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Sample Submission Information
        Electronic Sample Submission Form
       Sample Submission Form
Ionization Techniques




The coupling of new mass spectrometric techniques with new and significant research problems requires considerable interaction between mass spectrometrist and mass spectrometry user. For this reason, Purdue University created the Campus-wide Mass Spectrometry Center (CWMSC) in October of 1985, with the following goals: 

1) to coordinate the operation and maintenance of mass spectrometers which are located in different departments and are used for routine analyses, 
2) to provide research groups working on significant problems with access to all of the mass spectrometers on campus, 
3) to increase awareness in the University community of the opportunities for problem solving by mass spectrometry and
4) to coordinate the acquisition of new instrumentation as needs evolve. 

Decentralization and shared resources are important features of this facility. Key to the success of the facility is the Director, who supervises the staff mass spectrometrists providing routine service across campus, assists investigators in defining (and recognizing) their needs in mass spectrometry, coordinates access to research mass spectrometers and through clinics, research group seminars, and other means educates the University in mass spectrometry. The CWMSC which utilizes mass spectrometers located in the Departments of Biochemistry, Chemistry and Medicinal Chemistry and Pharmacognosy, insures a high level of quality control for the more routine types of analyses, and provides a collaborative analytical mass spectrometry capability to the Purdue research community. In order to more efficiently utilize the mass spectrometry resources on campus the CWMSC has pursued a plan designed to maximize the utilization of the mass spectrometers in the three departments. This is being done in a variety of ways: 

(a) the coordination of sample analyses, since differing capabilities are available in different departments (Biochemistry - capillary GC/MS, electron impact and chemical ionization probe, plasma desorption, matrix-assisted laser desorption; Chemistry - electron impact and positive and negative chemical ionization probe, desorption chemical ionization ICPMS; Medicinal Chemistry and Pharmacognosy - electrospray ionization, electron impact and chemical ionization probe, high resolution mass measurement), 
(b) the education of researchers campus-wide as to availability and capabilities of modern mass spectrometry,
(c) maintaining close investigator-operator ties such that the analysis is not done without the necessary background for providing quality results, and 
(d) the presence of a director to coordinate access to the mass spectrometers, address questions relating to the interpretation of the spectra, train instrument operators, assist users in their search for new research funds and provide troubleshooting expertise to minimize instrument downtime.

The CWMSC is organized as shown in Table 1. The department heads (or their designated representative) meet with the director individually on a regular basis and as a group at least once per year. They act as a resource for the Director as well as to provide their input from a departmental perspective for new initiatives in steering the direction of mass spectrometry at Purdue. Each department head (or their representative) is a mass spectrometry user and is committed to the decentralized, but coordinated concept of mass spectrometry at Purdue. This can be seen by the collaborative effort used to obtain funds from all three departments/schools to purchase the matrix-assisted laser desorption instrument located in the Department of Biochemistry. In addition, the central administration is strongly supportive of mass spectrometry. A former Vice President for Research launched the concept of a Campus-wide Mass Spectrometry Center and provided the Director's salary for the first three years.

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Status of Instruments

Mass Spectrometers at CWMSC
(click on the instrument to view picture)


Instrument Primary Use
Applied Biosystems Voyager DE PRO (Matrix-Assisted Laser Desorption) Nonvolatile components to m/z 100000
Agilent 5975C GC/MS (EI/CI probe and capillary GC/MS)
Volatile components to m/z 1000
Instrument Primary Use
ELEMENT2 (Inductively coupled Argon plasma)
Multi-element analyses
Hewlett Packard Engine (EI/CI probe and capillary GC/MS)
Volatile components to m/z 1000
Agilent 6320 Trap (Electrospray and Atmospheric Pressure Chemical Ionization, LC/MS/MS)

Nonvolatile components to m/z 50,000

Medicinal Chemistry & Molecular Pharmacology
Instrument Primary Use
FinniganMAT XL95 (High Resolution Mass Measurements)
EI, CI and ESl 
Thermoquest LCQ (Electrospray, LC/MS/MS)
Nonvolatile components to m/z 50,000

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Sample Submission Information

Samples can be submitted at any of the three mass spectrometry laboratories.  The electronic sample submission form can be accessed at: www.ras.itap.purdue.edu. First you will need to log-in with your career account. At this point you will want to ‘Create a new job’ which involves giving a sample name and selecting ‘next’. On the next page first time users will be asked for their phone number. Then you will need to provide your account information and the type of mass spectrometric service you require (drop down box). On the opposite side of the page you can provide a description if needed as well as relevant sample information including molecular formula, molecular weight, structure (at present as a downloaded file), solvent, etc. Once you hit submit, the system will check your account number and indicate to you all is okay, do you want to proceed. Assuming yes the next step is to print a copy of the sample submission form. Once printed all you need to do is select done. The final step is to bring the sample submission form and your sample to one of the mass spectrometry labs. At present I would request that you also draw the structure of your reaction and/or expected product on the sample form or provide it on a separate sheet of paper (we sometimes have problems reading the files you include). If you run into any difficulties please contact Karl V. Wood (kvw@purdue.edu).

If you have questions about the best method for obtaining mass spectral results, please give the Director or any of the staff mass spectrometrists a call to discuss.  This also includes any special needs that your sample might require like; being kept in the freezer, the need to analyze right after reaction is completed due to stability, some unique solubility issue, etc.

 If you need to utilize GC/MS or LC/MS capabilities we request that you first determine the methodology, for separation prior to submitting the sample.  In this way we can best try to duplicate your chromatogram and provide you with the information you need.  LC/MS is particularly demanding in terms of the sample and mobile phase requirements, as seen in the next few paragraphs.

 The following is needed to submit a sample for LC/MS  

1.     A new or clean (provide blank chromatogram) LC column and at least one liter of the mobile phase

2.     The LC elution conditions, including (a) flow rate (less than 1 ml per minute is preferred), (b) mobile phase, (c) stationary phase and (d) gradient

3.     The amount of sample injected and the concentration of the sample

4.     A copy of the LC chromatogram showing the peak(s) of interest as well as the wavelength used

5.     A standard where applicable

6.     The expected component(s) of interest, as well as the reactants and solvents involved

7.     The mass range of interest

8.     If possible supply at least 50 microliters of sample

For routine operation the sample size should be in the range 1-100 picomoles per microliter.

Brief commentary on acceptable buffering agents:  LC/MS can only utilize VOLATILE components (and only below acceptable molar concentrations) or else the electrospray capillary will become plugged.  This includes common solvents like methanol, water, acetonitrile and salts (below 25mM) like ammonium acetate and ammonium bicarbonate.  This also explains why acetic acid is preferred over trifluroacetic acid.

 NO PHOSPHATE salts/buffers or mineral acids can be used.

REMEMBER, the more information you can provide about your sample and its chemical characteristics the better mass spectra we can obtain for you.

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Ionization Techniques

The Following is a brief description of selected mass spectrometer ionization techniques:

Electron Impact (EI) utilizes 70eV electrons for ionization of volatile compounds.  This relatively harsh ionization technique can produce molecular ions (M+) as well as fragment ions.  If fragmentation is extensive little or no molecular ion intensity may be observed.

Chemical Ionization (CI) is a softer ionization technique for volatile compounds.  The basis for ionization centers on proton transfer from a reagent gas ion, present in great excess relative to the sample of interest.  Typically reagent gases are isobutane, methane and ammonia.

The following three ionization techniques are used to analyze non-volatile components.

Matrix-Assisted Laser Desorption Ionization (MALDI) typically utilizes a nitrogen laser at 337nM as the ionization source.  The sample is mixed with a matrix, and allowed to dry prior to insertion into the mass spectrometer.  Crystallization of the sample within the matrix is an important component of successful MALDI analysis.  A variety of matrices, present in great excess relative to the sample amount, are used to span the range of compounds classes amenable to MALDI mass analysis.  Formation of sample ions, upon laser irradiation, involves a proton transfer reaction involving the matrix (which absorbs the UV photon) and the analyte.  The ions are then accelerated into a time-of-flight mass analyzer for mass analysis.  Typical matrices include, a-cyano-4-hydroxycinnamic acid, sinapinic acid and 2,5-dihydroxybenzoic acid.  MALDI can be done routinely to m/z 100,000 and there are many examples of analyses going well above this mass range.

Electrospray (ESI) Samples can be analyzed by ESI using either direct injection or through liquid chromatographic introduction.  Typically ESI forms protonated molecules with little or no fragmentation.  Large molecular weight molecules can also be ionized using ESI.  In this case the molecule becomes multiply charged and the molecule of interest is observed at its respective m/z.  (For example a 20,000 molecular weight protein that has 20 protons attached would be detected at 20,020/20 or m/z 1001.)  The choice of solvents and related components, which must be volatile, are very important for obtaining quality electrospray spectra.  This results because sample introduction is through a liquid medium, but eventually the solvent needs to be volatilized away.  If a nonvolatile solvent or buffer is used the result is frequent plugging of the capillary tubing and/or some of the beam defining components.  In ESI the solvated sample is passed through a needle held at a high potential typically 3-10kV.  As the molecule exits from the needle, the resulting spray undergoes electrostatic nebulization, which places a charge(s) on the droplet.  The charged droplet passes through a variety of focusing elements, which are differentially pumped.  One result is desolvation of the droplet.  Depending on the size and chemical makeup of the analyte the resulting stable ion can have a single charge or may be multiply charged.  Mass analysis of this ion can be carried out with any type of mass analyzer, including magnetic sector, quadrupole, ion trap or time-of-flight.  Sample concentrations that can routinely be analyzed are 10-50picomoles / microliter, however the detection limit for many components is considerably lower.  ESI is amenable to liquid samples, for this reason it is used for liquid chromatography / mass spectrometry. The sample is typically dissolved in a volatile organic solvent, like methanol or acetonitrile, and then injected into the mass spectrometer through a small capillary. 

Plasma Desorption Mass Spectrometry (PDMS) utilizes fission fragments from 252Californium for ionization.  The sample is applied to a nitrocellulose matrix, either by droplet or electrospraying, allowed to dry and then inserted into the mass spectrometer.  The sample ions, which are formed, are accelerated into a time-of-flight mass spectrometer for mass analysis. The useful mass range for PDMS is up to m/z 5000.  Typically the observed ion is the protonated molecule, however, PDMS has proven to be well suited for the analysis of pre-charged species, like anthocyanidins. 

Inductively Coupled Argon Plasma (ICP) multi-element analyses are carried out using ICP.  The sample is vaporized an Argon plasma, with the resulting ions being analyzed.  Detection limits for selected elements can be sub part per trillion in-optimized experiments.

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Under Construction



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215 BCHM
150 WTHR
Medicinal Chemistry
518 RHPH
Please Direct Comments to Karl V. Wood
Last Updated on January 6, 2010
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