an example of such complex equipment is a liquid chromatography - tandem mass spectrometry ( lc - ms / ms ) system , which , in recent years has become a frequent addition to clinical laboratories for a variety of applications including testing for drugs of abuse , therapeutic drug monitoring and steroid analysis.[36 ] such devices offer high potential sample throughput , but , as they are not currently accompanied by vendor - supplied interfaces to enable them to be connected to a laboratory information system ( lis ) , they also impose a potentially burdensome requirement for manual data transfer with the concomitant risk of transcription errors . to the authors knowledge ,
the only commercially available software to software interface that exists for the mass spectrometer in use here , is from data innovations llc ( south burlington , vermont , usa ) .
the advantage of using a commercially available product is that the company already has software developed for a number of different instruments and the laboratory does not require expertise in computer programing to implement such an interface .
however , the disadvantages are the significant cost of such an interface and the decrease in control and ease of adaptability of such a product as far as the laboratory is concerned .
a group in the department of pathology at the university of pittsburgh medical center developed a data management interface to help solve this problem successfully interfacing a waters 2795 lc - ms / ms to a sunquest lis .
we describe here the implementation of the same data management interface using the same lis , but a different mass spectrometer that is in use in our laboratory and we extend their work by describing the pre - processor code that was required to convert the data output from the mass spectrometer into a format accepted by the lis .
the targeted analytical mass spectrometer was the ab sciex  5500 qtrap ( ab sciex , foster city , ca ) coupled to a shimadzu prominence uflc ( ultra - fast liquid chromatography , shimadzu scientific instruments , pleasanton , ca ) lc system .
the standalone computer running the lc - ms / ms was a dell optiplex 960 that uses the microsoft windows 7 operating system ( microsoft corporation , redmond , wa ) . the analyst 1.5.1 application ( ab sciex , foster city , ca ) acquires data from the mass spectrometer and generates a results table upon the user 's request .
a text file ( txt ) of the results table can then be exported from analyst by the user and saved in the appropriate folder .
the data management software was licensed from the university of pittsburgh ( automated file transfer for mim batch style interfaces ; id01516 ) .
the data management software and the other support modules are written in autohotkey ( ahk ) , a free open - source scripting language for automating activities on a computer operating under the windows operating system .
both the compiled executable programs and the source text files are included with the data management software .
the software program was installed solely on the computer running the lc - ms / ms system .
the lis utilized was sunquest ( sunquest information systems inc . , tuscon , az ) .
standard parameters such as analyzer and assay identification codes as well as quality control ( qc ) definitions for the lc - ms / ms assay were defined by adding them to the sunquest maintenance , using the straightforward and well - documented methods provided by the vendor .
the targeted analytical mass spectrometer was the ab sciex  5500 qtrap ( ab sciex , foster city , ca ) coupled to a shimadzu prominence uflc ( ultra - fast liquid chromatography , shimadzu scientific instruments , pleasanton , ca ) lc system .
the standalone computer running the lc - ms / ms was a dell optiplex 960 that uses the microsoft windows 7 operating system ( microsoft corporation , redmond , wa ) . the analyst 1.5.1 application ( ab sciex , foster city , ca ) acquires data from the mass spectrometer and generates a results table upon the user 's request .
a text file ( txt ) of the results table can then be exported from analyst by the user and saved in the appropriate folder .
the data management software was licensed from the university of pittsburgh ( automated file transfer for mim batch style interfaces ; id01516 ) . the data management software and the other support modules are written in autohotkey ( ahk ) , a free open - source scripting language for automating activities on a computer operating under the windows operating system .
both the compiled executable programs and the source text files are included with the data management software .
the software program was installed solely on the computer running the lc - ms / ms system .
the lis utilized was sunquest ( sunquest information systems inc . , tuscon , az ) .
standard parameters such as analyzer and assay identification codes as well as quality control ( qc ) definitions for the lc - ms / ms assay were defined by adding them to the sunquest maintenance , using the straightforward and well - documented methods provided by the vendor .
four discrete data are required to successfully transmit an individual patient result from the lc - ms / ms output text file to sunquest : the unique patient container identification number ( cid - a barcode affixed to the patient sample container that is scanned by a barcode reader , electronically entering the cid into the lc - ms / ms software ) ; the sunquest test code for the assay being performed ( in this case test code ptes for pediatric total testosterone ) ; the assay result for each patient and the qc data ( the total testosterone concentrations obtained from running 3 qc materials with each batch of patient samples with mean concentrations of 9 , 168 and 535 ng / dl respectively in this case ) .
the data management software consists of libraries of code that are called from a primary compiled program that handles the various aspects of export file management and transfer to the lis via file transfer protocol ( ftp ) .
the documentation included with the licensed data management software was comprehensive ; however , minor discrepancies were discovered between the documented installation file locations and the actual locations specified in the software source code ( included with the software ) .
accurate placement of the library and resource files in appropriate directories and subdirectories was required for the compiled program to find them . although the author was not familiar with ahk at the time of installation , its similarities to other scripting languages permitted casual review to catch these discrepancies .
the documentation supplied with the data management software clearly describes the process of integrating a pre - processor , which is required if the data output format from the lc - ms / ms software does not match the input format of the lis , but is not supplied with the data management software . in this case , pre - processing of
the text file exported from the analyst software was required in order for sunquest to accept the data and perl was chosen by the authors for writing the pre - processor .
perl is a popular and well - established open - source scripting language used in many contexts , including biomedicine , is freely available for multiple platforms and can be installed on windows platform ( as well as others ) via activeperl installer .
perl stands for  practical extraction and report language  and is highly suitable for parsing text , making it an ideal language to use for a pre - processor in the context of the analyst - sunquest interface .
a particularly helpful feature of perl utilized extensively in the pre - processor is its implementation of  regular expressions ,  which facilitates searching for particular patterns in a given text string and optionally replacing them with another string .
although the data management software includes a log file , we found that additional logging was helpful during the debugging process , and thus we added additional logging to the pittsburgh software source files , which were then recompiled . with this in mind , the pre - processor includes a separate log with output to verify that the various steps in the program occur each time it is run . a flow chart documenting the steps in the process
the source code for the pre - processor is shown in figure 2 , and an explanation of each line of the code can be found in table 1 . the workflow process from the analyst software to the pre - processor , the data management software and finally to the transfer by file transfer protocol to the laboratory information system source code written in perl to pre - process the text file output from the liquid chromatography - tandem mass spectrometry system to a format suitable for transfer to sunquest via file transfer protocol key to the purpose of each line of the source code that was used to pre - process the data output file from the liquid chromatography - tandem mass spectrometry system during the validation of the ptes assay , the interface was tested by exporting the text file containing calibrator , qc and patient assay results into a specific folder ; in this case the  report output folder  on the computer running the mass spectrometer .
the correct order of events is as follows : the text file containing the results will disappear from the  report output folder ;  when the pre - processing has been completed , a text file will then be found in the  converted folder ;  this file disappears from the  converted folder  and will then be found in the  sent folder ;  the original text file exported from the lc - ms / ms system will then be placed in the  archived folder .  in order to determine if the interface was performing as expected , when the pre - processed file was found in the  sent folder ,  the sunquest lis was accessed ( after a delay to allow sunquest to perform its periodic scan of the stipulated upload location for the data ) to determine if the qc results and patient assay results had indeed been transferred via ftp , and that the calibrator results were essentially ignored by the pre - processor .
as this process was working successfully , it was implemented once the ptes assay was placed into clinical use . to date , there have been no software problems or failures .
the interface has eliminated the need for manual data entry and any associated manual transcription errors .
four discrete data are required to successfully transmit an individual patient result from the lc - ms / ms output text file to sunquest : the unique patient container identification number ( cid - a barcode affixed to the patient sample container that is scanned by a barcode reader , electronically entering the cid into the lc - ms / ms software ) ; the sunquest test code for the assay being performed ( in this case test code ptes for pediatric total testosterone ) ; the assay result for each patient and the qc data ( the total testosterone concentrations obtained from running 3 qc materials with each batch of patient samples with mean concentrations of 9 , 168 and 535 ng / dl respectively in this case ) .
the data management software consists of libraries of code that are called from a primary compiled program that handles the various aspects of export file management and transfer to the lis via file transfer protocol ( ftp ) .
the documentation included with the licensed data management software was comprehensive ; however , minor discrepancies were discovered between the documented installation file locations and the actual locations specified in the software source code ( included with the software ) .
accurate placement of the library and resource files in appropriate directories and subdirectories was required for the compiled program to find them . although the author was not familiar with ahk at the time of installation , its similarities to other scripting languages permitted casual review to catch these discrepancies .
the documentation supplied with the data management software clearly describes the process of integrating a pre - processor , which is required if the data output format from the lc - ms / ms software does not match the input format of the lis , but is not supplied with the data management software . in this case , pre - processing of
the text file exported from the analyst software was required in order for sunquest to accept the data and perl was chosen by the authors for writing the pre - processor .
perl is a popular and well - established open - source scripting language used in many contexts , including biomedicine , is freely available for multiple platforms and can be installed on windows platform ( as well as others ) via activeperl installer .
perl stands for  practical extraction and report language  and is highly suitable for parsing text , making it an ideal language to use for a pre - processor in the context of the analyst - sunquest interface .
a particularly helpful feature of perl utilized extensively in the pre - processor is its implementation of  regular expressions ,  which facilitates searching for particular patterns in a given text string and optionally replacing them with another string .
although the data management software includes a log file , we found that additional logging was helpful during the debugging process , and thus we added additional logging to the pittsburgh software source files , which were then recompiled . with this in mind , the pre - processor includes a separate log with output to verify that the various steps in the program occur each time it is run . a flow chart documenting the steps in the process
the source code for the pre - processor is shown in figure 2 , and an explanation of each line of the code can be found in table 1 . the workflow process from the analyst software to the pre - processor , the data management software and finally to the transfer by file transfer protocol to the laboratory information system source code written in perl to pre - process the text file output from the liquid chromatography - tandem mass spectrometry system to a format suitable for transfer to sunquest via file transfer protocol key to the purpose of each line of the source code that was used to pre - process the data output file from the liquid chromatography - tandem mass spectrometry system
during the validation of the ptes assay , the interface was tested by exporting the text file containing calibrator , qc and patient assay results into a specific folder ; in this case the  report output folder  on the computer running the mass spectrometer .
the correct order of events is as follows : the text file containing the results will disappear from the  report output folder ;  when the pre - processing has been completed , a text file will then be found in the  converted folder ;  this file disappears from the  converted folder  and will then be found in the  sent folder ;  the original text file exported from the lc - ms / ms system will then be placed in the  archived folder .  in order to determine if the interface was performing as expected , when the pre - processed file was found in the  sent folder ,  the sunquest lis was accessed ( after a delay to allow sunquest to perform its periodic scan of the stipulated upload location for the data ) to determine if the qc results and patient assay results had indeed been transferred via ftp , and that the calibrator results were essentially ignored by the pre - processor .
as this process was working successfully , it was implemented once the ptes assay was placed into clinical use . to date , there have been no software problems or failures .
the interface has eliminated the need for manual data entry and any associated manual transcription errors .
we successfully implemented a licensed data management interface between sunquest and an ab sciex mass spectrometer that may allow the laboratory more control and adaptability than a commercially available software to software interface .
currently , this interface has only been used to transmit results from one test to individual patients , but the authors are confident in the adaptability of this interface in order to be able to handle more complex results , such as pharmacokinetic analysis consisting of a number of samples from the same patient over a given time period , each with a different concentration . although the licensed software from the university of pittsburgh was extremely useful in facilitating an interface between the lc - ms / ms system and the lis , local expertise in programming was necessary to perfect the data transfer process .
 background : interfacing complex laboratory equipment to laboratory information systems ( lis ) has become a more commonly encountered problem in clinical laboratories , especially for instruments that do not have an interface provided by the vendor . 
 liquid chromatography - tandem mass spectrometry is a great example of such complex equipment , and has become a frequent addition to clinical laboratories . as the testing volume on such instruments can be significant , manual data entry 
 will also be considerable and the potential for concomitant transcription errors arises . due to this potential issue , 
 our aim was to interface an ab sciex mass spectrometer to our sunquest lis.materials and methods : we licensed software for the data management interface from the university of pittsburgh , but extended this work as follows : the interface was designed so that it would accept a text file exported from the ab sciex  5500 qtrap mass spectrometer , pre - process the file ( using newly written code ) into the correct format and upload it into sunquest via file transfer protocol.results:the licensed software handled the majority of the interface tasks with the exception of converting the output from the analyst software to the required sunquest import format . 
 this required writing of a  
 pre - processor  by one of the authors which was easily integrated with the supplied software.conclusions:we successfully implemented the data management interface licensed from the university of pittsburgh . 
 given the coding that was required to write the pre - processor , and alterations to the source code that were performed when debugging the software , we would suggest that before a laboratory decides to implement such an interface , it would be necessary to have a competent computer programmer available . 