    E-mail：na...@be...
    TEL : 092-982-2566 FAX : 092-982-2677
    URL : https://be-force.co.jp
++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-+

What settings are you currently using? In particular, what format are you converting from and to?

> On Nov 9, 2024, at 12:23 AM, motonao nakao <na...@be...> wrote:
> 
> Dear temas
> 
> When converting MS data using MSconverterGUI, what settings can I use
> to remove the decimal points?
> I want to reduce the file size.
> 
> Sincerely
> --
> ++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-+
> Motonao Nakao
>    E-mail：na...@be...
>    URL : https://be-force.co.jp
> ++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-+
> 
> 
> _______________________________________________
> proteowizard-support mailing list
> pro...@li...
> https://lists.sourceforge.net/lists/listinfo/proteowizard-support

Dear temas

When converting MS data using MSconverterGUI, what settings can I use
to remove the decimal points?
I want to reduce the file size.

Sincerely
-- 
++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-+
Motonao Nakao
    E-mail：na...@be...
    URL : https://be-force.co.jp
++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-++-+

Dear Matthew and Andreas,

Apologies for the delayed response, I was out of the lab recently. I now
have answers to your questions:


   - Regarding the "non-MS detector," it results from using an Agilent HPLC
   system alongside a Thermo MS detector. To support the external metadata
   requirements, I’ll attach the relevant .D folder from the Agilent
   analysis corresponding to each Thermo RAW file.
   - The modulation time, which I set in the Agilent pump method, is 0.64
   seconds.
   - I didn’t find the curts.xml file in the .D folder. Do you have any
   suggestions on where I might find it?


My main objective is to identify the m/z precursor based on the retention
times in the peak list from the RAW files and explore any possibility to
correlate these retention times with those from the Agilent system.
Ideally, this will allow me to pinpoint the corresponding spots on the
LCxLC plot.

Please let me know if you need further clarification or additional data.
 001-P1-B1-CipN_AA25_ByphXPor_MS_NEG_01.D.zip
<https://drive.google.com/file/d/19cbCvuFKXg048cfnmvs3nYUQy5utvbo_/view?usp=drive_web>
 003-P1-B1-CipN_AA25_ByphXPor_MS_POS_02.D.zip
<https://drive.google.com/file/d/1t7JIWFtMi5a4C3wKqSC8hJ587cNkvMsl/view?usp=drive_web>



Il giorno gio 7 nov 2024 alle ore 17:31 Chambers, Matthew <
mat...@gm...> ha scritto:

> Hi Andreas, thanks for your insight! I'm curious why you think it
> shouldn't be done by msconvert? (Inserting cvParams for the LCxLC
> coordinates, I mean, not generating 2d chromatograms.) Looking at the time
> vs. m/z heatmap for the whole RAW, I can definitely see the periodicity. Do
> your 2d chromatograms collapse the m/z dimension (possibly filtered for
> some m/z range of interest) and then plot the first column RT vs second
> column RT with the summed intensity as color?
>
>
> On 11/7/2024 3:32 AM, BREIDBACH Andreas wrote:
>
> Hi, I use here a pretty similar setup for LCxLC-MS. The Agilent software
> creates a XML file in the respective acquisition directory (cuts.xml)
>  which contains the transfer times. That combined with the RAW file can
> then be used to construct the 2D-chromatogram. I personally do not think
> this is something that should belong in msconvert.
>
>
>
> Andreas Breidbach
>
>
>
> *From:* Chambers, Matthew <mat...@gm...>
> <mat...@gm...>
> *Sent:* Wednesday, November 6, 2024 8:09 PM
> *To:* Giovanna AQUINO <ga...@un...> <ga...@un...>
> *Cc:* su...@pr...
> *Subject:* Re: [proteowizard-support] Conversion orbitrap file
>
>
>
> Unfortunately I don't see any metadata in the file about LCxLC
> coordinates. I don't see any non-MS detector which would provide something
> like pump pressure or other QC traces like that. I'm pretty surprised about
> that actually as those are pretty common in modern RAW files. Does this set
> of RAW files have some external metadata file from the Agilent system that
> could allow mapping 1d scan time to LCxLC coordinates? This single RAW file
> is the output of an entire LCxLC gradient, right? Is the modulation time
> something you set in the Agilent pump's method? Hypothetically if I had the
> modulation time I might be able to derive the LCxLC coordinates from that
> and the 1d scan time, but I'm not sure how accurate that would be. LCxLC is
> definitely not something I'm experienced with.
>
> On 11/6/2024 11:04 AM, Giovanna AQUINO wrote:
>
>
>
> Il giorno mer 6 nov 2024 alle ore 16:55 Chambers, Matthew <
> mat...@gm...> ha scritto:
>
> Can you share an example RAW file and I'll see if I can extract those
> times from the metadata?
>
>
> On 11/6/2024 2:08 AM, Giovanna AQUINO via proteowizard-support wrote:
> > Dear Proteowizard support,
> >
> > I’m a PhD student from University of Salerno (Italy) and I’m writing for
> any suggestion on how to convert 2D LCxLC data acquired on an
> > Orbitrap Exploris 120 (Thermo).
> >
> > Our experiments were performed using an Agilent Infinity II 1290 LCxLC
> system coupled online to an Exploris120 Mass Spectrometer (Thermo
> > Scientific) in positive and negative ionization mode.
> >
> > Specifically, we would like to characterize a plant extract, and we
> would like to use MZmine and Sirius for a detailed annotation of the
> > metabolites.
> >
> > There are 3 CV parameters we would need:
> >
> > “MS:1002082“ -> First column elution time
> >
> > “MS:1002083“ -> Second column elution time
> >
> > “MS:1002042“ -> modulation time
> >
> >
> > Until now I only got the possibility to download the mass list and the
> related retention time, but they are refereed as a mono dimensional
> > run.
> >
> > There is a possibility to convert an Orbitrap .raw file to obtain these
> 3 CV parameters?
> >
> >
> > Kind regards,
> >
> > Giovanna
> >
>
>
>
>
>

Hi Andreas, thanks for your insight! I'm curious why you think it shouldn't be done by msconvert? (Inserting cvParams for the LCxLC 
coordinates, I mean, not generating 2d chromatograms.) Looking at the time vs. m/z heatmap for the whole RAW, I can definitely see the 
periodicity. Do your 2d chromatograms collapse the m/z dimension (possibly filtered for some m/z range of interest) and then plot the first 
column RT vs second column RT with the summed intensity as color?


On 11/7/2024 3:32 AM, BREIDBACH Andreas wrote:
>
> Hi, I use here a pretty similar setup for LCxLC-MS. The Agilent software creates a XML file in the respective acquisition directory 
> (cuts.xml)  which contains the transfer times. That combined with the RAW file can then be used to construct the 2D-chromatogram. I 
> personally do not think this is something that should belong in msconvert.
>
> Andreas Breidbach
>
> *From:*Chambers, Matthew <mat...@gm...>
> *Sent:* Wednesday, November 6, 2024 8:09 PM
> *To:* Giovanna AQUINO <ga...@un...>
> *Cc:* su...@pr...
> *Subject:* Re: [proteowizard-support] Conversion orbitrap file
>
> Unfortunately I don't see any metadata in the file about LCxLC coordinates. I don't see any non-MS detector which would provide something 
> like pump pressure or other QC traces like that. I'm pretty surprised about that actually as those are pretty common in modern RAW files. 
> Does this set of RAW files have some external metadata file from the Agilent system that could allow mapping 1d scan time to LCxLC 
> coordinates? This single RAW file is the output of an entire LCxLC gradient, right? Is the modulation time something you set in the 
> Agilent pump's method? Hypothetically if I had the modulation time I might be able to derive the LCxLC coordinates from that and the 1d 
> scan time, but I'm not sure how accurate that would be. LCxLC is definitely not something I'm experienced with.
>
> On 11/6/2024 11:04 AM, Giovanna AQUINO wrote:
>
>
>     Il giorno mer 6 nov 2024 alle ore 16:55 Chambers, Matthew <mat...@gm...> ha scritto:
>
>         Can you share an example RAW file and I'll see if I can extract those times from the metadata?
>
>
>         On 11/6/2024 2:08 AM, Giovanna AQUINO via proteowizard-support wrote:
>         > Dear Proteowizard support,
>         >
>         > I’m a PhD student from University of Salerno (Italy) and I’m writing for any suggestion on how to convert 2D LCxLC data acquired
>         on an
>         > Orbitrap Exploris 120 (Thermo).
>         >
>         > Our experiments were performed using an Agilent Infinity II 1290 LCxLC system coupled online to an Exploris120 Mass Spectrometer
>         (Thermo
>         > Scientific) in positive and negative ionization mode.
>         >
>         > Specifically, we would like to characterize a plant extract, and we would like to use MZmine and Sirius for a detailed
>         annotation of the
>         > metabolites.
>         >
>         > There are 3 CV parameters we would need:
>         >
>         > “MS:1002082“ -> First column elution time
>         >
>         > “MS:1002083“ -> Second column elution time
>         >
>         > “MS:1002042“ -> modulation time
>         >
>         >
>         > Until now I only got the possibility to download the mass list and the related retention time, but they are refereed as a mono
>         dimensional
>         > run.
>         >
>         > There is a possibility to convert an Orbitrap .raw file to obtain these 3 CV parameters?
>         >
>         >
>         > Kind regards,
>         >
>         > Giovanna
>         >
>

What I forgot to mention: I have a R script to do this for me, construct 2D chromatograms from cuts.xml and the respective mzML file

Andreas Breidbach
------------------
European Commission
Joint Research Centre
Reference Materials
https://ec.europa.eu/jrc/
Retieseweg 111, B-2440 Geel (Belgium)
Tel +32 (0)14 571 -205

The views expressed are purely those of the writer and may not in any circumstances be regarded as stating an official position of the European Commission.

From: BREIDBACH Andreas via proteowizard-support <pro...@li...>
Sent: Thursday, November 7, 2024 9:33 AM
To: Chambers, Matthew <mat...@gm...>; Giovanna AQUINO <ga...@un...>
Cc: su...@pr...
Subject: Re: [proteowizard-support] Conversion orbitrap file

Hi, I use here a pretty similar setup for LCxLC-MS. The Agilent software creates a XML file in the respective acquisition directory (cuts.xml)  which contains the transfer times. That combined with the RAW file can then be used to construct the 2D-chromatogram. I personally do not think this is something that should belong in msconvert.

Andreas Breidbach
------------------
European Commission
Joint Research Centre
Reference Materials
https://ec.europa.eu/jrc/
Retieseweg 111, B-2440 Geel (Belgium)
Tel +32 (0)14 571 -205

The views expressed are purely those of the writer and may not in any circumstances be regarded as stating an official position of the European Commission.

From: Chambers, Matthew <mat...@gm...<mailto:mat...@gm...>>
Sent: Wednesday, November 6, 2024 8:09 PM
To: Giovanna AQUINO <ga...@un...<mailto:ga...@un...>>
Cc: su...@pr...<mailto:su...@pr...>
Subject: Re: [proteowizard-support] Conversion orbitrap file

Unfortunately I don't see any metadata in the file about LCxLC coordinates. I don't see any non-MS detector which would provide something like pump pressure or other QC traces like that. I'm pretty surprised about that actually as those are pretty common in modern RAW files. Does this set of RAW files have some external metadata file from the Agilent system that could allow mapping 1d scan time to LCxLC coordinates? This single RAW file is the output of an entire LCxLC gradient, right? Is the modulation time something you set in the Agilent pump's method? Hypothetically if I had the modulation time I might be able to derive the LCxLC coordinates from that and the 1d scan time, but I'm not sure how accurate that would be. LCxLC is definitely not something I'm experienced with.
On 11/6/2024 11:04 AM, Giovanna AQUINO wrote:

[Image removed by sender.] CipN_2D_BYPxPOR_CH3COOH_NEG_01.raw<https://urldefense.com/v3/__https:/drive.google.com/file/d/1fMqpywz-f85NAODefbNzFl4DwTD6LAbA/view?usp=drive_web__;!!DOxrgLBm!CNz8NzxbBDjc1aeq6T2af2fE9TEmzM5TN7M6AHgIM79sOgGbKDhI2jlVY9w93H_TNLJXuGzs0v7GneCUggEP1hiL_n139VtcJWU$>

[Image removed by sender.] CipN_2D_BYPxPOR_CH3COOH_POS_02.raw<https://urldefense.com/v3/__https:/drive.google.com/file/d/13hTuhDVxMsre3YqbQBN4z6h63VI_sWba/view?usp=drive_web__;!!DOxrgLBm!CNz8NzxbBDjc1aeq6T2af2fE9TEmzM5TN7M6AHgIM79sOgGbKDhI2jlVY9w93H_TNLJXuGzs0v7GneCUggEP1hiL_n13vFDWZPo$>
Thank you for your answer.
Here are the requested RAW files.


Il giorno mer 6 nov 2024 alle ore 16:55 Chambers, Matthew <mat...@gm...<mailto:mat...@gm...>> ha scritto:
Can you share an example RAW file and I'll see if I can extract those times from the metadata?


On 11/6/2024 2:08 AM, Giovanna AQUINO via proteowizard-support wrote:
> Dear Proteowizard support,
>
> I’m a PhD student from University of Salerno (Italy) and I’m writing for any suggestion on how to convert 2D LCxLC data acquired on an
> Orbitrap Exploris 120 (Thermo).
>
> Our experiments were performed using an Agilent Infinity II 1290 LCxLC system coupled online to an Exploris120 Mass Spectrometer (Thermo
> Scientific) in positive and negative ionization mode.
>
> Specifically, we would like to characterize a plant extract, and we would like to use MZmine and Sirius for a detailed annotation of the
> metabolites.
>
> There are 3 CV parameters we would need:
>
> “MS:1002082“ -> First column elution time
>
> “MS:1002083“ -> Second column elution time
>
> “MS:1002042“ -> modulation time
>
>
> Until now I only got the possibility to download the mass list and the related retention time, but they are refereed as a mono dimensional
> run.
>
> There is a possibility to convert an Orbitrap .raw file to obtain these 3 CV parameters?
>
>
> Kind regards,
>
> Giovanna
>

Hi, I use here a pretty similar setup for LCxLC-MS. The Agilent software creates a XML file in the respective acquisition directory (cuts.xml)  which contains the transfer times. That combined with the RAW file can then be used to construct the 2D-chromatogram. I personally do not think this is something that should belong in msconvert.

Andreas Breidbach
------------------
European Commission
Joint Research Centre
Reference Materials
https://ec.europa.eu/jrc/
Retieseweg 111, B-2440 Geel (Belgium)
Tel +32 (0)14 571 -205

The views expressed are purely those of the writer and may not in any circumstances be regarded as stating an official position of the European Commission.

From: Chambers, Matthew <mat...@gm...>
Sent: Wednesday, November 6, 2024 8:09 PM
To: Giovanna AQUINO <ga...@un...>
Cc: su...@pr...
Subject: Re: [proteowizard-support] Conversion orbitrap file

Unfortunately I don't see any metadata in the file about LCxLC coordinates. I don't see any non-MS detector which would provide something like pump pressure or other QC traces like that. I'm pretty surprised about that actually as those are pretty common in modern RAW files. Does this set of RAW files have some external metadata file from the Agilent system that could allow mapping 1d scan time to LCxLC coordinates? This single RAW file is the output of an entire LCxLC gradient, right? Is the modulation time something you set in the Agilent pump's method? Hypothetically if I had the modulation time I might be able to derive the LCxLC coordinates from that and the 1d scan time, but I'm not sure how accurate that would be. LCxLC is definitely not something I'm experienced with.

On 11/6/2024 11:04 AM, Giovanna AQUINO wrote:

[Image removed by sender.] CipN_2D_BYPxPOR_CH3COOH_NEG_01.raw<https://urldefense.com/v3/__https:/drive.google.com/file/d/1fMqpywz-f85NAODefbNzFl4DwTD6LAbA/view?usp=drive_web__;!!DOxrgLBm!CNz8NzxbBDjc1aeq6T2af2fE9TEmzM5TN7M6AHgIM79sOgGbKDhI2jlVY9w93H_TNLJXuGzs0v7GneCUggEP1hiL_n139VtcJWU$>

[Image removed by sender.] CipN_2D_BYPxPOR_CH3COOH_POS_02.raw<https://urldefense.com/v3/__https:/drive.google.com/file/d/13hTuhDVxMsre3YqbQBN4z6h63VI_sWba/view?usp=drive_web__;!!DOxrgLBm!CNz8NzxbBDjc1aeq6T2af2fE9TEmzM5TN7M6AHgIM79sOgGbKDhI2jlVY9w93H_TNLJXuGzs0v7GneCUggEP1hiL_n13vFDWZPo$>
Thank you for your answer.
Here are the requested RAW files.


Il giorno mer 6 nov 2024 alle ore 16:55 Chambers, Matthew <mat...@gm...<mailto:mat...@gm...>> ha scritto:
Can you share an example RAW file and I'll see if I can extract those times from the metadata?


On 11/6/2024 2:08 AM, Giovanna AQUINO via proteowizard-support wrote:
> Dear Proteowizard support,
>
> I’m a PhD student from University of Salerno (Italy) and I’m writing for any suggestion on how to convert 2D LCxLC data acquired on an
> Orbitrap Exploris 120 (Thermo).
>
> Our experiments were performed using an Agilent Infinity II 1290 LCxLC system coupled online to an Exploris120 Mass Spectrometer (Thermo
> Scientific) in positive and negative ionization mode.
>
> Specifically, we would like to characterize a plant extract, and we would like to use MZmine and Sirius for a detailed annotation of the
> metabolites.
>
> There are 3 CV parameters we would need:
>
> “MS:1002082“ -> First column elution time
>
> “MS:1002083“ -> Second column elution time
>
> “MS:1002042“ -> modulation time
>
>
> Until now I only got the possibility to download the mass list and the related retention time, but they are refereed as a mono dimensional
> run.
>
> There is a possibility to convert an Orbitrap .raw file to obtain these 3 CV parameters?
>
>
> Kind regards,
>
> Giovanna
>

Unfortunately I don't see any metadata in the file about LCxLC coordinates. I don't see any non-MS detector which would provide something 
like pump pressure or other QC traces like that. I'm pretty surprised about that actually as those are pretty common in modern RAW files. 
Does this set of RAW files have some external metadata file from the Agilent system that could allow mapping 1d scan time to LCxLC 
coordinates? This single RAW file is the output of an entire LCxLC gradient, right? Is the modulation time something you set in the Agilent 
pump's method? Hypothetically if I had the modulation time I might be able to derive the LCxLC coordinates from that and the 1d scan time, 
but I'm not sure how accurate that would be. LCxLC is definitely not something I'm experienced with.


On 11/6/2024 11:04 AM, Giovanna AQUINO wrote:
>
> CipN_2D_BYPxPOR_CH3COOH_NEG_01.raw <https://drive.google.com/file/d/1fMqpywz-f85NAODefbNzFl4DwTD6LAbA/view?usp=drive_web>
>
> CipN_2D_BYPxPOR_CH3COOH_POS_02.raw <https://drive.google.com/file/d/13hTuhDVxMsre3YqbQBN4z6h63VI_sWba/view?usp=drive_web>
> Thank you for your answer.
> Here are the requested RAW files.
>
>
> Il giorno mer 6 nov 2024 alle ore 16:55 Chambers, Matthew <mat...@gm...> ha scritto:
>
>     Can you share an example RAW file and I'll see if I can extract those times from the metadata?
>
>
>     On 11/6/2024 2:08 AM, Giovanna AQUINO via proteowizard-support wrote:
>     > Dear Proteowizard support,
>     >
>     > I’m a PhD student from University of Salerno (Italy) and I’m writing for any suggestion on how to convert 2D LCxLC data acquired on an
>     > Orbitrap Exploris 120 (Thermo).
>     >
>     > Our experiments were performed using an Agilent Infinity II 1290 LCxLC system coupled online to an Exploris120 Mass Spectrometer
>     (Thermo
>     > Scientific) in positive and negative ionization mode.
>     >
>     > Specifically, we would like to characterize a plant extract, and we would like to use MZmine and Sirius for a detailed annotation of
>     the
>     > metabolites.
>     >
>     > There are 3 CV parameters we would need:
>     >
>     > “MS:1002082“ -> First column elution time
>     >
>     > “MS:1002083“ -> Second column elution time
>     >
>     > “MS:1002042“ -> modulation time
>     >
>     >
>     > Until now I only got the possibility to download the mass list and the related retention time, but they are refereed as a mono
>     dimensional
>     > run.
>     >
>     > There is a possibility to convert an Orbitrap .raw file to obtain these 3 CV parameters?
>     >
>     >
>     > Kind regards,
>     >
>     > Giovanna
>     >
>

 CipN_2D_BYPxPOR_CH3COOH_NEG_01.raw
<https://drive.google.com/file/d/1fMqpywz-f85NAODefbNzFl4DwTD6LAbA/view?usp=drive_web>

 CipN_2D_BYPxPOR_CH3COOH_POS_02.raw
<https://drive.google.com/file/d/13hTuhDVxMsre3YqbQBN4z6h63VI_sWba/view?usp=drive_web>
Thank you for your answer.
Here are the requested RAW files.


Il giorno mer 6 nov 2024 alle ore 16:55 Chambers, Matthew <
mat...@gm...> ha scritto:

> Can you share an example RAW file and I'll see if I can extract those
> times from the metadata?
>
>
> On 11/6/2024 2:08 AM, Giovanna AQUINO via proteowizard-support wrote:
> > Dear Proteowizard support,
> >
> > I’m a PhD student from University of Salerno (Italy) and I’m writing for
> any suggestion on how to convert 2D LCxLC data acquired on an
> > Orbitrap Exploris 120 (Thermo).
> >
> > Our experiments were performed using an Agilent Infinity II 1290 LCxLC
> system coupled online to an Exploris120 Mass Spectrometer (Thermo
> > Scientific) in positive and negative ionization mode.
> >
> > Specifically, we would like to characterize a plant extract, and we
> would like to use MZmine and Sirius for a detailed annotation of the
> > metabolites.
> >
> > There are 3 CV parameters we would need:
> >
> > “MS:1002082“ -> First column elution time
> >
> > “MS:1002083“ -> Second column elution time
> >
> > “MS:1002042“ -> modulation time
> >
> >
> > Until now I only got the possibility to download the mass list and the
> related retention time, but they are refereed as a mono dimensional
> > run.
> >
> > There is a possibility to convert an Orbitrap .raw file to obtain these
> 3 CV parameters?
> >
> >
> > Kind regards,
> >
> > Giovanna
> >
>

Can you share an example RAW file and I'll see if I can extract those times from the metadata?


On 11/6/2024 2:08 AM, Giovanna AQUINO via proteowizard-support wrote:
> Dear Proteowizard support,
>
> I’m a PhD student from University of Salerno (Italy) and I’m writing for any suggestion on how to convert 2D LCxLC data acquired on an 
> Orbitrap Exploris 120 (Thermo).
>
> Our experiments were performed using an Agilent Infinity II 1290 LCxLC system coupled online to an Exploris120 Mass Spectrometer (Thermo 
> Scientific) in positive and negative ionization mode.
>
> Specifically, we would like to characterize a plant extract, and we would like to use MZmine and Sirius for a detailed annotation of the 
> metabolites.
>
> There are 3 CV parameters we would need:
>
> “MS:1002082“ -> First column elution time
>
> “MS:1002083“ -> Second column elution time
>
> “MS:1002042“ -> modulation time
>
>
> Until now I only got the possibility to download the mass list and the related retention time, but they are refereed as a mono dimensional 
> run.
>
> There is a possibility to convert an Orbitrap .raw file to obtain these 3 CV parameters?
>
>
> Kind regards,
>
> Giovanna
>

Dear Proteowizard support,

I’m a PhD student from University of Salerno (Italy) and I’m writing for
any suggestion on how to convert 2D LCxLC data acquired on an Orbitrap
Exploris 120 (Thermo).

Our experiments were performed using an Agilent Infinity II 1290 LCxLC
system coupled online to an Exploris120 Mass Spectrometer (Thermo
Scientific) in positive and negative ionization mode.

Specifically, we would like to characterize a plant extract, and we would
like to use MZmine and Sirius for a detailed annotation of the metabolites.

There are 3 CV parameters we would need:

“MS:1002082“ -> First column elution time

“MS:1002083“ -> Second column elution time

“MS:1002042“ -> modulation time


Until now I only got the possibility to download the mass list and the
related retention time, but they are refereed as a mono dimensional run.

There is a possibility to convert an Orbitrap .raw file to obtain these 3
CV parameters?


Kind regards,

Giovanna

Hi Xavier,

If you need vendor file conversion on a Mac, you can either use Parallels or some other VM to run a real Windows instance, or you can use 
our Docker container which runs the Windows version of ProteoWizard with Wine:
https://hub.docker.com/r/proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses

If you don't need vendor file conversion, it is possible to build and run pwiz natively on MacOS, but I don't think we have any official 
release for it because we don't have a build agent set up to build one.

Hope this helps,
-Matt


On 10/29/2024 10:41 AM, Xavier Brazzolotto wrote:
> Hi Proteowizard developers
>
> I would like to know if you plan to have a MacOS version of ProteoWizard available for the mac community ?
>
> Best
> Xavier
>
> *Xavier Brazzolotto, PhD*
> *Département de Toxicologie et Risques Chimiques*
> *Institut de Recherche Biomédicale des Armées*
> 1 Place du Général Valérie André
> *91220 Brétigny sur Orge*
> *France*

Hi Proteowizard developers

I would like to know if you plan to have a MacOS version of ProteoWizard available for the mac community ?

Best
Xavier

Xavier Brazzolotto, PhD
Département de Toxicologie et Risques Chimiques
Institut de Recherche Biomédicale des Armées
1 Place du Général Valérie André
91220 Brétigny sur Orge
France

Phone		+33 (0) 1 78 65 14 00
Alt Phone	+33 (0) 4 57 42 87 19
Cell			+33 (0) 6 58 36 39 09

https://irba.sante.defense.gouv.fr/

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

Thank you for the information.

On Thu, 24 Oct, 2024, 9:38 pm Brian Pratt, <bs...@pr...> wrote:

> We're not aware of any such issues on our end, sorry.
>
> I'd say investigate the .d file using SeeMS to see if you're getting the
> fragmentation you expect compared with your other systems, possibly you
> need to optimize collision energies etc. It's more likely that it's a
> process issue than a data conversion issue.
>
>
>
> On Wed, Oct 23, 2024 at 11:30 PM roshitha k r <ros...@gm...>
> wrote:
>
>> Hello Team Lead,
>>
>> I find this possibility, but we notice that our data obtained from
>> systems other than the Agilent QTOF system works well for library matching,
>> this is why we thought we might face issues due to the data conversion.
>> Moreover, the GNPS website also mentioned that the chance of trouble in
>> data converted from the Agilent system is verified with reported issues.
>>
>> Is there any option to clarify the same? Please advise in this regard or
>> redirect me to a more suitable alternative support.
>> [image: image.png]
>> Warm Regards,
>> *Roshitha K R*
>> *PhD Research Scholar*
>> *Pharmaceutical Analysis*
>> *NIPER Hyderabad*
>>
>>
>>
>>
>> On Mon, Oct 21, 2024 at 9:21 PM Brian Pratt <bs...@pr...>
>> wrote:
>>
>>> If you think the issues are related to data conversion with msconvert,
>>> we can help you with that.
>>>
>>> Downstream from there, you'll need to consult with the developers of
>>> those tools. I guess that's the GNPS folks in this case?
>>>
>>> Best of luck to you!
>>>
>>> Brian
>>>
>>> On Mon, Oct 21, 2024 at 6:37 AM roshitha k r <ros...@gm...>
>>> wrote:
>>>
>>>> Hi Brian,
>>>>
>>>> Good to hear from you,
>>>>
>>>> Here are some screenshots of our trials.
>>>>
>>>> I used to get a progress chart, and the analysis used to run for more
>>>> than a day a few times, otherwise as shared in the picture, not even the
>>>> progress chart would appear. The sad part is till now,  there have been no
>>>> more than 3 compounds matched in my files which show multiple compounds in
>>>> mass hunter software.
>>>>
>>>> Warm Regards,
>>>> *Roshitha K R*
>>>> *PhD Research Scholar*
>>>> *Pharmaceutical Analysis*
>>>> *NIPER Hyderabad*
>>>>
>>>>
>>>>
>>>>
>>>> On Sun, Oct 20, 2024 at 10:09 PM Brian Pratt <bs...@pr...>
>>>> wrote:
>>>>
>>>>> Hi Roshita K R,
>>>>>
>>>>> Let's see what we can do - show us what you've tried, and what errors
>>>>> you're seeing. Screenshots are the easiest way to do that.
>>>>>
>>>>> Best regards,
>>>>>
>>>>> Brian Pratt
>>>>>
>>>>>
>>>>> On Sun, Oct 20, 2024 at 1:33 AM roshitha k r <ros...@gm...>
>>>>> wrote:
>>>>>
>>>>>> Dear proteowizard team ,
>>>>>>
>>>>>> I cannot get the library matching or molecular networking on the data
>>>>>> converted from the Agilent QTOF system's .d file format to mzMl format.
>>>>>>
>>>>>> I am struggling to process my data.  Please help me out in this
>>>>>>
>>>>>> Warm Regards,
>>>>>> *Roshitha K R*
>>>>>> *PhD Research Scholar*
>>>>>> *Pharmaceutical Analysis*
>>>>>> *NIPER Hyderabad*
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> proteowizard-support mailing list
>>>>>> pro...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/proteowizard-support
>>>>>>
>>>>>

We're not aware of any such issues on our end, sorry.

I'd say investigate the .d file using SeeMS to see if you're getting the
fragmentation you expect compared with your other systems, possibly you
need to optimize collision energies etc. It's more likely that it's a
process issue than a data conversion issue.



On Wed, Oct 23, 2024 at 11:30 PM roshitha k r <ros...@gm...> wrote:

> Hello Team Lead,
>
> I find this possibility, but we notice that our data obtained from systems
> other than the Agilent QTOF system works well for library matching,
> this is why we thought we might face issues due to the data conversion.
> Moreover, the GNPS website also mentioned that the chance of trouble in
> data converted from the Agilent system is verified with reported issues.
>
> Is there any option to clarify the same? Please advise in this regard or
> redirect me to a more suitable alternative support.
> [image: image.png]
> Warm Regards,
> *Roshitha K R*
> *PhD Research Scholar*
> *Pharmaceutical Analysis*
> *NIPER Hyderabad*
>
>
>
>
> On Mon, Oct 21, 2024 at 9:21 PM Brian Pratt <bs...@pr...> wrote:
>
>> If you think the issues are related to data conversion with msconvert, we
>> can help you with that.
>>
>> Downstream from there, you'll need to consult with the developers of
>> those tools. I guess that's the GNPS folks in this case?
>>
>> Best of luck to you!
>>
>> Brian
>>
>> On Mon, Oct 21, 2024 at 6:37 AM roshitha k r <ros...@gm...>
>> wrote:
>>
>>> Hi Brian,
>>>
>>> Good to hear from you,
>>>
>>> Here are some screenshots of our trials.
>>>
>>> I used to get a progress chart, and the analysis used to run for more
>>> than a day a few times, otherwise as shared in the picture, not even the
>>> progress chart would appear. The sad part is till now,  there have been no
>>> more than 3 compounds matched in my files which show multiple compounds in
>>> mass hunter software.
>>>
>>> Warm Regards,
>>> *Roshitha K R*
>>> *PhD Research Scholar*
>>> *Pharmaceutical Analysis*
>>> *NIPER Hyderabad*
>>>
>>>
>>>
>>>
>>> On Sun, Oct 20, 2024 at 10:09 PM Brian Pratt <bs...@pr...>
>>> wrote:
>>>
>>>> Hi Roshita K R,
>>>>
>>>> Let's see what we can do - show us what you've tried, and what errors
>>>> you're seeing. Screenshots are the easiest way to do that.
>>>>
>>>> Best regards,
>>>>
>>>> Brian Pratt
>>>>
>>>>
>>>> On Sun, Oct 20, 2024 at 1:33 AM roshitha k r <ros...@gm...>
>>>> wrote:
>>>>
>>>>> Dear proteowizard team ,
>>>>>
>>>>> I cannot get the library matching or molecular networking on the data
>>>>> converted from the Agilent QTOF system's .d file format to mzMl format.
>>>>>
>>>>> I am struggling to process my data.  Please help me out in this
>>>>>
>>>>> Warm Regards,
>>>>> *Roshitha K R*
>>>>> *PhD Research Scholar*
>>>>> *Pharmaceutical Analysis*
>>>>> *NIPER Hyderabad*
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> proteowizard-support mailing list
>>>>> pro...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/proteowizard-support
>>>>>
>>>>

If you think the issues are related to data conversion with msconvert, we
can help you with that.

Downstream from there, you'll need to consult with the developers of those
tools. I guess that's the GNPS folks in this case?

Best of luck to you!

Brian

On Mon, Oct 21, 2024 at 6:37 AM roshitha k r <ros...@gm...> wrote:

> Hi Brian,
>
> Good to hear from you,
>
> Here are some screenshots of our trials.
>
> I used to get a progress chart, and the analysis used to run for more than
> a day a few times, otherwise as shared in the picture, not even the
> progress chart would appear. The sad part is till now,  there have been no
> more than 3 compounds matched in my files which show multiple compounds in
> mass hunter software.
>
> Warm Regards,
> *Roshitha K R*
> *PhD Research Scholar*
> *Pharmaceutical Analysis*
> *NIPER Hyderabad*
>
>
>
>
> On Sun, Oct 20, 2024 at 10:09 PM Brian Pratt <bs...@pr...>
> wrote:
>
>> Hi Roshita K R,
>>
>> Let's see what we can do - show us what you've tried, and what errors
>> you're seeing. Screenshots are the easiest way to do that.
>>
>> Best regards,
>>
>> Brian Pratt
>>
>>
>> On Sun, Oct 20, 2024 at 1:33 AM roshitha k r <ros...@gm...>
>> wrote:
>>
>>> Dear proteowizard team ,
>>>
>>> I cannot get the library matching or molecular networking on the data
>>> converted from the Agilent QTOF system's .d file format to mzMl format.
>>>
>>> I am struggling to process my data.  Please help me out in this
>>>
>>> Warm Regards,
>>> *Roshitha K R*
>>> *PhD Research Scholar*
>>> *Pharmaceutical Analysis*
>>> *NIPER Hyderabad*
>>>
>>>
>>> _______________________________________________
>>> proteowizard-support mailing list
>>> pro...@li...
>>> https://lists.sourceforge.net/lists/listinfo/proteowizard-support
>>>
>>

Hi Roshita K R,

Let's see what we can do - show us what you've tried, and what errors
you're seeing. Screenshots are the easiest way to do that.

Best regards,

Brian Pratt


On Sun, Oct 20, 2024 at 1:33 AM roshitha k r <ros...@gm...> wrote:

> Dear proteowizard team ,
>
> I cannot get the library matching or molecular networking on the data
> converted from the Agilent QTOF system's .d file format to mzMl format.
>
> I am struggling to process my data.  Please help me out in this
>
> Warm Regards,
> *Roshitha K R*
> *PhD Research Scholar*
> *Pharmaceutical Analysis*
> *NIPER Hyderabad*
>
>
> _______________________________________________
> proteowizard-support mailing list
> pro...@li...
> https://lists.sourceforge.net/lists/listinfo/proteowizard-support
>

Dear proteowizard team ,

I cannot get the library matching or molecular networking on the data
converted from the Agilent QTOF system's .d file format to mzMl format.

I am struggling to process my data.  Please help me out in this

Warm Regards,
*Roshitha K R*
*PhD Research Scholar*
*Pharmaceutical Analysis*
*NIPER Hyderabad*

Maybe try a newer or older version of Docker? I've never encountered that error myself.


On 10/18/2024 6:57 PM, Charlie Bayne wrote:
>
> Hey Matt,
>
> Thanks for the quick response!
>
> Sorry I wasn’t clearer; I was using the actual paths to my data on my ubuntu host, which were as follows.
>
> docker run -it --rm -e WINEDEBUG=-all -v /home/nanopore-catalyst/scratch_analysis/15_DIA_HEK_Test_CB/raw_data:/data 
> chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert /data/DG23663.raw
>
> Also, I checked to make sure the file was present in the container at /data/DG23663.raw, and it was.
>
> Best,
>
> Charlie
>
> *From: *Chambers, Matthew <mat...@gm...>
> *Date: *Friday, October 18, 2024 at 3:26 PM
> *To: *Charlie Bayne <ch...@he...>, su...@pr... <su...@pr...>
> *Subject: *Re: [proteowizard-support] msconvert docker container
>
> Hi Charlie,
>
> You need to substitute "/your/data" with an actual path to your data on your Ubuntu host. Don't change the "/data" part (either after : or 
> for /data/file.raw). I assume you're not actually just passing file.raw, you're using a real filename?
>
> -Matt
>
> On 10/18/2024 4:46 PM, Charlie Bayne via proteowizard-support wrote:
>
>     Hi,
>
>     I have run into a problem using the docker container on Ubuntu when trying to follow the provided instructions
>     (https://hub.docker.com/r/chambm/pwiz-skyline-i-agree-to-the-vendor-licenses
>     <https://urldefense.com/v3/__https:/hub.docker.com/r/chambm/pwiz-skyline-i-agree-to-the-vendor-licenses__;!!LLK065n_VXAQ!iHcFfDlYkhGH3I2QdDfuthYs0u798UnPeNwFhaMZE4BxVT_9IZ7JweS-VXk58SjUR_F1XzaQR-v1xJyd6VQ8rswr6u8$>)
>
>
>     I am trying to can convert .raw files to mzML using:
>
>     docker run -it --rm -e WINEDEBUG=-all -v /your/data:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert /data/file.raw
>
>
>     Unfortunately, when I run the command, I get the error wine: socket: Function not implemented. Would you be able to help me figure out
>     how to resolve this issue? Thank you!
>
>     Best,
>
>     Charlie
>
>
>
>
>     _______________________________________________
>
>     proteowizard-support mailing list
>
>     pro...@li...
>
>     https://lists.sourceforge.net/lists/listinfo/proteowizard-support <https://urldefense.com/v3/__https:/lists.sourceforge.net/lists/listinfo/proteowizard-support__;!!LLK065n_VXAQ!iHcFfDlYkhGH3I2QdDfuthYs0u798UnPeNwFhaMZE4BxVT_9IZ7JweS-VXk58SjUR_F1XzaQR-v1xJyd6VQ8dGSgsLs$>
>

Hey Matt,

Thanks for the quick response!

Sorry I wasn’t clearer; I was using the actual paths to my data on my ubuntu host, which were as follows.

docker run -it --rm -e WINEDEBUG=-all -v /home/nanopore-catalyst/scratch_analysis/15_DIA_HEK_Test_CB/raw_data:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert /data/DG23663.raw

Also, I checked to make sure the file was present in the container at /data/DG23663.raw, and it was.


Best,
Charlie

From: Chambers, Matthew <mat...@gm...>
Date: Friday, October 18, 2024 at 3:26 PM
To: Charlie Bayne <ch...@he...>, su...@pr... <su...@pr...>
Subject: Re: [proteowizard-support] msconvert docker container
Hi Charlie,

You need to substitute "/your/data" with an actual path to your data on your Ubuntu host. Don't change the "/data" part (either after : or for /data/file.raw). I assume you're not actually just passing file.raw, you're using a real filename?

-Matt

On 10/18/2024 4:46 PM, Charlie Bayne via proteowizard-support wrote:
Hi,

I have run into a problem using the docker container on Ubuntu when trying to follow the provided instructions (https://hub.docker.com/r/chambm/pwiz-skyline-i-agree-to-the-vendor-licenses<https://urldefense.com/v3/__https:/hub.docker.com/r/chambm/pwiz-skyline-i-agree-to-the-vendor-licenses__;!!LLK065n_VXAQ!iHcFfDlYkhGH3I2QdDfuthYs0u798UnPeNwFhaMZE4BxVT_9IZ7JweS-VXk58SjUR_F1XzaQR-v1xJyd6VQ8rswr6u8$>)

I am trying to can convert .raw files to mzML using:

docker run -it --rm -e WINEDEBUG=-all -v /your/data:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert /data/file.raw

Unfortunately, when I run the command, I get the error wine: socket: Function not implemented. Would you be able to help me figure out how to resolve this issue? Thank you!


Best,
Charlie




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