Re: [spctools-discuss] Error generation while converting raw files

2021-01-24 Thread 'Luis Mendoza' via spctools-discuss 
Hello Giangiacomo,

You can use the Lib2html tool to convert an splib into a webpage with
clickable links to library spectra.  You can launch this tool from
SpectraST Tools -> Convert Libraries to HTML.

Hope this helps,
--Luis


On Thu, Jan 21, 2021 at 12:09 AM giangiacomo beretta <
giangiacomo.berett...@gmail.com> wrote:

> Hi David, sorry for the mistypos!
>
> Yes I run PeptideProphet under Analyze Peptides, and no relevant messages
> were generated :)
>
> However, I forgot to mention that the problem is related to
> interact.pep.xml processing in SpectraST in its command line version
> (independent from TPP).
>
> I am sorry, I did not notice that TPP includes an option for spectral
> library generation that works perfectly fine, and this is what I needed..!
>
> Just last question, is there any tool for visualisation/inpection of
> spectra in splib libraries ?
>
> Lots of thanks,
>
> Giangiacomo
>
> Il giorno giovedì 21 gennaio 2021 alle 01:24:47 UTC+1 David Shteynberg ha
> scritto:
>
>> I am not sure I know a tool called "ProptideProphet" ;) Perhaps you tried
>> to run PeptideProphet but it generated no results for you?  When you run
>> "Analyze Peptides" in the TPP interface, it should create a file called
>> interact.pep.xml by default, that will contain probabilities among other
>> information.  Did you run "Analyzed Peptides"?  Were there any messages
>> reported by the analysis?
>>
>> On Wed, Jan 20, 2021 at 1:30 AM giangiacomo beretta <
>> giangiacom...@gmail.com> wrote:
>>
>>> Hi David! It works nicely, thank you !
>>>
>>> Now I am experiencing another issue of mine :)
>>>
>>> I run ProptideProphet on the XML fiel generated by XTandem. I need this
>>> file presuming that PP will add probabilities to the identified peptides as
>>> this is requested by SpectraST to generate the corresponding spectral
>>> library (this is actually my final goal).
>>>
>>> However, when I try to do it, SpectraST reports: WARNING -- PEPXML
>>> IMPORT: Importing a .pep.xml file with no probabilities. PeptideProphet
>>> probably needs to be run on .pep.xml first.
>>>
>>> Maybe probabilities are used for data processing but not appendend to
>>> the XML output file?
>>>
>>> Thanks a lot in advance!
>>>
>>> G
>>>
>>> Il giorno martedì 19 gennaio 2021 alle 20:53:57 UTC+1 David Shteynberg
>>> ha scritto:
>>>
 Dear Giangiacomo,

 Thanks for trying the TPP and reporting the problem.  TPP uses the
 proteowizard's msconvert tools for this step.  You can remedy the problem
 by either upgrading to a newer version of proteowizard's msconvert tool or
 use  --ignoreUnknownInstrumentError option with your current version.  On
 the generate mzML page you can specify this option in the"Enter
 additional options to pass directly to the command-line" text box, just
 enter the text  --ignoreUnknownInstrumentError

 Hope it works!

 Cheers,
 -David


 On Tue, Jan 19, 2021 at 8:10 AM giangiacomo beretta <
 giangiacom...@gmail.com> wrote:

> Hi, when I try to convert raw files, the conversion tool stops
> immediately reporting the following error:
>
> Reader_Thermo::fillInMetadata] unable to parse instrument model;
> please report this error to the ProteoWizard developers with this
> information: model(Orbitrap Eclipse) name(Orbitrap Eclipse); if want to
> convert the file anyway, use the ignoreUnknownInstrumentError flag
>
> It appears that the system is not recognizing the instrument model
> that produced the raw files. Is there any option to overcome this issue?
>
> Actually I have converted the same files with ProteoWizard without
> troubles.
>
> Thanks in advance!
>
> G
>
> --
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> 
> .
>
 --
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>>> 
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>>>
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Re: [spctools-discuss] Error generation while converting raw files

2021-01-21 Thread giangiacomo beretta 
Hi David, sorry for the mistypos!

Yes I run PeptideProphet under Analyze Peptides, and no relevant messages 
were generated :)

However, I forgot to mention that the problem is related to 
interact.pep.xml processing in SpectraST in its command line version 
(independent from TPP).

I am sorry, I did not notice that TPP includes an option for spectral 
library generation that works perfectly fine, and this is what I needed..! 

Just last question, is there any tool for visualisation/inpection of 
spectra in splib libraries ?

Lots of thanks,

Giangiacomo
 
Il giorno giovedì 21 gennaio 2021 alle 01:24:47 UTC+1 David Shteynberg ha 
scritto:

> I am not sure I know a tool called "ProptideProphet" ;) Perhaps you tried 
> to run PeptideProphet but it generated no results for you?  When you run 
> "Analyze Peptides" in the TPP interface, it should create a file called 
> interact.pep.xml by default, that will contain probabilities among other 
> information.  Did you run "Analyzed Peptides"?  Were there any messages 
> reported by the analysis?
>
> On Wed, Jan 20, 2021 at 1:30 AM giangiacomo beretta <
> giangiacom...@gmail.com> wrote:
>
>> Hi David! It works nicely, thank you ! 
>>
>> Now I am experiencing another issue of mine :)
>>
>> I run ProptideProphet on the XML fiel generated by XTandem. I need this 
>> file presuming that PP will add probabilities to the identified peptides as 
>> this is requested by SpectraST to generate the corresponding spectral 
>> library (this is actually my final goal).
>>
>> However, when I try to do it, SpectraST reports: WARNING -- PEPXML 
>> IMPORT: Importing a .pep.xml file with no probabilities. PeptideProphet 
>> probably needs to be run on .pep.xml first.
>>
>> Maybe probabilities are used for data processing but not appendend to the 
>> XML output file?
>>
>> Thanks a lot in advance!
>>
>> G
>>
>> Il giorno martedì 19 gennaio 2021 alle 20:53:57 UTC+1 David Shteynberg ha 
>> scritto:
>>
>>> Dear Giangiacomo,
>>>
>>> Thanks for trying the TPP and reporting the problem.  TPP uses the 
>>> proteowizard's msconvert tools for this step.  You can remedy the problem 
>>> by either upgrading to a newer version of proteowizard's msconvert tool or 
>>> use  --ignoreUnknownInstrumentError option with your current version.  On 
>>> the generate mzML page you can specify this option in the"Enter 
>>> additional options to pass directly to the command-line" text box, just 
>>> enter the text  --ignoreUnknownInstrumentError 
>>>
>>> Hope it works!
>>>
>>> Cheers,
>>> -David   
>>>
>>>
>>> On Tue, Jan 19, 2021 at 8:10 AM giangiacomo beretta <
>>> giangiacom...@gmail.com> wrote:
>>>
 Hi, when I try to convert raw files, the conversion tool stops 
 immediately reporting the following error:

 Reader_Thermo::fillInMetadata] unable to parse instrument model; please 
 report this error to the ProteoWizard developers with this information: 
 model(Orbitrap Eclipse) name(Orbitrap Eclipse); if want to convert the 
 file 
 anyway, use the ignoreUnknownInstrumentError flag 

 It appears that the system is not recognizing the instrument model that 
 produced the raw files. Is there any option to overcome this issue?

 Actually I have converted the same files with ProteoWizard without 
 troubles.

 Thanks in advance!

 G

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 https://groups.google.com/d/msgid/spctools-discuss/2134bb9e-bb7e-4f52-9afc-bf59b75f21aen%40googlegroups.com
  
 
 .

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>>
> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/spctools-discuss/95da30b4-f9d1-49cc-896e-fe734ba0cac4n%40googlegroups.com
>>  
>> 
>> .
>>
>

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Re: [spctools-discuss] Error generation while converting raw files

2021-01-20 Thread 'David Shteynberg' via spctools-discuss 
I am not sure I know a tool called "ProptideProphet" ;) Perhaps you tried
to run PeptideProphet but it generated no results for you?  When you run
"Analyze Peptides" in the TPP interface, it should create a file called
interact.pep.xml by default, that will contain probabilities among other
information.  Did you run "Analyzed Peptides"?  Were there any messages
reported by the analysis?

On Wed, Jan 20, 2021 at 1:30 AM giangiacomo beretta <
giangiacomo.berett...@gmail.com> wrote:

> Hi David! It works nicely, thank you !
>
> Now I am experiencing another issue of mine :)
>
> I run ProptideProphet on the XML fiel generated by XTandem. I need this
> file presuming that PP will add probabilities to the identified peptides as
> this is requested by SpectraST to generate the corresponding spectral
> library (this is actually my final goal).
>
> However, when I try to do it, SpectraST reports: WARNING -- PEPXML IMPORT:
> Importing a .pep.xml file with no probabilities. PeptideProphet probably
> needs to be run on .pep.xml first.
>
> Maybe probabilities are used for data processing but not appendend to the
> XML output file?
>
> Thanks a lot in advance!
>
> G
>
> Il giorno martedì 19 gennaio 2021 alle 20:53:57 UTC+1 David Shteynberg ha
> scritto:
>
>> Dear Giangiacomo,
>>
>> Thanks for trying the TPP and reporting the problem.  TPP uses the
>> proteowizard's msconvert tools for this step.  You can remedy the problem
>> by either upgrading to a newer version of proteowizard's msconvert tool or
>> use  --ignoreUnknownInstrumentError option with your current version.  On
>> the generate mzML page you can specify this option in the"Enter
>> additional options to pass directly to the command-line" text box, just
>> enter the text  --ignoreUnknownInstrumentError
>>
>> Hope it works!
>>
>> Cheers,
>> -David
>>
>>
>> On Tue, Jan 19, 2021 at 8:10 AM giangiacomo beretta <
>> giangiacom...@gmail.com> wrote:
>>
>>> Hi, when I try to convert raw files, the conversion tool stops
>>> immediately reporting the following error:
>>>
>>> Reader_Thermo::fillInMetadata] unable to parse instrument model; please
>>> report this error to the ProteoWizard developers with this information:
>>> model(Orbitrap Eclipse) name(Orbitrap Eclipse); if want to convert the file
>>> anyway, use the ignoreUnknownInstrumentError flag
>>>
>>> It appears that the system is not recognizing the instrument model that
>>> produced the raw files. Is there any option to overcome this issue?
>>>
>>> Actually I have converted the same files with ProteoWizard without
>>> troubles.
>>>
>>> Thanks in advance!
>>>
>>> G
>>>
>>> --
>>> 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-discu...@googlegroups.com.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/spctools-discuss/2134bb9e-bb7e-4f52-9afc-bf59b75f21aen%40googlegroups.com
>>> 
>>> .
>>>
>> --
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> 
> .
>

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Re: [spctools-discuss] Error generation while converting raw files

2021-01-20 Thread giangiacomo beretta 
Hi David! It works nicely, thank you ! 

Now I am experiencing another issue of mine :)

I run ProptideProphet on the XML fiel generated by XTandem. I need this 
file presuming that PP will add probabilities to the identified peptides as 
this is requested by SpectraST to generate the corresponding spectral 
library (this is actually my final goal).

However, when I try to do it, SpectraST reports: WARNING -- PEPXML IMPORT: 
Importing a .pep.xml file with no probabilities. PeptideProphet probably 
needs to be run on .pep.xml first.

Maybe probabilities are used for data processing but not appendend to the 
XML output file?

Thanks a lot in advance!

G

Il giorno martedì 19 gennaio 2021 alle 20:53:57 UTC+1 David Shteynberg ha 
scritto:

> Dear Giangiacomo,
>
> Thanks for trying the TPP and reporting the problem.  TPP uses the 
> proteowizard's msconvert tools for this step.  You can remedy the problem 
> by either upgrading to a newer version of proteowizard's msconvert tool or 
> use  --ignoreUnknownInstrumentError option with your current version.  On 
> the generate mzML page you can specify this option in the"Enter 
> additional options to pass directly to the command-line" text box, just 
> enter the text  --ignoreUnknownInstrumentError 
>
> Hope it works!
>
> Cheers,
> -David   
>
>
> On Tue, Jan 19, 2021 at 8:10 AM giangiacomo beretta <
> giangiacom...@gmail.com> wrote:
>
>> Hi, when I try to convert raw files, the conversion tool stops 
>> immediately reporting the following error:
>>
>> Reader_Thermo::fillInMetadata] unable to parse instrument model; please 
>> report this error to the ProteoWizard developers with this information: 
>> model(Orbitrap Eclipse) name(Orbitrap Eclipse); if want to convert the file 
>> anyway, use the ignoreUnknownInstrumentError flag 
>>
>> It appears that the system is not recognizing the instrument model that 
>> produced the raw files. Is there any option to overcome this issue?
>>
>> Actually I have converted the same files with ProteoWizard without 
>> troubles.
>>
>> Thanks in advance!
>>
>> G
>>
>> -- 
>> 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-discu...@googlegroups.com.
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/spctools-discuss/2134bb9e-bb7e-4f52-9afc-bf59b75f21aen%40googlegroups.com
>>  
>> 
>> .
>>
>

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Re: [spctools-discuss] Error generation while converting raw files

2021-01-19 Thread 'David Shteynberg' via spctools-discuss 
Dear Giangiacomo,

Thanks for trying the TPP and reporting the problem.  TPP uses the
proteowizard's msconvert tools for this step.  You can remedy the problem
by either upgrading to a newer version of proteowizard's msconvert tool or
use  --ignoreUnknownInstrumentError option with your current version.  On
the generate mzML page you can specify this option in the"Enter
additional options to pass directly to the command-line" text box, just
enter the text  --ignoreUnknownInstrumentError

Hope it works!

Cheers,
-David


On Tue, Jan 19, 2021 at 8:10 AM giangiacomo beretta <
giangiacomo.berett...@gmail.com> wrote:

> Hi, when I try to convert raw files, the conversion tool stops immediately
> reporting the following error:
>
> Reader_Thermo::fillInMetadata] unable to parse instrument model; please
> report this error to the ProteoWizard developers with this information:
> model(Orbitrap Eclipse) name(Orbitrap Eclipse); if want to convert the file
> anyway, use the ignoreUnknownInstrumentError flag
>
> It appears that the system is not recognizing the instrument model that
> produced the raw files. Is there any option to overcome this issue?
>
> Actually I have converted the same files with ProteoWizard without
> troubles.
>
> Thanks in advance!
>
> G
>
> --
> 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/2134bb9e-bb7e-4f52-9afc-bf59b75f21aen%40googlegroups.com
> 
> .
>

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