Upgrade Decisions

A data system consists of three primary elements:

  • Computer
  • Data processing package
  • Acquisition software and electronics

Introduction of a new PC to an older instrument provides extraordinary gains. Consider these PC features:

  • Operating system, Windows 8®, Windows 7®, Windows Vista®, or Windows XP.
  • Large hard drives for data storage, e.g., 1TB and greater.
  • Fast, multi-core processors.
  • Powerful but easy networking, usually built in.
  • Versatile local and network printer support.
  • Data archival media such as CD-R and DVD±R.
  • Large, eye-friendly displays.

Older data systems based on PC technology, usually cannot take advantage of today's PCs, due to hardware timing issues or incompatible interface buses. Even without these issues, getting an old MS-DOS, Windows 3.x, or Windows 9x based system to run a new PC is usually difficult, and typically isn't worthwhile since the data system remains obsolete.

A replacement data system needs to have access to a strong data processing package.  Vx Acquisition can generate Agilent MSD ChemStation, Varian WorkStation, and Andi NetCDF data files.  This allows your laboratory to choose the optimal data processing package.

The heart of the data system is its acquisition package. The Adron data system is supports a wide range of mass spectrometers, chromatographs and auto samplers. These components can be mixed and matched as required. For different instrument configurations, our software offers a consistent user interface.

Our data system provides versatile instrument control, including computer control of many chromatographs and autosamplers. (See our  instrument page  for supported instruments.)
Consider these aspects:

  • Instrument condition
  • Original data system condition
  • Replacement data system benefits
  • Replacement data system costs

Consider these axioms:

“Invest only in solid instruments!”
If your instrument performs well, is reliable, and generates good data, consider a replacement data system.
“Invest only in strategic instruments!”
What role does this instrument play in your laboratory?
The value of your older instrumentation on the resale market may be relatively modest.

However, your older instrumentation may have high value to your company's operation.  This is particularly true if your instrumentation has been, and continues to be, a strong revenue generator for your lab. Instrumentation replacement costs usually are much higher than the cost of a replacement data system.

Consider your staffs' knowledge. If your lab's personnel know how to maintain, and repair your vintage machines, this is a tremendous value. If your lab utilizes several similar instruments, these benefits are compounded.

The goal of our data systems is to extend the useful life of these vintage machines, so they can continue to be strong revenue generators for your lab.

We use the term “vintage” in recognition that many older quadrupoles and ion traps are good performers; generating excellent data with good reliability.

Data Systems

A combination of improved mass scanning electronics, more sensitive (and less noisy) ion input electronics, signal averaging and signal filtering can contribute to improve mass spectrometer performance. This applies to analog quadrupole instruments (Finnigan, Extrel, Nermag) controlled by our TEK-803 board. See the next two questions regarding  sampling rate  and  ion signal resolution.

Additionally, today's PC offer greatly improved I/O speed and processing power compared with the original data system. Increased I/O speed allows data from the instrument to be pulled in more quickly. Less time pulling in data means more time is available for scanning, signal averaging and filtering. A performance gain for digitally controlled instruments such as Hewlett-Packard quadrupoles, Finnigan and Varian iontraps.
The sampling rate of the Teknivent analog acquisition unit is 33 kHz. This sampling rate can be utilized (“partitioned”) in different ways during a scan.

Scan speed (in terms of amu/sec) is developed by parsing these samples across the acquired mass range.

The first parameter that must be specified is how many sample points are needed to characterize a mass spectral ion peak. On a quadrupole instrument (with unit resolution), the peaks are usually one amu wide, and typically 8 points are needed per peak in order to characterize it well enough for a peak detector to consistently determine peak centroid value and position.

On a 1000 amu scan, 8000 points (8 points per amu x 1000 amu) would be needed. At the 33 kHz rate, this would allow the scan to be completed in about 0.25 second. A rate of 4000 amu/sec would be possible based on our electronics.

In most quadrupole instruments, this rate is not achievable based on the mass filter electronics within the spectrometer. In these cases, the speed can be “slowed down” by taking multiple points at each amu step and averaging or summing these values together. For our example above, if we took 4 samples at each amu point it would take 32 sample conversions (8 points per amu x 4 sample readings per point) to acquire a single amu. In this case, to scan 1000 amu would take 32,000 points or approximately 1 seconds based on the 33 kHz overall sample rate.

The combination of points per amu and number of conversions per point directly determine the scan speed. For most applications, 1000 amu/sec scan speed is more than enough and easily falls within the bandwidth of our system.
The incoming analog ion signal from the mass spectrometer enters the analog-to-digital (A2D) circuitry within our interface electronics. Once there, an autoranging input circuit of different gain ranges (x1, x10, x100) determines the best gain channel for the signal. For instance, signals below 100 mV are amplified by the x100 channel, signals between 100 mV and 1 V by the x10 channel, and signals above 1 V by the x1 channel. The “preconditioning” amplified signal passes through a 16 bit A/D (65535 points) convertor and is numerically scaled to represent the original incoming signal.

The system has a input dynamic range of 1 : 6553500 counts on a single sample reading allowing digitizing of analog values down to around 1.5 µV (10 V full scale input / 6553500 points).
For serial control of your chromatograph, you need a Varian serial interface board and a compatible Varian CPU board. These boards reside in slots on the left side of the instrument. Slot "S I/O" is for the serial board. The revision number for the CPU board can be noted when the chromatograph first starts or "INSTR TEST" is invoked. The number is of the form:


where "xxx" is the number of interest. These boards usually work:

  • 336
  • 514
  • 526
  • 544  some work fine; others don't!
  • 586
  • 617
  • 684

The following boards  do not work:

  • 240
  • 254
  • 316
  • 447  has a timing issue
  • 456

Generally, boards in the "5xx" and "6xx" series do work. We haven't found any boards in the "2xx" serial that work. For other boards in the "3xx" and "4xx" series, we just don't know!

Note: For the Varian 3400, Vx Acquisition defaults to 2400 baud. On the Varian S I/O board, locate switch S3.  For 2400 baud, set #2 of the DIP switch to the ON (up) position. Set all other positions of the DIP switch to the OFF (down) position.
The recommended cable is available from  Adron Systems LLC.

Adron's part number is V3400-CBL. This is a custom 3 meter cable.

The computer side has a female (receptacle) 9-pin D-sub connector that attaches to the PC's serial (COM) port. On the GC side is a male (plug) IEEE-488 style connector (AMP CHAMP) that attaches to the Varian S I/O card. The GC connector has a grounding strap that connects to the chassis of the Varian 3400. The grounding strap is attached to the cable's shield.

Note:  Equivalent cables are no longer manufactured by Thermo-Fisher Scientific or Varian.
The recommended cable is available from  L-com® Connectivity Products.

L-com's part number is CSNULL259MF-10 with the description “Deluxe Null Modem Cable, DB25 Male / DB9 Female, 10 ft.”

This cable is compatible with the HP7673A and HP7673B autosampler models. This cable is also used for serial control of the HP5890 Series II GC when using the DICE interface connector.
The recommended cable is available from  L-com® Connectivity Products.

L-com's part number is CMZ10-IBM with the description “Molded AT Modem Cable, DB25 Male / DB9 Female, 10 ft.”
Wild Hare Computer Systems  specializes in Data General computers such as those used by older Finnigan MAT GC/MS systems. Wild Hare provides media conversion services for these systems.  Wild Hare can transfer data from backup tapes to new media such as CDs or DVDs.

An inexpensive but time-consuming approach for moving data off of your Data General computer relies on using a PC as a terminal. The PC, running a terminal emulation program, allows data to be transferred from the Data General computer.

Our colleagues at MasCom Technologies GmbH provide the GetRun scripts for pulling Finnigan MI,MX files off of the DG-10 computer. The script files can be modified with a text editor to match your needs.

We would suggest trying the E-Term32 terminal emulation program from DCSi. This terminal emulator supports MasCom's GetRun scripts.

Note: E-Term32 doesn't support the VTMODE command in the GetRun ECF scripts, so you'll need to delete the VTMODE lines.

Note: If your Finnigan data is in MI,MX or TI,TX,CT format, then check out our  Vx Capture™ GC/MS data conversion program. Vx Capture  can convert these Finnigan file formats over to Agilent MSD ChemStation, Varian WorkStation and Andi NetCDF data files.

Send Adron Systems one of your Finnigan data files and we'll return a converted file to you.
An “analog” mass spectrometer is controlled by voltage or current settings.  For example, the mass scan signal is often controlled by a 0 to 10 voltage.  This voltage maps to (corresponds to) the ion mass being scanned. Analog controlled instruments are generally older machines.

In contrast, a “digital” mass spectrometer is controlled by digital signals from the data system, typically over a GPIB, LAN or proprietary connection.  Newer mass spectrometers have total digital control by their data system. Information (data) from the instrument is returned as digital signals.

It is possible to have an instrument requiring both digital and analog control or digital and analog return signals.
Adron Systems does not provide Finnigan or Varian software for these ion traps.

Vx Acquisition provides extensive control of these ion traps under Windows 7® and Windows XP. Please visit our product page for detailed information.
Magnum_Traces.pdf  contains ion gate plus RF sweep signals for various ion trap operating modes.

Although not posted as a question, the operating modes of the Finnigan ion trap are confusing, especially to new users. Hopefully these oscillographic traces will aid in understanding the ion trap's operation.
In quadrupole instruments, a mass scan takes place in one continuous sweep.

Ion traps, such as the Finnigan Magnum and Varian Saturn, can sweep a mass range much faster. For signal-to-noise improvements, several “micro-scans” are averaged together, forming the apparent mass scan. More micro-scans means better quality mass spectra are generated for the ion trap.

In Vx Acquisition, the number of micro-scans can be monitored while running an acquisition method.

Vx Acquisition™

We've taken the "V" from our Vector series of data systems. The "x" because its our neXt data system.
Adron Systems is emphasizing that Vx is focused on controlling and pulling in data from the instrument, i.e., the acquisition of data.

Processing of data is left to another package such as Agilent's MSD ChemStation, Varian WorkStation, Thermo XCalibur, or another user specified package. Vx works with a variety of processing packages because it can generate target data files in a variety of formats.
Vx Acquisition is a native Windows application targeting Windows 7, Windows Vista, and Windows XP. Vx provides versatile instrument configuration. The user interface for Vx takes advantage of modern Window user interface elements. For a preview, go to our Vx product page.
Suggested PC:

  • Windows 7
    • 2 gigahertz (GHz) minimum processor
    • Dual-core Intel or AMD processor minimum; Quad-core or higher recommended
    • 2 gigabyte (GB) RAM minimum for 32-bit Windows 7
    • 4 gigabyte (GB) RAM minimum for 64-bit Windows 7

  • Windows XP
    • 1.2 gigahertz (GHz) minimum processor
    • Dual-core Intel or AMD processor recommended
    • 1 gigabyte (GB) RAM minimum

  • 2 serial ports (one for chromatograph; one for autosampler)
  • 1 USB port
  • 1 full-height PCI port (for National Instruments' PCI-GPIB card)

  • or

  • 1 full-height PCI Express slot (for National Instruments' PCIe-GPIB card)

Suggested Monitor:

  • 17" minimum, 19" or greater recommended,
  • 1280x1024 resolution or greater

Operating Systems:

  • Windows 7 (32-bit or 64-bit) or Windows XP Pro
Vx Acquisition, Vx Capture and Vx Extract support the new Microsoft Windows 7 operating system, 32-bit and 64-bit editions.

Interested in Microsoft Windows 8® support? Contact Adron Systems for further assistance.
The “Getting Started” document is written for ion trap users and contains detailed steps for tuning the ion trap.
We would also suggest looking at the screenshots in Magnum_Images.pdf.
Vx Acquisition will save the data in its native format (Adron TKF) and optionally convert to the user specified target form.

If you rely on a “post-acquisition” macro for data conversion, this macro is not called. In this case, you would manually need to invoke the macro to convert your data.

You can also use Vx Capture to convert from the Adron TKF format over to a desired target format.
Dear Confused,

AGC, or automatic gain control, is a mode that attempts to keep the same number of ions present in the ion trap during each scan. As chromatographic peaks elute from the capillary column, the molecular concentration in the ion trap changes drastically. With AGC enabled (on), the ionization window (gate) is shortened as molecular concentration increases.

The ion trap accomplishes this by doing a “pre-scan”. Essentially, a very quick scan is taken to determine concentration. The result of the pre-scan adjusts the ionization gate for the actual scan. With AGC, the actual ionization time can vary from 100μs to 25000μs. (This range is adjustable in the Vx Tune section, under the Init_EI setpoints.)

With AGC enabled, masses less than the AGC_ON_BackMass value are tossed away.  AGC_ON_BackMass is typically set at 50 m/z.

To monitor air and water peaks, AGC needs to be disabled. Otherwise, due to the AGC_ON_BackMass value, these ions would be thrown away. The AGC_OFF_Ion_Time is a fixed ionization time used when AGC is disabled.
First, make sure you've specified a calibration file in the Method's “Scan Setup” page. Without a calibration file, setpoints configured in Tune are not loaded!

Second, make sure to enable the mass spec in the “Scan Table” section.  Without this, the mass spec is never turned on. See the following picture: Method - Scan Setup.
The evaluation version of Vx Acquisition is supplied with a USB licensing key. If this key has expired, or has not been installed correctly, then the program reverts to “demo” mode. This is what you are experiencing.  The following document may clarify things: Adron_USB_Key.pdf.

Adron USB (HASP) drivers are available at:

Current HASP drivers are also available from the SafeNet website.

Vector/2™ & EnviroLink™

From an acquisition standpoint, Vector/2 and EnviroLink are nearly identical.  Instrument tuning, calibration and data acquisition are the same. A few instrument control parameters are hidden in the EnviroLink system to aide good laboratory practices.

Vector/2 has its own native processing, library and quantitation packages.

EnviroLink, as a derivative of Vector/2, was introduced to take advantage of the HP (Agilent) MSD ChemStation quantitation package for data processing.

EnviroLink and Vector/2 normally ship with copies of Agilent MSD ChemStation unless the purchaser specifies otherwise.
We refer our Vector/2 and EnviroLink customers to Vx Acquisition since this is our latest product; offering easy instrument configuration and control.

Many Vector/2 and EnviroLink customers prefer their original platform. For these customers, we offer the “On Windows” versions of Vector/2 and EnviroLink.

EnviroLink on Windows and Vector/2 on Windows products allow OS/2 EnviroLink and OS/2 Vector/2 to run on top of Windows XP using “virtual pc” technology.

Agilent MSD ChemStation runs directly on the Windows desktop, easing user interaction and printing.
Suggested PC:

  • Windows XP
    • 2 gigahertz (GHz) minimum processor
    • 512 megabyte (MB) RAM minimum
    • 40 gigabyte (GB) or greater harddrive

  • CD-ROM or CD-RW or DVD±R
  • 2 serial ports (one for chromatograph; one for autosampler)
  • 1 parallel port
  • 1 full-height PCI port (for National Instruments' PCI-GPIB card)

Suggested Monitor:

  • 17" minimum, 19" or greater recommended,
  • 1280x1024 resolution or greater

Operating Systems:

  • Windows XP Pro
Adron Systems' staff is very familiar with Teknivent and its products.

Adron Systems provides the only upgrade option for Vector/2 and EnviroLink users through its Vx Acquisition product. Please visit our product page for more information.

Vx Acquisition supports the Finnigan Incos 50, 500 and XL instruments.

If your instrument already has Vector/2 or EnviroLink, your investment in Teknivent hardware is preserved with the Vx upgrade. In this case, an upgrade consists of a new Windows 7 computer and National Instrument GPIB card. An optional upgrade to Agilent MSD ChemStation is available.

Teknivent Corporation ceased operations in 1996.