| Beiträge 1-10 des Diskussionsthemas "Convert HP ChemStation 3D MSD data to ASCII?" |
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Dear all,
I am new to the list and do not know if the problem has been voiced an answered
before. If yes, pls point me to the right direction.
I am looking for a way to convert the entire HP Chemstation MSD data file into
ASCII format. It can be a macro or an independent program. I have found in the
ChemStation itself only a feature to convert either selected chromatogram or
spectrum to an ASCII file. Does anyone have experience with the same problem?
Thanks a lot for your help,
Dr. Pham Tuan Hai
Unilever Research Vlaardingen
Central Analytical Sciences / A4471
Postbox 114
3130 AC Vlaardingen
The Netherlands
Tel: 0031-10-460 55 46
Fax: 0031-10-460 56 71
__________________________________________________
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Oh, I have but did not find the right answer. Maybe somebody else has done it.
Thanks anyway.
Hai
--- stms <cminvms@acme.gatech.edu> wrote:
} Try the archived questions/answers at the sci.techniques.mass-spec website
} at <http://www.chemistry.gatech.edu/stms> under archives-by-topic in the
} computer section.
} Thanks,
} Sarah Shealy
} backup moderator for sci.techniques.mass-spec
}
} At 05:02 AM 8/14/01 -0700, you wrote:
} }Dear all,
} }
} }I am new to the list and do not know if the problem has been voiced an
} }answered
} }before. If yes, pls point me to the right direction.
} }
} }I am looking for a way to convert the entire HP Chemstation MSD data file into
} }ASCII format. It can be a macro or an independent program. I have found in the
} }ChemStation itself only a feature to convert either selected chromatogram or
} }spectrum to an ASCII file. Does anyone have experience with the same problem?
} }
} }Thanks a lot for your help,
} }Dr. Pham Tuan Hai
} }Unilever Research Vlaardingen
} }Central Analytical Sciences / A4471
} }Postbox 114
} }3130 AC Vlaardingen
} }The Netherlands
} }Tel: 0031-10-460 55 46
} }Fax: 0031-10-460 56 71
} }
} }__________________________________________________
} }Do You Yahoo!?
} }Make international calls for as low as $.04/minute with Yahoo! Messenger
} }http://phonecard.yahoo.com/
}
__________________________________________________
Do You Yahoo!?
Make international calls for as low as $.04/minute with Yahoo! Messenger
http://phonecard.yahoo.com/
There is a program from ChemSW that will do this. http://www.chemsw.com. The
program is called GC GCMS File Translator. There are two versions. You
probably can get by with the cheaper one. There is also a program available
from Palisade software, http://www.palisade.com, for a lot more money. This
is called Mass Transit.
The subject line of your message makes me think that you believe that both
MS and chromatographic data are stored in a GC/MS or LC/MS data file. This
is incorrect. The data stored are mass spectral data of m/z value and
intensity pairs for each spectrum acquired. Chromatograms are reconstructed
from these mass spectral data either by summing all the intensities with in
each mass spectrum and plotting this summed intensity as a function of the
spectrum number, which is also a function of time (the reconstructed total
ion current chromatogram -- RTICC) or by plotting the intensities of one are
more ions with in each mass spectrum as a function of time (the mass
chromatogram -- or RIC on the ChemStation).
Regards;
David
--
O. David Sparkman
Consultant-At-Large
ods@compuserve.com
"Pham Tuan Hai" <PhamTuanHai@rocketmail.com> wrote in message
news:9lbljl$tp$1@news-int.gatech.edu...
} Oh, I have but did not find the right answer. Maybe somebody else has done it.
} Thanks anyway.
} Hai
}
} --- stms <cminvms@acme.gatech.edu> wrote:
} } Try the archived questions/answers at the sci.techniques.mass-spec website
} } at <http://www.chemistry.gatech.edu/stms> under archives-by-topic in the
} } computer section.
} } Thanks,
} } Sarah Shealy
} } backup moderator for sci.techniques.mass-spec
} }
} } At 05:02 AM 8/14/01 -0700, you wrote:
} } }Dear all,
} } }
} } }I am new to the list and do not know if the problem has been voiced an
} } }answered
} } }before. If yes, pls point me to the right direction.
} } }
Lesen Sie den Rest der Nachricht... (38 zusätzliche Zeilen)
On Tue, 14 Aug 2001 05:02:03 -0700 (PDT), Pham Tuan Hai wrote:
} I am looking for a way to convert the entire HP Chemstation MSD data file into
} ASCII format. It can be a macro or an independent program.
I don't know what you want to do with these ASCII data, and I don't
know in which form you need them, so I have to guess ... but three
possibilities come to mind:
(1) Export dataset as netCDF file, then use 'MSGraph' (available at
http://www.mysunrise.ch/users/joerg.hau/sci/msgraph/). This program can
export mass spectra, chromatograms or a complete run (!) as ASCII
data. However, it's limited to integer mass processing.
(2) Export dataset as netCDF file (as above), then use a home-made
program to access the netCDF data directly. 'cdf2msg' is available at
the same URL as above (with source code) and will require only a few
modifications to do what you need.
(3) ... and of course you could [have someone] write a macro that writes
them out spectrum-by-spectrum, but that's programming-at-large again.
HTH,
-- Joerg
------------------------------------------------------------
joerg.hau(at)swissonline.ch * Lausanne, Switzerland
http://www.diax.ch/users/joerg.hau/
"All standard disclaimers apply".
Pham Tuan Hai wrote:
} I am looking for a way to convert the entire HP Chemstation MSD data file into
} ASCII format. It can be a macro...
Nazdar,
!HP2ASCII.MAC starts here
name HP2ASCII
!***
!*** this macro fully converts a HP Chemstation file to ASCII or JCAMP-DX
!*** (c)TK4ICBINB
!*** if an error occours during macro execution:false line break in macro
!***
!***(1) load a GC-MS file in HP Chemstation
!***(2) Choose Options Dialog Box --> Command line
!***(3) enter "macro" at command line and load HP2ASCII
!***(4) enter HP2ASCII at the command line to start
!***(5) Choose an option TIC+MS, TIC, JCAMP-DX
!***(6) Read in with XCL with ";" separator
!*** (from the actual HP data path)
!***
!*** possible files are : xMSspec.txt, xspecrow.txt,
!*** xTIConly.txt , JCMPGCMS.jdx
!*** BEWARE: XCL can read only a 256x65536 matrix!!! Yes 3x!
LOCAL label, button, choice
SDim label, 4
SDim button, 3
label[1] = "TIC+spectra nice output"
label[2] = "TIC+spectra ín one line"
label[3] = "Only TIC"
label[4] = "JCAMP 4 Lib2NIST"
button[1] = ""
button[2] = "OK"
button[3] = ""
choice = 1
INPUT6 3, 4,"HP2ASCII", label, button, choice
mychoice = choice
POINTS R0 ! Get scan range in NPOINTS
lowscan = 1
highscan = NPOINTS
if (mychoice = 1) then
NiceOutput
endif
if (mychoice = 2) then
LineOutput
endif
if (mychoice = 3) then
TICOutput
endIF
if (mychoice = 4) then
JCAMP4Lib2NIST
endIF
CLOSE #1
Alert "Beware: EXCEL is only 8-bit!",2
return
name NiceOutput
fileName$ = _DATAPATH$+_DATAFILE$ + "\xMSspec.txt"
OPEN fileName$ FOR OUTPUT AS #1
!change for header line output
PRINT USING #1,"%;%;%;%;%;%/","Scan","Time","TIC","MSPeaks","Mass","Abund"
i = 1
while i <= highscan
scan i
points x !get the number of spectra points
!***array starts from 0 , scans start from 1 aarrgghh
PRINT USING #1, "#;#.###;#;#/",i,r0[i-1,0],r0[i-1,1],NPOINTS
!*****************************************
!*** write out the mass pairs
masscount = 0 !array starts from zero
while masscount < NPOINTS
!*** take care !
!*** if you want true mass values use #.###
!*** and remove the round() function
!*** give out mass, abundance
print using #1 ,";;;;#.##;#/",round(x[masscount,0]),x[masscount,1]
masscount = masscount+1
endwhile
!*****************************************
i = i+1
print i
endwhile
return
name LineOutput
fileName$ = _DATAPATH$+_DATAFILE$ + "\xspecrow.txt"
OPEN fileName$ FOR OUTPUT AS #1
!header line output
PRINT USING #1,"%;%;%;%;%;%/","Scan","Time","TIC","MSPeaks","Mass","Abund"
i = 1
while i <= highscan
scan i
points x !get the number of spectra points
!***array starts from 0 , scans start from 1 aarrgghh
PRINT USING #1, "#;#.###;#;#",i,r0[i-1,0],r0[i-1,1],NPOINTS
!*****************************************
!*** write out the mass pairs
masscount = 0 !array starts from zero
while masscount < NPOINTS
! All spectra in one line
print using #1 ,";#.##;#",round(x[masscount,0]),x[masscount,1]
masscount = masscount+1
endwhile
!*****************************************
print using #1, "/"
i = i+1
print i
endwhile
return
name TICOutput
fileName$ = _DATAPATH$+_DATAFILE$ + "\xTIConly.txt"
OPEN fileName$ FOR OUTPUT AS #1
PRINT USING #1, "%;%;%;%;/","Scan","Time","TIC","MSPeaks"
i = 1
while i <= highscan
scan i
points x !get the number of spectra points
!***array starts from 0 , scans start from 1 aarrgghh
PRINT USING #1, "#;#.###;#;#/",i,r0[i-1,0],r0[i-1,1],NPOINTS
i = i+1
print i
endwhile
return
name JCAMP4Lib2NIST
! HP Chemstation GC-MS file to JCAMP-DX (HP2JCAMP)
! my contribution to the IUPAC year :-)
! but anyway, it would be better to use AMDIS32 and Lib2NIST
! and use only pure extracted peaks...
! for JCAMP look at
! http://wwwchem.uwimona.edu.jm:1104/software/jcampdx.html
! http://www.isas-dortmund.de/projects/jcamp/
! no compressed format -> ever built a hashtable in Chemstation ?
fileName$ = _DATAPATH$+_DATAFILE$ + "\JCMPGCMS.jdx"
OPEN fileName$ FOR OUTPUT AS #1
i = 1
while i <= highscan
scan i
points x !get the number of spectra points
!***array starts from 0 , scans start from 1 aarrgghh
PRINT USING #1, "% % %#/","##TITLE=",_DATAFILE$,"Scan ",i
PRINT #1, "##JCAMPDX= Revision 5.0"
PRINT #1, "##DATA TYPE= MASS SPECTRUM"
PRINT #1, "##DATA CLASS= PEAK TABLE"
PRINT #1, "##XUNITS= m/z"
PRINT #1, "##YUNITS= RELATIVE ABUNDANCE"
PRINT USING #1, "% #/", "##NPOINTS=", NPOINTS
PRINT #1, "##PEAK TABLE= (XY..XY)"
!*****************************************
!*** write out the mass pairs
masscount = 0 !array starts from zero
while masscount < NPOINTS
!*** take care !
!*** if you want true mass values use #.###
!*** and remove the round() function
!*** give out mass, abundance
print using #1 ,"# #/",round(x[masscount,0]),x[masscount,1]
masscount = masscount+1
endwhile
!*****************************************
i = i+1
print i
endwhile
return
!*** HP2ASCII.MAC ends here
With kind regards
Tobias Kind
PS:
I still can´t decide wether to take ICBINB
http://www.tasteyoulove.com/product/index.html
or My Three Suns
http://home.nikocity.de/stoesser/Tierrechte/txt/futurama.html
:-)
Just to be pedantic :-) ChemStation files actually store the RTICC
information in the data file. Each scan has a header record which specifies
the number of peaks in the scan, the base peak, retention time, etc, and
also the TIC for that scan.
--
Dave White
SpectraChrom Software
www.spectrachrom.com
dave(underscore)white@spectrachrom.com replace the (underscore) with _ to
e-mail directly
"David Sparkman" <ods@compuserve.com> wrote in message
news:9lj5ls$auj$1@news-int.gatech.edu...
snip
} is incorrect. The data stored are mass spectral data of m/z value and
} intensity pairs for each spectrum acquired. Chromatograms are reconstructed
} from these mass spectral data either by summing all the intensities with in
} each mass spectrum and plotting this summed intensity as a function of the
} spectrum number, which is also a function of time (the reconstructed total
} ion current chromatogram -- RTICC) or by plotting the intensities of one
are
Tobias,
Good stuff, however Pham requires a macro for the LC/MS CHEMSTATION and it
ain't the same
macro language or at least a lot different !!
Phil
"Tobias Kind" <kind@rziris.rz.uni-leipzig.de> a écrit dans le message news:
9lm5im$7h1$1@news-int.gatech.edu...
}
}
} Pham Tuan Hai wrote:
}
} } I am looking for a way to convert the entire HP Chemstation MSD data file into
} } ASCII format. It can be a macro...
}
}
}
} Nazdar,
}
} !HP2ASCII.MAC starts here
}
} name HP2ASCII
} !***
} !*** this macro fully converts a HP Chemstation file to ASCII or JCAMP-DX
} !*** (c)TK4ICBINB
} !*** if an error occours during macro execution:false line break in macro
} !***
} !***(1) load a GC-MS file in HP Chemstation
} !***(2) Choose Options Dialog Box --> Command line
} !***(3) enter "macro" at command line and load HP2ASCII
} !***(4) enter HP2ASCII at the command line to start
} !***(5) Choose an option TIC+MS, TIC, JCAMP-DX
} !***(6) Read in with XCL with ";" separator
} !*** (from the actual HP data path)
} !***
} !*** possible files are : xMSspec.txt, xspecrow.txt,
} !*** xTIConly.txt , JCMPGCMS.jdx
} !*** BEWARE: XCL can read only a 256x65536 matrix!!! Yes 3x!
}
}
}
} LOCAL label, button, choice
} SDim label, 4
} SDim button, 3
} label[1] = "TIC+spectra nice output"
Lesen Sie den Rest der Nachricht... (183 zusätzliche Zeilen)
Ehmmm ... to be even more pedantic ;-) the ChemStation data
file also has so called "directory records" behind all the spectral
records which consist of
1 - a pointer to the spectral record,
2 - retention time, and
3 - total ion abundance at this retention time.
Neglecting the pointer, this basically is the Total Ion Chromatogram!
This and more details were documented in the HP-UX ChemStation
manual, for instance.
Volker Haeupl - vh@quasium.com
"Dave White" <dave_white@spectrachrom.com> wrote in message
} news:9lm5k0$7h4$1@news-int.gatech.edu...
} Just to be pedantic :-) ChemStation files actually store the RTICC
} information in the data file. Each scan has a header record which specifies
} the number of peaks in the scan, the base peak, retention time, etc, and
} also the TIC for that scan.
}
} --
} Dave White
} SpectraChrom Software
} www.spectrachrom.com
} dave(underscore)white@spectrachrom.com replace the (underscore) with _ to
} e-mail directly
Hi Tobias, Phil, Joerg et all.
Yes, sorry that I did not make it clear in the first message (call for help). I
was talking about the LC/MS data and it seems that the macro you've sent me is
not compatible. I tried to load it into the ChemStation and got the syntax
error message.
The HP ChemStation does not have to ability to export data set into net CDF
file, so the option to use MSgraph is also not OK.
I should explain a bit more about the purpose of having data in the ASCII
format. We want to play around with retention time shifting problem, then do
the PCA analysis for a set of data. This will be done by an data science guy in
our group. I am responsible for providing the data, but he will need them in
ASCII format to play around. Data taken on the MassLynx system has no such
problem due to the built in option for conversion. HP does not provide an
explicite function. That why I am asking for help.
Hai
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Phil wrote:
} Tobias,
}
} Good stuff, however Pham requires a macro for the LC/MS CHEMSTATION and it
} ain't the same
} macro language or at least a lot different !!
Dear Phil,
yes! But my data system also has a RP18 column in the Agilent picture book. :-)
or :-(
[Maybe Pham Tuan Hai can answer if he has HP G1047A LC/MS Software or G2710AA
system ?
he already answered ]
And I know Lin DeNoyer claims to know how to read HP LC/MS ChemStation data.
And maybe he can send the header format and I will write a converter for a
piece of ICBINB...
PS:
Mmmhh... Philippe I found you in 167 out of my 1400 macros - so I guess
you also know the HP 3D LC/MS Chemstation format ?? :-)
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