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NOTICE ______ MSFORMS is a copyrighted product and as such is protected by the copyright laws of the United States. You are therefore asked NOT to give copies of your MSFORMS REGISTERED disk away to anyone. You may, and indeed are encouraged, to give away copies of your MSFORMS EVALUATION disk, providing, of course, that you adhere to the limits contained in the license agreement. Your cooperation in this matter is greatly appreciated. Declan Cowley August 1987 MSFORMS Version 3.10 copyright 1986, 1989 by Declan Cowley (CHAOS COMPUTING) 801 Seminole Blvd. Geneva, Fl 32732 407-896-6645 (work) MSFORMS page 1 NOTICE ------ BEFORE PROCEEDING ANY FURTHER YOU ARE ENCOURAGED TO MAKE A BACKUP COPY OF YOUR EVALUATION DISK. THE FILE MAINTAINENCE SECTION OF THE PROGRAM WILL ALTER SOME OF THE FILES SUPPLIED WITH THIS PROGRAM - SO USE OF YOUR BACKUP COPY FOR EXPERIMENTING IS ENCOURAGED. MSFORMS page 2 YOUR MSFORMS LICENSE MSFORMS is copyrighted and is NOT in the public domain. Even though the program is distributed under the SHAREWARE concept, and can be freely copied, there are still some limitations to protect the quality of the distribution and to support future development. Users of MSFORMS may make copies of this program for trial use by others on a PRIVATE NON-COMMERCIAL BASIS. This program may not be sold by anyone other than the author. By accepting and using this software, you acknowledge that this software may not suit your particular requirements or be completely trouble free. With proper application, this software will perform as described. However I will not be responsible for your specific application or any problems resulting from the use of this software. If the software does not perform as described, my liability to you is limited to replacing the software or refunding the purchase price (if purchased and registered). I have no liability to you or any other person or entity for any damage or loss, including special, incidental or consequential damages, caused by this software, directly or indirectly. This agreement is governed by the laws of the State of California. Should any part of this agreement be held invalid, the remainder of the agreement will still be in effect. This agreement can only be modified by written statement signed by me. Under this license you may NOT: 1) Distribute the program in connection with any other product or service, as part of a corporate or institutionally sponsored distribution. 2) Charge anything for MSFORMS. An exception is made for registered user groups who may charge a cost based fee (not to exceed $10) to cover their own costs. 3) Distribute the program in modified form, or without the accompanying demo files and this document file. Declan Cowley August 1987 MSFORMS page 3 THE SHAREWARE CONCEPT --------------------- MSFORMS is distributed through a unique marketing concept called SHAREWARE. The diskette with programs on it can be freely copied and shared. It is also available directly from the author for $50, shipping and handling included. We ask you to help us distribute MSFORMS by sharing unmodified and complete copies of the EVALUATION RELEASE with others. We also encourage you and those to whom you have distributed the program, to register your copy if you find the program of use. Registration has a number of benefits to you: 1) You will receive the most recent version of the program. -the registered version has a few enhancements over this shareware release - mainly ... * it does not have the SHAREWARE notice. * fixes of any found or reported bugs. * recent improvements/additions. * you may request to receive the source code - QuickBASIC source and the C and assembler library modules. 2) You will be notified of updates. 3) (MAINLY) You will be supporting the concept that allowed you to receive MSFORMS in the first place. Only through user support can I continue to improve MSFORMS and perhaps develop other programs. Only by supporting the program authors who release valuable programs as shareware can you encourage others to do the same. Supporting shareware will encourage other authors which will result in more low cost quality software for you to enjoy. If ASHTON-TATE and LOTUS had their way we would all be spending upwards of $500 for each software package and not even be allowed to make backup copies for our own protection under threat of legal prosecution. Fortunately not all of us think this way - hence SHAREWARE. MSFORMS page 4 HARDWARE REQUIREMENTS --------------------- An IBM PC or MS-DOS compatible computer with 512K of RAM and running MS-DOS V2.0 or higher, dual 360K floppies (with a hard disk recommended). A serial port and a parallel printer port are also required. SUGGESTED DISK CONFIGURATIONS ----------------------------- A hard disk is the best configuration to work with, as there is a lot of disk activity during program execution as MSFORMS reads in the various files it needs and creates data files. I suggest capturing your QUAN reports onto a floppy, or into their own subdirectory. It makes erasing the files easier (since there is no real reason to keep the captured QUAN reports)- and more foolproof. If you have a dual drive system, then MSFORMS and its files should be on the same floppy. The QUAN reports on another. Before proceeding, I would suggest that you make a backup copy of the distribution disk. Use the backup for normal everyday use and put your original away in a safe place. Once you have customized MSFORMS to your parameter lists, make a backup of the support files for safe keeping. MSFORMS page 5 MSFORMS - AN OVERVIEW --------------------- MSFORMS reads in an ASCII QUAN report that has been generated on a FINNIGAN(tm) mass spectrometer using Finnigan TCA software, and produces a finished report suitable for giving to a client. This is accomplished by attaching the RS-232 communications cable from the GC/MS NOVA computer to the serial port of your PC. You then load a suitable terminal emulator program on your PC and capture as individual ASCII files the FINNIGAN TCA QUAN reports onto your PC's disk. (Also supports the ITD). MSFORMS is then loaded and the QUAN filenames passed to the program, along with other information, including matrix type and dilution factors. MSFORMS reads in the QUAN report, parses it and then gives you the opportunity to edit the results or add flags before it prints out a results form suitable for presenting to a client. In addition, MSFORMS will also generate an MS/MSD report and a surrogate summery report. A CONFIGURATION menu allows the user to set up default parameters for the program to use and to define your printer control codes. The FILE MAINTAINCE section is used to set up the files MSFORMS requires while processing the QUAN report. These files include 'library' name lists - two for each analysis (soil and water matrix) - complete with MDL's (method detection limits), a surrogate file that tells MSFORMS how many internal standards and surrogate standards you use in your analysis and the concentrations of your surrogates and a print header file that contains the name and address that will appear on the top of the report, and an MS/MSD info file. In addition, this section is used to create a BATCH file that MSFORMS can use to process multiple QUAN reports unattended. MSFORMS is not all encompassing (unfortunately), therefore it places certain restrictions on you and your system in order for you to be able to use it. These restrictions are not very severe and can be easily incorporated into your method of operation. The restrictions will be pointed out to you during the course of the rest of this manual. Finally, this is not a substitute, for FINNIGAN's QAFORMASTER(tm). Although, perhaps one day!!! It is intended for any GC/MS lab that employs FINNIGAN mass spectrometers and uses FINNIGAN's AUTOQUAN(tm) software. Its function is to aid the analyst in processing the mass spectrometer QUAN results into a presentable form, suitable for giving to a client. MSFORMS page 6 MSFORMS was written primarily because I used to spend so much time transcribing data from QUAN reports to work sheets and calculating values based on dilution factors which I then hand to a secretary who types it again. One day I discovered how easy it was to interface a PC to the MS and download a QUAN report. That was the beginning - this (MSFORMS V2.61) is the middle (and the fifth evaluation release). The end may not be for quit a while as I have many ideas for changes and additions to MSFORMS. What really spurred me on was FINNIGAN's $4000 QAFORMASTER program. That program is very comprehensive (suitable of FINNIGAN), with a manual that boggles the mind. I thought an inexpensive and easy to use program might find some favor. I refer you to the EPA CLP STATEMENT of WORK for ORGANIC ANALYSIS Multi-Media, Multi-Concentration 10/86 revision, as a guide to what I am trying to achieve. So if some of my explanations of what the program does or what I am trying to achieve with it are less than lucid, then if you refer to this document, I hope it will become clearer. Finally, I am a practicing scientist and programmer, not a writer. So please bear with me as I do my best to create a lucid description of this program and how to use it. MSFORMS page 7 DEMO/TRIAL RUN of MSFORMS ------------------------- Like most people, you are anxious to see what you have in MSFORMS. So this section is a quick demo of the MSFORMS program. On your distribution disk are all the files that are needed for this demo. You should have the following:- NAMES.VOW MSFORMS.EXE NAMES.VOS NAMES.BNW MSFORMS.CFG NAMES.BNS PRINTER.CFG NAMES.PCW EPSON.PRN HPLJET.PRN SURROGAT.VO SURROGAT.BN BATCH.MSF SURROGAT.PC MATRIX.VO MATRIX.BN MATRIX.PC REPORTS.FRM QUAN1.VO QUAN2.VO QUAN3.VO QUAN4.BN QUAN5.BN QUAN6.BN First we will generate the volatile organics report. Start by inserting your backup copy of the distribution disk into drive A, then enter MSFORMS at the DOS A> prompt, followed by a carriage return. The SHAREWARE notice will appear followed shortly by the MSFORMS opening screen and shortly following it the main menu. Select 'QUAN REPORT GENERATOR' with the cursor keys, then the parameter entry screen will appear. The cursor will be positioned at the first entry - QUAN FILENAME. Type QUAN1.VO followed by a carriage return (<CR>). For the following eight entries enter anything you want. At the nineth entry (SAMPLE TYPE) enter 'W'. For now enter one's for the dilution factors. After a very short pause the screen will change and the data will be displayed for modification. The data can be displayed in pages using the PgUp PgDn keys, or you can go to the top and bottom of the data by using the HOME and END keys respectively. To select a result for editing, press the cursor up or cursor down keys. The selected result will be highlighted, continue to use the cursor keys to select the item of interest. When you have moved the cursor to the item of interest press the <F1> key to edit the result, or press the <F2> key to edit the flag (two flag characters are allowed). Once you have finished editing the results, press the ESC key to start the printing of the form. MSFORMS page 8 At this time there should be a fair amount of disk activity - this is normal. Very shortly the printer will fire up and the report will be printed. Basically that's all there is to it. Now repeat the above exercise, only use QUAN4.BN for the QUAN FILENAME entry. This time you will get a semi-volatiles report. Repeat the exercise again, only this time use GC.PC for the QUAN FILENAME entry (and water for the MATRIX). This is the way to specify that no quan report exists, it will then read in the NAMES.PCW file and present you with an edit screen without results. Edit in the results, then print the report. This is the mechanism that can be used for generating GC reports, or reports for any other instrument that has a list of compounds. Repeat the exercise again, only enter BATCH for the QUAN FILENAME entry. This will automatically produce both reports using the QUAN1.VO and QUAN4.BN files. Note that this time no data is presented for editing. This is discussed later in the manual. Now select 'MS/MSD REPORT GENERATOR' from the menu. The MS/MSD parameter screen will appear. Enter QUAN1.VO, QUAN2.VO and QUAN3.VO for the filenames (in that order), complete the rest of the entries and an MS/MSD report is generated. Repeat the above for the three .BN QUAN files (4,5,6 in that order) and you will get a BNA MS/MSD report. Select the 'MS/MSD REPORT GENERATOR' again. This time enter GC.PC for the first QUAN filename. The cursor will now skip the next two fields. Proceed as normal with the rest of the entries. This time three screens will be presented for EDITing. Editing in the spike results will allow you to enter data from a GC run for an MS/MSD report. The first screen is for the results from the unspiked sample, the second for the spike and the third for the spike duplicate. Now select 'SURROGATE REPORT GENERATOR' from the menu, answer VO and a surrogate summery report will be printed. Selecting it again and answering BN will produce another surrogate report. MSFORMS page 9 FILE MAINTAINENCE ----------------- Since the FILE MAINTAINENCE section creates files that MSFORMS requires in order to work, we shall discuss it first. FILE MAINTAINENCE is used to create six files, three of which must be present for MSFORMS to work. The files are:- 1) NAMES.xxW 2) NAMES.xxS 3) SURROGAT.xx 4) MATRIX.xx 5) REPORTS.FRM 6) BATCH.MSF - where xx is any two letter extention, user defined. All these files are present on the distribution disk. However, you will need to create your own in order to customize the system to your operation. The files present on the distribution disk also include six ASCII QUAN reports downloaded from my 4600. They are QUAN1(2&3).VO and QUAN4(5&6).BN and they are VOA and SVO reports respectively. You may use these files together with the other files above to do 'test runs' of the program. Selecting 4 at the main menu will select FILE MAINTAINENCE. You will be presented with a menu. The selections are:- 1) CREATE NEW NAME LIST 2) EDIT NAME LIST ENTRY 3) INSERT/DELETE ENTRY 4) ADD NEW ENTRY TO LIST 5) CREATE SURROGATES FILE 6) CREATE MATRIX SPIKE FILE 7) CREATE REPORTS FILE 8) CREATE BATCH FILE 9) RETURN TO MAIN MENU The first four entries create or edit the NAMES.xxS or NAMES.xxW files. MSFORMS page 10 1) CREATE NEW NAME LIST ------------------------ Selecting this item on the menu will bring up a screen asking for the two letter extention (xx (above)) of the file you wish to create and the matrix. Your selection here will create a file named either NAMES.xxW or NAMES.xxS. Once selected a new entry screen is displayed:- 2 LETTER FILE EXTENTION .-- ENTRY NUMBER : --- MDL ------- UNITS ------------------------ COMPOUND NAME ------------------------------ CODE # ---- CAS # ---------- BASE MULTIPLIER ---- The entry number is filled in for you - it is a counter to help you keep track. The MDL (method detection limit) is entered first. Entering a 0 (zero) will terminate entry and write the file to disk. The MDL value to enter should correspond to your reportable MDL for your standard analysis weight/volumn. As per the VOA CPL contract this would correspond to 5 (ug/l or ug/kg) for MOST compounds. As per the BNA CPL contract this would correspond to 10(ug/l) for MOST compounds. Since the normal dilution factor for water is 2 it will be necessary to half the CLP values to 5 in order to get the correct MDL (when using a dilution factor of 2) on the printed report. The MDL used in SVO analysis of soils with a normal soil sample weight corresponding to 30gm, the CLP contract level of 330 (ug/kg) for MOST compounds (this also corresponds to a normal dilution factor of one for a 30gm soil sample extracted and concentrated to 1ml). If you are not doing CLP work then the MDL you enter is determined by your standard operating procedures. The reportable units that will appear on the report form is taken from the UNITS entry. *** NOTE *** The program actually only reads the UNITS field and the BASE MULTIPLIER field from the FIRST entry in each file - this is why the input routine will not prompt you for them a second time, but carries the input over into all subsequent entries. MSFORMS page 11 Next is the compound name. Here you enter the compound name AS YOU WANT IT TO APPEAR on the printed report. If you want it capitalized on your report - make sure you capitalize it when you enter it. *** NOTE *** This is one of the restrictions (actually three) the program will make on your system. 1) The internal standards MUST be the first 'x' compounds in your name list. 2) The surrogate standards MUST be the next 'y' compounds in your name list. 3) The balance of the compounds in your TCA list MUST BE ENTERED IN THE ORDER THEY APPEAR IN THE QUAN REPORT. 3a) This restriction (3) also applies to your IS and SS. This means that your QUAN report MUST list the compounds in the following order:- a: Internal Standards b: Surrogate Standards c: rest of the TCA compounds Why is this? Because MSFORMS does not have the ability (yet) to determine which compound is where. Therefore it expects the order of compounds in the QUAN report to correspond to the order in this name list. It further discards the first 'x' compounds (the internal standards) and processes the second 'y' compounds (the surrogate standards) and generates % recovery results for them. The balance of the compounds are treated as TCA compounds. MDL values for the internal standards and surrogates -- you cannot enter zero (as this would terminate entry) so I suggest a suitably small non zero but positive value, such as 0.1. If you intend to use the ND option on your report then the MDL value entered in the FIRST entry of the name list is used on the report. One final restriction - the QUAN report must be complete with NOT FOUNDS if necessary. That means the QUAN report MUST NOT have had the NOT FOUND's compressed out by EDSL (U;W;E. The reason for this restriction is related to the programs current inability to determine what compound is where. The processing of the QUAN report involves discarding all text only lines from the QUAN report, leaving only lines containing results. Then the number on the left is read in and this tells the program what compound it is, which it then reads from the name file. MSFORMS page 12 This is why the order is important. If you compress out the NOT FOUND's with EDSL (U;W , the entries are renumbered and that number no longer points to the correct compound in the name list. For those of you not familiar with how to preserve the QUAN list intact, especially if you have automatic procedures that do additional data processing on an analytical run that compresses out the NOT FOUND's, incorporate the following before and after the procedure: FTP (CO;$1.QL;TEMP.QL;E procedure FTP (CO;TEMP.QL;$1.QL;E This obviously presupposes that the file you are processing is in $1. If it isn't you will need to set it up beforehand. Finally, if you are unclear as to the above I suggest you take a look at the two QUAN reports supplied with this program and the name lists also supplied. Next is an entry entitled CODE. At present this is not used. It is present in order to provide forward compatability between the files generated now with future versions of MSFORMS. The next entry is the CAS #. This is a report option. The last entry is BASE MULTIPLIER. The BASE MULTIPLIER is a constant factor that you wish applied to the data results (it does not effect the surrogates) to bring the QUAN report values up to the reportable UNITS. For instance the MDL for CLP soils is 330 ug/kg. However only 30 grams are extracted. To convert 30 grams to kilograms a multiplier of 33 is required. Entering 33 as the base multiplier takes care of this automatically. The only thing the analyst needs to worry about are dilution factors. This also allows the program to be customized to unusual extraction volumns and final extract volumns. Once these are standardized, calculate the factor to convert the QUAN results to reportable results and enter it into the BASE MULTIPLIER. Thereafter you need only concern yourself with dilution factors (ie: variations from your standardized extraction volumns and final extract volumns). If you do not need to use a BASE MULTIPLIER, enter a value of one. MSFORMS page 13 2) EDIT NAME LIST ENTRY ----------------------- Menu item 2 (EDIT LIST) allows you to select an entry in the appropriate name list for editing. You supply the entry number - the program then displays the entry for editing. You need not re-enter all data for that entry - hitting return does default to the original data. Enter data only if you wish to make a change. You may modify the UNITS field and the BASE MULTIPLIER field in this option. REMEMBER entry #1 is the record the program reads to get the UNITS and BASE MULTIPLIER fields and MDL entry. 3) INSERT/DELETE ENTRY ---------------------- This section allows you to delete an entry from the name list and to insert an entry into the name list. After selecting the file to change the entries are displayed for selection in order from first to last. You have three choices: Keep - keeps the entry (no change) Delete - deletes the displayed entry Insert - allows you to insert a new entry in FRONT of the displayed entry. Finally, you are asked to confirm your changes. Answering No will not make the changes permanent. Yes, will. 4) ADD NEW NAMES TO LIST ------------------------ Menu item 4 (ADD NEW ENTRIES TO LIST) allows you to add additional compounds to your selected name list. This item will append the new entry to the END of the name list. Bear in mind that all entries in the name list will appear on the report form. Just to reiterate, the compound entry numbers in this module must correspond to the compound name and the number that appears on the left of your QUAN report. The program expects these to be the same, and indeed uses these numbers to get the compound name and MDL from the appropriate name list, NAMES.xxW or NAMES.xxS. *** NOTE *** As MSFORMS is designed to handle a maximum of 160 compounds per report, the NAMES program will terminate user input after the 160th entry has been input (in modules 1 and 3). The file will be written to disk and closed with 160 compound entries in it. MSFORMS page 14 5) CREATE SURROGATES FILE ------------------------- Menu item 5 will create a disk file that will tell MSFORMS how many internal standards and surrogate standards are in the NAMES.xxx file and corresponding QUAN report. At the moment the assumption is that the same number of internal standards and surrogates are used in both soil and water analysis. The entry screen looks like: VOA(V) or BNA(B) or GC(G) - 2 LETTER FILE EXTENTION .-- NUMBER OF INTERNAL STANDARDS --- NUMBER OF SURROGATE STANDARDS --- SURROGATE NUMBER --- TRUE (UNDILUTED) SURROGATE VALUE --- The true (undiluted) value corresponds to the surrogate concentration at a dilution factor of one. A value of zero is a valid entry if you should use no surrogates (or internal standards). MSFORMS page 15 6) CREATE MATRIX SPIKE FILE --------------------------- Menu item 6 will create a disk file of the information MSFORMS needs in order to process matrix spike/matrix spike duplicates. The screen display looks like: 2 LETTER FILE EXTENTION : .-- QUAN REPORT ENTRY NUMBER : --- COMPOUND NAME : ------------------------------ COMPOUND CODE : ---- CONCENTRATION : ---- QUAN REPORT ENTRY NUMBER - this is the same as in the name lists, if the compound is number 32 on your QUAN report then enter 32 here. MSFORMS uses this number to select out of the QUAN report only those entries it needs. COMPOUND NAME - this is self explanatory, again enter it exactly as you want it on your report. COMPOUND CODE - at this time, this entry is not used, but is included to allow forward compatability at a later date. CONCENTRATION - enter the spiking concentration of the compound. This value will be used to compute the percent recoveries. This is the true (undiluted) value. 7) CREATE REPORTS FILE ---------------------- Menu item 7 will create a disk file that contains the name, address and phone number of your lab. This information is read in by MSFORMS and placed at the top of the printed report. In addition a footer can be added to your report, such as a disclamer (or a Christmas greeting). The footer can be up to 122 characters long. Input is divided in two fields 61 characters long. Enter your footer until you reach the end of the field, then hit return and enter the second field. When entering, ignore the artifical boundery at the end of the field - type until you reach it then hit return and continue. If you have to break a word in the middle, that's okay, just continue on the next line where you left off. The footer will be automatically centered on the report form. MSFORMS page 16 8) CREATE BATCH FILE -------------------- Menu item 8 will create a disk file with all the report parameters for multiple files. This will allow MSFORMS to do data processing on multiple files unattended. The data entry screen which appears is almost identical to the MSFORMS data entry screen. The only difference is the presence of 'ENTRY # :' that appears in the upper left of the screen. This keeps track of how many files you have entered. The entry screen looks like this : QUAN FILE NAME : -------------- BLANK FILE ID : -------------- CLIENT NAME : ------------------------------ LAB SAMPLE NUMBER : -------------- CLIENT SAMPLE NUMBER : ------------------------ DATE RECEIVED : ---------- DATE SAMPLED : ---------- DATE EXTRACTED : ---------- DATE ANALYSED : ---------- SAMPLE TYPE (SOIL/WATER/AIR) : - DILUTION FACTOR SAMPLE : -------- SURROGATES : -------- The only required entries are QUAN FILE NAME, SAMPLE TYPE and the DILUTION FACTORS. There are restrictions as to what you may enter here, and the program checks for valid input. QUAN FILE NAME: Valid entries require any two letter extension. This is how MSFORMS determines what name list to use. The only other limitation is that it be a valid DOS filename. NOTE: the GC.xx entry is not valid here, as this requires the edit screen input. BLANK FILE ID: This is the mass spec instrument file name. (extraction date (BNA) and analysis date (VOA) are already present on the report) The sample instrument file name is extracted by the parser and will appear on the report under the blank id. SAMPLE TYPE: Only an 'S' or 'W' or 'A' is valid. The 'A' will use the appropriate .xxW name list. However, result units will read 'total nanograms' in place of whatever is in the name list for UNITS. DILUTION FACTORS: Any numeric entry greater than 0 (zero) is accepted. The range of values is .0000001 to 99999999. MSFORMS page 17 MSFORMS ------- MSFORMS is started from the DOS prompt by typing MSFORMS followed by a carriage return. The opening screen is the SHAREWARE notice. If you register your copy of MSFORMS, you will receive the latest edition of the program, complete with serial number and without the SHAREWARE notice. The second screen is the real opening screen, and the one on which your serial number will appear. This screen also tells you what version it is. The third screen is the main menu. At present it has only six offerings. Item 1 is the parameter entry screen for report generation and is virtually identical to the batch file entry screen in FILE MAINTAINENCE. Item 2 is the SURROGATE SUMMERY REPORT. Item 3 is the MS/MSD entry screen and item 4 is EPA CLP REPORTS MENU. Item 5 is the FILE MAINTAINENCE MENU. Item 5 is the CONFIGURATION menu. Item 6 exits to DOS. For menu item 1, QUAN REPORT GENERATOR the same restrictions apply as in FILE MAINTAINENCE. The same four entries are required, the others are optional. All non required entries supply information that will appear in the header of the printed report. Lab sample number and date analysed are passed to the surrogate summery report. Again, the QUAN FILE NAME MUST end with any valid two letter extention, however, here a third entry is also valid. Entering BATCH will transfer control to the file we created with item 7 in FILE MAINTAINENCE and proceed to automatically process the files named therein. Entering GC.xx is also valid. Essentially this is the 'blank' report. The xx is any valid two letter extention for which all the appropriate files have been created. The 'GC' tells the program that a QUAN file does not exist. The program then goes out and creates a blank report by reading in the NAMES.xx file and assigns zero to each result. On the edit screen you then get to edit in the results. The GC.xx entry is NOT valid in BATCH. If you have entered GC.xx for the QUAN FILENAME, a window will open requesting the METHOD. This is to allow the user to specify the GC method number (ie: 601, 8010 etc.). On the report form, the method number will replace the QUAN FILE ID. MSFORMS page 18 If 'A' is entered for sample type, a window will open at the top of the screen requesting additional input. -- AIR ANALYSIS -- Result Units (total nanograms) extract volumn(ml) (1000) MATRIX (AIR) The values in brackets are default values and can be kept by simply hitting return, else enter the changes required. The volumn entry is based on 1000ml for calculations (1000ml gives a factor of one). Anternate entries will adjust the results accordingly - especially useful if reporting results in wt/litre volumn. This works in ADDITION to the dilution factors. If 'S' is entered for sample type, a window will open at the bottom of the screen requesting additional input. -- SOIL ANALYSIS -- Percent Moisture (0) The value in brackets is default, and corresponds to NO percent moisture correction. This works in ADDITION to the dilution factor. If the sample matrix is soil, then one of two additional messages appear underneath the RESULT UNITS: on the report. Either "Results reported on a wet weight basis" or "Results reported on a dry wight basis", depending upon your answer to the percent moisture question. Once the final item on this screen has been entered MSFORMS will read in and parse the named QUAN report. Then a fourth screen appears which will present a listing of CMPD # and its VALUE for editing before the report is printed. This will allow the analyst to remove erroneous data from the QUAN report or correct results that have been recalculated. To remove a false hit from the report simply enter the compound number. You will then have the compound number and its value displayed at the bottom of the screen and be prompted for the new value. The minimum allowable value is 0. Once finished editing the data, MSFORMS then processes the results data and prints the finished report. MSFORMS will multiply the MDL by the dilution factor for the sample in keeping with CLP protocol. Also in keeping with CLP protocol, MSFORMS supplies the letter 'U' after the MDL value when it is reported as the result. Result values between 0.5MDL and the MDL are reported with a 'J' appended. Result values less than 0.5MDL are reported as the MDL. MSFORMS page 19 One final note. If the BATCH mode is invoked, the editing screen is bypassed. If you need to edit any QUAN reports prior to processing and you want to use the BATCH mode, then you can edit your QUAN reports using WORDSTAR(tm) in its non document mode. Of course, any other ASCII file text editor will also work. Printed results are rounded to two significant figures. If you call up a screen you do not want to be in, pressing return without entering anything will return you to the main menu. During the execution of the program, if you find that MSFORMS returns an error telling you that a file does not exist or if you forget a filename, it is possible to get a directory listing. During MOST fielded input, pressing the <F10> key will cause a window to open. Enter the Drive:\Path for which you need a listing and press return. The filenames for that Drive:\Path will be displayed. If there are more entries than can be displayed in the window, pressing PgDn and PgUp will display the rest. HOME will allow another Drive:\Path to be entered. END will close the window and return you to the input field you were at prior to calling the directory window. Menu item 2, SURROGATE SUMMERY REPORT will ask for the two letter extention for which to generate the summery report. The surrogate summery file is generated automatically each time a report is processed from item 1, unless, of course, zero surrogates is specified in its surrogat.xx file. When the surrogate summery report is printed the file containing the surrogate summary (SURRHOLD.xx) is renamed to SR??????.xx for archival purposes (or for your QC officer). The data in this file contains information not currently printed. The data is contained in the following format: num, lab id, date analysed, time analysed, date extracted, instrument filename, matrix, (surrogate results .....) num = 6 + (number of surrogates) ie: VOA analysis uses 3 surrogates, therefore num = 6 + 3 == 9. MSFORMS page 20 Menu item 3, MS/MSD REPORT GENERATOR will call up the following input screen: SAMPLE QUAN FILENAME : -------------- MATRIX SPIKE QUAN FILENAME : -------------- MSD QUAN FILENAME : -------------- SAMPLE ID : -------------- MATRIX (Soil/Water/Air) : - DATE ANALYSED : ---------- DILUTION FACTOR : --------- The SAMPLE QUAN FILENAME refers to the unspiked sample. The next refer to the two spiked samples. The program checks to see that all three have the SAME file name extention (ie: .VO or .BN). An entry of GC.xx is a valid input here. Again, this tells the program that you wish to generate an MS/MSD report for an analysis, but that there are no QUAN files to read in. Since there are no quan files to read in, the QUAN filename for the MS and MSD will be bypassed. The program will request other field items, then you will be presented with the edit screen to edit in the results for the SAMPLE, then MATRIX SPIKE and then the MATRIX SPIKE DUPLICATE, each in turn. Watch the box over the compound names to tell which is currently requested. The SAMPLE ID is for laboratory sample identification on the report. MATRIX and DATE ANALYSED are self explanatory. Input on these three items is optional. DILUTION FACTOR is as it implies. The assumption made here is that all three samples were run using the same dilution factor. The program will subtract the unspiked sample values from the spiked values and then use the concentrations entered into the MATRIX.xx files created in FILE MAINTAINENCE to calculate percent recoveries. All values are multiplied by the entered dilution factor before any calculations are made. The program uses the spike and spike duplicate results to compute the RPD. Calculations are done on the results unmodified, but the results are rounded only prior to printing. *** NOTE *** MSFORMS uses the computer's system clock to generate the REPORT DATE on the forms. So make sure the system date is set correctly when the computer is turned on. MSFORMS page 21 Menu item 4, EPA CLP REPORTS MENU. This will display a menu of EPA CLP forms. At this release only the first entry is functional, the HSL REPORT - FORM I. The other forms are currently under development. Selecting the HSL FORM I REPORT will display the header screen: ORGANICS ANALYSIS DATA SHEET EPA SAMPLE NUMBER QUAN FILENAME:............... ............. Lab Name:......................... Contract:........... Lab Code:....... Case No:...... SAS No:....... SDG:...... Matrix: (soil/water) ...... Lab Sample ID:............. Sample wt/vol:..... (g/ml).... Lab File ID:........... Level:(low/med)...... Date Received:........ % Moisture: not dec.... dec.... Date Extracted:........ Extraction:(SepF/Cont/Sonc).... Date Analysed:........ GPC Cleanup:(Y/N)... pH:..... CONC UNITS: ..... Column:(pack/cap)...... (ug/l or ug/Kg) Dilution Factor: Sample:........ Surrogates:........ If you have conpleted the EPA HEADER in the configuration menu, then the lab name, contract, lab code, case no., sas no., sdg no., level, extraction, GPC and column will be filled in from the file information. Otherwise you will need to supply the information. Hitting return will accept any existing data. Some items (matrix, sample (g/ml), level, extraction, GCP, column and conc units) have specific required entries. To speed entry in these fields, it is only necessary to enter one letter. The accepted letters are: FIELD LETTER DISPLAY -------------------------------------------- MATRIX: S SOIL W WATER SAMPLE (g/ml): G G M ML LEVEL: L LOW M MED EXTRACTION: F SEPF C CONT S SONC GPC: Y Y N N COLUMN: P PACK C CAP CONC UNITS: L UG/L K UG/KG Once you conplete the entries, the QUAN report is read in and the EDIT screen is displayed. The entry results can be edited at this time. Hitting ESC will print the form. An EPA CLP FORM I is printed. This matches the CLP format report in most ways. The few descrepiencies are: fixed 34 compounds per page, the report footer does not say 1/87 Rev and the SV page 2 does not have the diphenylamine note. The header form number says only 1 instead of 1A or 1B or 1C etc. MSFORMS page 22 CONFIGURATION MENU ------------------ This selects the configuration menu, which offers the following options: CONFIGURE MSFORMS CONFIGURE MENU CONFIGURE EPA HEADER RETURN TO MAIN MENU CONFIGURE MSFORMS ----------------- This allows you to set the DRIVE:\PATH specifications for where MSFORMS will look for its own files (NAMES.xxx etc.), as well as where it will look for your QUAN files. This will eliminate the need to enter a drive specifier, as well as allow you to keep the files in another subdirectory, if you so desire. Enter drive specifiers as 'A:' or 'A:\' not simply 'A'. Enter path specifiers as 'A:\path' or 'A:\path\' or '\path\'. The preceding backslash is required if no drive specifier is included. The trailing backslash can be omitted because CONFIGURE will add it if omitted. The report options are: a: PRINT 'J' VALUES - a yes/no answer is required. If you answer NO the 'ND' will be printed in place of the 'MDL' or 'J' values. The form footer information will be changed from the 'U', 'J' info to read "ND = indicates the compound was analysed for, but not detected at a detection limit of 'x'". Where 'x' is the MDL value found in the first record (IS#1) of the NAMES.xxx file. This value will be adjusted for dilution. b: U/J CUTOFF - enter percent (1 - 100). If you answer Yes (a: above), then you will be asked for the 'U/J' cutoff (This step is omitted if you answered No). The U/J cutoff is the percentage of the MDL value you wish J values reported to. ie: If the MDL is 10 and you wanted to report J values down to 1, then enter 10 (10% of 10 = 1. 100% would only report MDL's and no J values). c: NUMBER OF LINES/PAGE - a numeric value greater than zero. This tells the printing routine how many LINES OF RESULTS to print per page. d: TWO COLUMNS - a Yes/No answer is required. 'Y' will cause two columns of results to be printed per page in 15 cpi print format. 'N' will cause only a single column of results to be printed per page in 10 cpi print format. MSFORMS page 23 e: PRINT CAS # - a Yes/No answer is required. Turns on or off the printing of CAS#. f: PRINT SURROGATES - a Yes/No answer required. Turns on or off the printing of the surrogate percent recoveries. If surrogate printing is turned off, the program will continue to calculate surrogate percent recoveries and append them to the surrogate summary file. g: PRINT DILUTION FACTOR - a Yes/No answer required. Turns on or off the printing of the dilution factor used for analysis. This will appear on the bottom of the report opposite the RESULT UNITS:. h: PRINT % MOISTURE - a Yes/No answer required. Turns on or off the printing of the % moisture value. This will appear on the bottom of the report underneath DILUTION FACTOR. A % moisture will be printed only if one is entered. When the screen comes up, the current settings are displayed. In most cases hitting return without entering anything will retain the current setting. The two settings that require explicit entry each time, are the two Path:\directory entries. This is because a null path IS a valid entry and the computer cannot distinguish between retaining the current entry or changing it to a null. Last but not least, you are asked if you want to save the configuration info. 'Y' saves it to a disk file (MSFORMS.CFG). 'N' does not save it, but puts the changes into effect for the duration of the session. At startup, MSFORMS will read in the configuration info and put the values into effect. MSFORMS will require the MSFORMS.CFG file to be in the same directory as itself. CONFIGURE PRINTER ----------------- The printer configuration screen will allow you to configure the program to work with your printer. The following entries are required: BELL LINEFEED FORMFEED COMPRESSED (17 cpi) DOUBLE WIDTH UNDERLINE ON UNDERLINE OFF EMPHASIZED ON EMPHASIZED OFF 10 cpi (PICA) RESET MSFORMS page 24 The filename MSFORMS reads in at startup is PRINTER.CFG. Two printer configurations are supplied, EPSON (EPSON.PRN) and HP laserjet II (HPLJET.PRN). Copy the appropriate file to PRINTER.CFG, or create your own configuration file. The control code sequence MUST be entered as the decimal values separated by commas. NO SPACES ARE ALLOWED. The HP laserjet does not support double width printing - so 'NONE' is entered in this field (see file). When the screen comes up, the current entries are displayed. Hitting return without entering anything will retain the current values. CONFIGURE EPA HEADER -------------------- This section accepts data that remains fairly constant in the header of the EPA reports. It will create a file for later retrieval during program execution. The display wiil be: LAB NAME: ......................... CONTRACT: ........... LAB CODE: ....... CASE NO: ...... SAS NO: ....... SDG NO: ...... LEVEL:(low/med) ...... VOLATILES COLUMN: (pack/cap) ........ SEMIVOLATILES: EXTRACTION: (SepF/Cont/Sonc) .... GPC CLEANUP: (Y/N) ... The same single letter entries mentioned above, also applies here. There is no entry validation performed here. MSFORMS page 25 COMPLETE SYSTEM OPERATION ------------------------- We have covered MSFORMS, now lets cover the complete operation from getting the QUAN report from the MS to generating the printed report. To start, it is necessary to connect the PC up to the NOVA computer and use it as the system terminal. To do this you need to disconnect the communications cable from the back of the mass spec terminal and connect it to the SERIAL port of your PC. Next you will need a suitable communications terminal emulator program which is capable of capturing data displayed to the screen into a disk file on your PC. At the very least the program should be able to emulate a DEC VT-52 or VT-100 and best of all should be able to emulate a Tektronix 4010. Although most all text only type emulators should work - I have only tried the DEC and TEK emulators. The communications parameters will need to be set up properly if you hope to have a meaningful communication with the NOVA. The parameters are: BAUD RATE : 9600 DATA BITS : 7 STOP BITS : 1 DUPLEX : HALF PARITY : SPACE A note about parity - the WESTWARD terminal uses SPACE parity and TekTERM supports SPACE parity. However some communications programs do not - so experiment with what is available. I would like to recommend a program that is in the public domain. It is called TekTERM and it is a DEC VT-100 emulator with a tektronix 4010 emulator built in. This program is outstanding. It is incredibly easy to use (the 'manual' is one page), offers high resolution text (VT-100 mode) and best of all, complete tektronics 4010 emulation WITH FULL GRAPHICS!!! The PC display does not have the resolution of the tektronix, but all the information is there - highly readable. In addition, the cross-hairs work perfectly. You can display CHRO, use the cross-hairs to select a scan and go into SPEC and look at the spectra. It's all there. The program is in the public domain and available from user groups. It is disk # 441 from PC-SIG (1030 E. Duane Ave. Suite D, Sunnyvale, Ca 94086 @ $6 + 6.5% sales tax in Ca. each). I will also be happy to provide the program free to all who register MSFORMS. Since there are many communications programs that you could use, I cannot even begin to give detailed instructions as to how to go about downloading a QUAN report that would be meaningful. Therefore my discussion will use the TekTERM program mentioned above. MSFORMS page 26 Assuming the PC has been properly connected to the NOVA, the TekTERM program is started by entering TT at the DOS prompt. The opening screen displays with the four possible commands listed at the bottom. ALT-L will ask for the configuration file (4600 in my case), then ALT-C will connect you (put you on line with the NOVA). If you do not get the MSDS prompt(>) or IDOS prompt(+) right away, press return. If that does not bring it up check your communications parameters. (Make sure your COM port is properly assigned in both the program and in the computer - no conflicts.) Assuming we have a prompt, you will need to be in MSDS. To list a QUAN report on the screen you would type QUAN <filename>. This will display the requested QUAN report. However this will also pause after each page and wait for a RETURN before displaying the next page. This is fine on the screen, but we want to capture the displayed QUAN report to a disk file so it would be nice not to have to keep pressing return. I have two very short procedures on my MS to handle VOA and SVO QUAN reports. They are: DUMPVO.PR = QUAN $(D;;;;E DUMPBN.PR = QUAN $(D;;;;G2;;;E These will display the QUAN reports without having to keep entering RETURNS. Back at our display we have the MSDS prompt (>) and we wish to capture the QUAN report for file 86M1BN0245. 1) Type DUMPBN 86M1BN0245 - do NOT hit return yet. 2) Press F4 - this starts the capture routine. - a prompt will appear asking for the name to give the captured file. - enter QUAN245.BN (remember the file name restrictions). - press RETURN 3) Now you are back at the MSDS display with the cursor under the captured filename prompt. NOW press RETURN. 4) After a brief delay, the QUAN report will scroll by. There should be intermittent disk activity as the QUAN report is written to disk. 5) Once it is finished and you have the MSDS prompt back - press F4 again (this closes the captured file). That's all there is to it. The captured file is now ready to be processed by MSFORMS. It shouldn't take much to see that downloading a lot of files can be automated somewhat by using an MSDS procedure driven by a name list. MSFORMS page 27 FINAL NOTES ___________ The captured files can be processed without further manipulation by MSFORMS. As I mentioned earlier, MSFORMS provides a results editor for the analyst to correct false hits, etc. If the BATCH mode is employed, this results editor is bypassed to allow multiple files to be processed unattended. If it is necessary to edit any of the files to be processed in BATCH mode then an ASCII text editor will be required. WORDSTAR(tm) when used in it's non document mode is an excellent choice. Points to remember regardless of which editor is used. The position (column) is important, so be sure to overwrite what is there - not insert. Since the position of compounds in the QUAN list MUST match the positions of compounds in the NAMES name list it will be necessary to reposition any compounds to their correct position in the list if they are added after the QUAN report has been created. I achieve this (very infrequently - if your library lists are set up properly) by setting $8 to a shortened filename. Then append the missed compounds to this list. When all the missed compounds have been found, a procedure similar to the following will insert the compound into the correct place. XYZ.PR = EDQL 86M1VO0281,DEC(-4,42;W;E EDQL 281,DEC(A;E EDQL 86M1VO0281,DEC(-1,4;A;E EDQL DEC,86M1VO0281 Then review it and W;E if its correct. Newer versions of Finnigan software allow sorting the quan list by library number - this is much faster than the method above!!! Lastly, the name assigned to the captured file. In my lab the GC/MS runs are assigned filenames like: 86M1BN0245 - the first two characters (86) signify the year. - the second two characters (M1) the instrument number. - the third two characters (BN) the analysis type. - the last four characters (0245) a sequential number assigned at run time. All of that will not fit into a DOS filename. So it must be concatenated into something meaningful within the limits of DOS (8 characters). Remember I limit your choice of extension to two letters. The maximum number of entries currently supported (at least on the edit screen {2 screens}) is 160. Raw result values up to (8 digits) will be correctly parsed. Values larger than that will be truncated on the left. MSFORMS page 28 FINALLY ------- This program began in July of 1986 as a programming exercise I set myself. First I discovered how easy it was to connect a PC to the mass spec, then I wanted to find out what would be involved in processing a captured QUAN file. Therein began the start of this program. As I proceeded with my project it grew bit by bit until it reached its present form. I use it daily in my laboratory, and it has increased my productivity considerably. I no longer need spend hours processing yesterdays data. I can now complete the data in about half the time, and with fewer errors. I decided to distribute the program as I felt other labs could make use of it also. However, the future of the program depends on you the end user. User support through registration will assure continued development and phone support (but only for registered users). Your comments and suggestions are not only welcome but encouraged. Please let me know what you like about the program, and what you dislike (with suggestions for improvement, please). Let me know what you would like to see added in future versions. If a sufficient number of people request a particular change, then I will do my best to implement it. All other suggestions will be considered, and implemented where feasible. BUGS!!! Although I have been using this program in my own lab for a while now and even though I have done my best to detect and eliminate these pesky creatures, I am sure some of you will manage to find some. Please let me know if you do. I also need to know what produced the bug and what it did. I'll do my best to fix any bugs in a timely manner. What am I looking at doing in future revisions? 1) Non dependent positions of the compounds in the QUAN report. Probably through the use of a code that would have to be in your library compound name - ie: the first four characters. Now you know what that CODE entry in NAMES is leading up to! Comments? 2) Another module to generate QC SAMPLE reports. 3) Support for the CAS # on the printed report. (CLP forms) **** completed March 1988 **** 4) Automatic page breaks if you have more than about 70 reportable compounds. **** completed June 1988 **** ***** user definable page breaks also ***** 5) Builtin terminal emulator. MSFORMS page 29 TECHNICAL NOTES --------------- 1: FILE CHECKING QuickBASIC's error handling is terrible. Unfortunately it has deteriorated with QB4, rather than improving. As a result of this, I have written a file checking routine that checks for the presence (existance) of a file in the specified DRIVE:\path, immediately after you enter the filename. If the file does not exist, the error is reported and you are asked to reinput the filename. In addition, certain critical MSFORMS files are also checked. Their absence will usually abort the procedure (reporting the error and the missing filename to you first). The file checking is fairly transparant with a hard disk, but quite noticable if you are using floppies. 2: MSFORMS is written in QuickBASIC and requires version 4. The screens and most fielded input is written in assembler. The windowing routines were written in assembler in previous versions. From version 2.10 on, the windowing routine is written in C, as is the file checking procedure and some fielded input and all function key input. Microsoft C version 5 is required for linking (MEDIUM memory model library). Because of the requirement of the C library, I will not automatically be supplying the source code. Instead, I have included a place on the registration form for requesting it. ONLY the QuickBASIC source code will be supplied. The rest (the assembler and C procedures) will be supplied as linkable libraries. However in order to recomplile the program you will have to have the following: Microsoft QuickBASIC 4 Microsoft C compiler version 5 or QuickC Microsoft LINK version 3 or later (supplied with the above compilers) You should also have: Microsoft Library Manager (LIB) Microsoft MAKE Microsoft CODEVIEW version 2 (these are supplied with MSC 5) Remember one of the above C compilers IS REQUIRED to recompile the source code because the C MEDIUM memory model library is used. MSFORMS page 30 REGISTRATION FORM ----------------- If you purchased MSFORMS directly from me in your own name, then your copy is already registered and you will receive all the benefits of registration. You do not need to send in a registration form. If you received MSFORMS some other way, you may register your copy by filling out the following form and mailing it to the listed address along with $50 (shipping and handling included). You will promptly receive the latest version of MSFORMS. (Request TekTERM if you wish a copy). You will also be placed in database of registered users so that you will automatically be notified of any MSFORMS updates. Mail to: Declan Cowley 801 Seminole Blvd. Geneva, Fl 32732 NAME : __________________________________________ COMPANY : _______________________________________ ADDRESS : _______________________________________ CITY/STATE : ____________________________________ ZIP : _______________ PHONE : _____________________________ WHICH VERSION OF MSFORMS DO YOU HAVE : __________________________ WHICH MODEL MASS SPEC DO YOU USE : ______________________________ WHAT REVISION OF INCOS DO YOU USE : _____________________________ DO YOU WANT THE QuickBASIC SOURCE CODE YES( ) NO( ) How did you first learn about MSFORMS or where did you first obtain a copy of MSFORMS? __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ MSFORMS page 31 CUSTOM VERSIONS OF MSFORMS -------------------------- Do you like the program generally, but certain parts do not meet your specific needs adequately? Well if so, then a custom version may be what you need. I am willing to do customizing of MSFORMS if the project is reasonably practical to implement. You will need to call me and discuss it on an individual basis. Any costs involved would be based on the amount of time and effort required to implement your request. As the saying goes, 'Nothing is impossible - it just takes a little longer to implement!' Declan Cowley December 1986 MSFORMS page 32