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Mass Spec Tips

Tip

Mass Spec Tips is a collection of tips relating to the operation and service of mass spectrometers. Some of these Tips have been reported in our newsletter, "The Mass Spec Source." If you have a question relating to the operation or service of mass spectrometers and would like to have it included in this forum, please Contact Us. Input to this database of MS Tips is needed from our readers to complete this section.


A new 24 page booklet is available written by John Manura of Scientific Instrument Services on the techniques and steps that have been taken to improve the performance and signal-to-noise ratios on the HP 5971 MSD's in our labs. This article combines the experience of more than 20 years of expertise in mass spec to operate the mass spec at its peak performance. The article also describes the improvement in performance by using new higher sensitivity multipliers, high grade vacuum pump oils and other products available from S.I.S.. Call or write for your FREE copy.

Application Notes

A series of 32 application notes on the use of our Short Path Thermal Desorption System and GC Cryo-Trap are available. Applications include the analysis of volatiles in food, forensic samples, plastics, air and commercial products. These application notes are available FREE on request.

The Mass Spec Source Newsletter

Our newsletter 'The Mass Spec Source' is published twice a year. This newsletter is designed for the mass spec community and features articles of interest to the mass spec user, mass spec tips, new products available and other items of general interest to the mass spectrometer user. The newsletter is FREE on request.


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  • 1 - Freon for use in Mass Spectrometer Leak Checking1 - Freon for use in Mass Spectrometer Leak Checking
    MS TIP No. 1 - Freon for use in Mass Spectrometer Leak Checking Author: John J. Manura Affiliation: Scientific Instrument Services Many mass spectroscopists have routinely utilized Freon (Dichlorodifluor-methane) for locating mass spectrometer vacuum leaks around flanges, feedthroughs, probe inlet seals, diffusion pumps and other seals on the mass spectrometer vacuum system. The product was convenient to use since it was supplied in a small compressed air can with a nozzle (DustOff by Falcon Pro
  • 2 - Mass Spectrometer Probe Cooling2 - Mass Spectrometer Probe Cooling
    MS TIP No. 2 - Mass Spectrometer Probe Cooling Author: John J. Manura Affiliation: Scientific Instrument Services The probe shafts on many mass spec probes can become excessively hot when the probes are used. Many probe tips reach temperatures in excess of 500 degrees C. In addition the probe tip and shaft can be further heated via thermal conductivity from the mass spectrometer source to which it is mated. When the probe is removed from the source, if the probe shaft is in excess of 200 degrees
  • 3 - Sample Vials for Direct Probes3 - Sample Vials for Direct Probes
    MS TIP No. 3 - Sample Vials for Direct Probes Author: Christopher Baker Affiliation: Scientific Instrument Services Sample vials for use in direct probes have been made of a variety of materials including aluminum, gold, quartz and Pyrex glass. Quartz, gold and aluminum vials are fairly expensive and therefore many users elect to reuse the vials after cleaning between samples. This is time consuming and care must be taken to insure that the vials are completely clean to eliminate cross contamina
  • 4 - Selection of Vacuum Pump Oils for Lowest Mass Spec Background4 - Selection of Vacuum Pump Oils for Lowest Mass Spec Background
    MS TIP No. 4 - Selection of Vacuum Pump Oils for Lowest Mass Spec Background Author: John J. Manura Affiliation: Scientific Instrument Services Significant background peaks are present in the mass chromatogram especially when using the mass spectrometer to detect and identify samples in the sub nanogram levels. These peaks occur due to backstreaming of the hydrocarbons from the oils into the mass spectrometer source. In both the rough pumps and the diffusion pumps, oils are used which can contri
  • 5 - Determination Linkages in Biomolecules of Disulfide5 - Determination Linkages in Biomolecules of Disulfide
    MS TIP No. 5 - Determination of Disulfide Linkages in Biomolecules Author: Anonymous Affiliation: Pharmaceutical Industry A fast and easy way to detect the presence of disulfide linkages in peptides during static FAB or LISIMS analysis is to dissolve the analyte in a sulfur containing matrix (i.e., thioglycerol, magic bullet, etc.) and add a trace amount of dilute ammonium hydroxide. We have found that this mixture causes immediate reduction of disulfide linkages (converting them to free-SH grou
  • 6 - Transfer of H.P. ChemStation MS and GC Chromatograms from PC to MAC Computer6 - Transfer of H.P. ChemStation MS and GC Chromatograms from PC to MAC Computer
    MS TIP No. 6 - Transfer of H.P. ChemStation MS and GC Chromatograms from PC to MAC Computer Biomolecules Author: John J. Manura Affiliation: Scientific Instrument Services In our laboratory we presently utilize two H.P. 5971 mass spectrometers and one H.P. 5989 Engine for the analysis of samples from our Short Path Thermal Desorption and also in our mass spectrometer probe development work. All the data is collected on PC computers utilizing the H.P. ChemStation Software used in the Windows envi
  • 7 - Repairing Clogged Thermospray Probes7 - Repairing Clogged Thermospray Probes
    MS TIP No. 7 - Repairing Clogged Thermospray Probes Christopher Baker Scientific Instrument Services Probe inserts for the thermospray interfaces used by Vestec, Hewlett-Packard and others become clogged by salts, polymers and particles. Use of an in-line filter before the probe removes the particles, but will not completely eliminate the problem. The probe, with its small inner diameter, typically 100 microns, is still susceptible to clogging. We have designed a probe insert in which clogged ca
  • 8 - Tuning a Finnigan 5100 to Meet BFB or DFTPP Criteria8 - Tuning a Finnigan 5100 to Meet BFB or DFTPP Criteria
    MS TIP No. 8 - Tuning a Finnigan 5100 to Meet BFB or DFTPP Criteria Author: Dennis Beauchamp Affiliation: Roy F. Weston FC43 TUNING AND CALIBRATION It is best to reproduce the same conditions for tuning every time you tune. For best results I always make sure that the GC is at the same temperature every time I look at FC43, usually the initial temperature of the GC program used to direct inject the BFB or DFTPP. Also the system should be under vacuum for at least 8 hours. Although the exact rati
  • 9 - H.P. 5971 Transfer Line Tip for Direct Introduction of Capillary Column9 - H.P. 5971 Transfer Line Tip for Direct Introduction of Capillary Column
    MS TIP No. 9 - H.P. 5971 Transfer Line Tip for Direct Introduction of Capillary Column into MSD Source for Improved Performance Author: John J. Manura Affiliation: Scientific Instrument Services In the original gold plated transfer line tip on the H.P. 5971 MSD (H.P. Part # 05971-20305), the GC capillary column is purged inside this fitting and diverted through side vents and then vented into the MSD source. This original H.P. design exposes the analytes being chromatographed to a hot metal surf
  • 10 - Troubleshooting Finnigan 5100 GC/MS Systems10 - Troubleshooting Finnigan 5100 GC/MS Systems
    MS TIP No. 10 - Troubleshooting Finnigan 5100 GC/MS Systems Author: Dennis Beauchamp Affiliation: Roy F. Weston In the lab where I work, we have many GC/MS systems but the majority of the systems are Finnigan 5100's. Many things can go wrong with mass spectrometers but the most common problem is when an analyst injects something and sees nothing. I call this "No Peaks". No Peaks This can be caused by many different things. Troubleshoot the problem with the following procedure. Is the R
  • 11 - Leak Checking Mass Spectrometers11 - Leak Checking Mass Spectrometers
    MS TIP No. 11 - Leak Checking Mass Spectrometers Author: Richard A. Berger Affiliation: Washington University School of Medicine The November, 1993 issue of THE MASS SPEC SOURCE contained a Mass Spec Tip concerning the use of Freon for leak checking Mass Spectrometers. We had used Freon-12 (Dichlorodifluoromethane) for this purpose until it was implicated in the ozone layer depletion phenomena. While Argon (MW 40) works well for leak detection in electron ionization (EI) mode, it does not work w
  • 12 - Elimination of Memory Peaks and GC Background Noise12 - Elimination of Memory Peaks and GC Background Noise
    MS TIP No. 12 - Elimination of Memory Peaks and GC Background Noise Author: John J. Manura Affiliation: Scientific Instrument Services S.I.S. has recently completed an investigation into the causes of memory peaks and background noise in the total ion chromatograms from a Hewlett Packard 5890 Series II gas Chromatograph. A technical bulletin describing the entire study is available from Scientific Instrument Services. A short description of this study is summarized below. To obtain a free copy o
  • 13 - SuperIncos Mapped Software Print Buffer Lockup13 - SuperIncos Mapped Software Print Buffer Lockup
    MS TIP No. 13 - SuperIncos Mapped Software Print Buffer Lockup Noise Author: Dennis Beauchamp Affiliation: Weston Analytics If your Finnigan system has dual terminal operation chances are you have Mapped software. This software is a big improvement over the older revisions but it does have a few quirks. The one that I have had the most is that the printer stops printing. Turning the printer on and off and Rebooting the computer won't fix the problem but the following will. Enter IDOS (+) In IDOS
  • 14 - Reduction of Peak Tailing14 - Reduction of Peak Tailing
    MS TIP No. 14 - Reduction of Peak Tailing Affiliation: Scientific Glass Engineering The occurrence of peak tailing and poor reproducibility can occur with standard syringe injection of liquid samples into the GC injection port. This is a common problem which is consistent with slow volatilization of the sample and/or slow transfer of all of the sample onto the column. It occurs with microvolume syringes when the minute sample being delivered from the syringe forms droplets which wet the syringe
  • 15 - Electron Multiplier Sensitivity15 - Electron Multiplier Sensitivity
    MS TIP No. 15 - Electron Multiplier Sensitivity by John J. Manura, Affiliation: Scientific Instrument Services With the prolific addition of new manufacturers of electron multipliers (mass spec detectors) for mass spectrometers, the competition among manufacturers is becoming fierce. Each manufacturer claims that their multiplier is the most sensitive or has the longest life or the greatest dynamic range. In order to provide mass spectrometers with the optimum sensitivity, the mass spectrometer
  • 16 - INCOS Procedure for Calibrating on the Finnigan 450016 - INCOS Procedure for Calibrating on the Finnigan 4500
    MS TIP No. 16 - INCOS Procedure for Calibrating on the Finnigan 4500 by John Delaney Affiliation: Betz Laboratories I subscribe to the Mass Spec Source and have found it to contain lots of useful information and timely tips. This tip describes an Incos procedure to use while calibrating that your readers should find valuable. While tuning and calibrating on a Finnigan 4500 (operating under SuperIncos) it is desirable to maximize the intensity of the FC43 ions, or any other cal gas for that matte
  • 17 - Extending Electron Multiplier Life17 - Extending Electron Multiplier Life
    MS TIP No. 17 - Extending Electron Multiplier Life 4500 by John J. Manura, Scientific Instrument Services Electron multiplier life is dramatically effected by its operating environment. Vacuum level, pressure surges, solvent plugs and air plugs all can drastically reduce multiplier life. In our labs we have two H.P 5971 instruments, in which we have increased multiplier life to greater than 2 years. This compared to the normal operation by most users of 9 months to 1 year for electron multiplier
  • 18 - What techniques or methods do you use to determine if the electron multiplier18 - What techniques or methods do you use to determine if the electron multiplier
    MS TIP No. 18 - What techniques or methods do you use to determine if the electron multiplier is in need of replacement? How do you determine multiplier gain? What is an acceptable signal to noise level? Answer 1 by John J. Manura, Affiliation: Scientific Instrument Services We posed these questions in our last newsletter because they are often asked by mass spec users. The determination of the gain or proper operation of the electron multiplier may be quite difficult to determine. Factors such
  • 19- What techniques or methods do you use to detect vacuum leaks in your mass spectrometer19- What techniques or methods do you use to detect vacuum leaks in your mass spectrometer
    MS TIP No. 19 - What techniques or methods do you use to detect vacuum leaks in your mass spectrometer? Answer 1 by: William Schutzer Affiliation: Oregon State University We use a HP 5890 GC with a J&W DB5-MS column interfaced to a 5971A MS running under HP ChemStation software. We make it a habit to run an air and water check once a week. When either values for mw 18 (water) or mw 32 (nitrogen/air) rise above 2%, we know we have a leak. Almost always, the leak is due to a loose fitting wher
  • 20 - Extending Lenear Range of the Mass Spec20 - Extending Lenear Range of the Mass Spec
    MS TIP No. 20 - As a detector for GC, mass spectrometry generally has a smaller linear dynamic range than FID. Is there any technique or method to extend the linear range? by: James B. EdwardsAffiliation: Enviroscan Corp. As a principally environmental laboratory, my company does primarily target compound analysis using standard EPA methodologies. We use a Finnigan INCOS 50B with a CTC A200S autosampler for semi-volatiles, and a Finnigan ITS-40 with Tekmar LSC200/ALS2016 for volatiles. As such,
  • Article - Improving Sensitivity in the HP 5971 Mass Spectrometer - Part 1 and Part 2Article - Improving Sensitivity in the HP 5971 Mass Spectrometer - Part 1 and Part 2
    SISWEB Technical Note C. Improving Sensitivity in the H.P. 5971 MSD and Other Mass Spectrometers - Part I of II John J. Manura Scientific Instrument Services, Inc. 1027 Old York Road, Ringoes, NJ 08551 (Part I | Part II - Increasing Mass Spec Sensitivity) Introduction The H.P. MSD instruments (Models 5970, 5971 and 5972) have proven to be very efficient, low cost, highly sensitive and versatile mass spectrometers. Due to their low cost as a complete GC/MS system, the HP MSD's have become the mos
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