LIMS integration

[tonydas]

Hi,

Our lab is interested in integrating our agilent instruments with our labware lims software. Basically, I want to know how to get this process started. We primarily want to integrate our FID and GC-MS TIC's and also the MS spectra.

Also, want to know if there is any way to alter the search algorithm for MS chemstation matching. As well, is there any program that can check the peaks RRT's and mass spectrum against a database and say if it is a match.

Sorry if this is confusing, I just want the computer or software to do a tech review or checks on the RRT's and spectra that the instrument produce. Want this to be automated.

Thanks.

[tonydas]

Can no one help? Any advice would help.

[zegockie]

One of the approaches could be to do checks using chemstation software, save reports as pdfs and then store pdfs in LIMS. I have no idea what automated MS searching algorithm beside PBM you can use for this purpose.
Ask your LIMS support how to store pdf documents in lims.
To make all this working smoothly will take quite a while. Good luck.

[tonydas]

The issue is we have very little support from labware lims directly, but is there no way to get a software to check the RRT's against a database. Would you know how to setup a calibration table in MSD chemstation to get the peaks to label?

Would you know how to get your blanks to print out automatically alongside on every single TIC of samples run after a blank? Do you have any reports I could try out.

I have tried uploading PDF's to LIMS and am aware how to do it.

Thank you for replying.

[antonk]

AMDIS works with Agilent libraries and data files.
AMDIS can export data in .msp - text file
AMDIS can be run in batch mode - you create .job file, invoke AMDIS - get reports.
Job control and MSP file formats described in help

[eselmeister]

You could try to utilize OpenChrom:
https://openchrom.net

A new release is scheduled for end of this month. OpenChrom is able to process MSD as wellas FID data. We also offer an AMDIS connector with additional filter settings as well as the possibility to use *.msl libraries for own purposes.

Please contact us for additional information.

[zegockie]

If you know Chemstation macros it is not difficult (but will take some time) to design a macro which will do PBM library search, compare RT's with database (list of compounds and their RTs), and printout TIC or what so ever of your samples with marked peaks. You can design print output how ever you want, including blanks etc and print them on paper or as PDFs. I designed such things for my lab purposes.

[tonydas]

Thank you for your replies. I am familiar with macros to a certain extent. Would you have any sample reports I could build upon if you don't mind sharing? I just need a start to help me in the right direction.

Basically, we a .mac file in the msexe folder of the gc-ms software that can be called up from the data analysis program using the command bar to print certain macros/reports from the .mac file.

How would you get a blank TIC to print out alongside (same page) every single sample TIC that was run after the blank. There are multiple users for each GC-MS here.

I really hope you can help.

[zegockie]

What instrument(s) and Chemstation are you using? Are you in US or abroad?

[tonydas]

So we have 7890A and 7890B's with 5975C and 5977's.

Our chemstations range from E.02.02.1431 to F.01.01.2317.

Is it even possible to get a blank TIC to print out on the same page as a sample TIC and have it be automated after the sample run is done?

Do you know what the sample type selection does when making a sequence? Does it have any significance when choosing 'blank' or 'sample'? Would this be a means to do what I am asking for?

Thanks a lot.

[zegockie]

I have experience with E02.02 and have no idea about F version. They may be compatible or not (you can ask Agilent). Regarding macros: it is possible to do what you are asking but it is time consuming. Unless you are comfortable with macro design and willing to invest considerable time to accomplish this it is better to hire a professional. Good luck.

[varossf]

It might be that what you are seeking is now available in OpenLAB 2.1.
GC/MS control and data acquisition
RRT peak identification
AUtomated comparison against a stored spectrum peak compound (in the compound table)
Ion Qualifiers
Automated searches against NIST/AMDIS