Public Release: 

Virtual mass spectrometry laboratory transforms learning experience

Product of Carnegie Mellon University and University of Pittsburgh collaboration

Carnegie Mellon University

At $1 million, many schools cannot afford the latest spectrometry equipment to help students conduct experiments such as determining the composition of a polymer, detecting the presence of cocaine in a hair sample or identifying an anesthetic. But that may soon change, thanks to collaboration between Carnegie Mellon University and the University of Pittsburgh on the development of the first virtual mass spectrometry system.

This interactive Internet educational tool has the potential to enable thousands of students and researchers to learn how to solve real problems from different scientific disciplines. Dubbed the Virtual Mass Spectrometry Laboratory (VMSL), this computerized tool is being presented Sunday, March 23, at the 225th meeting of the American Chemical Society (ACS), March 23-27, in New Orleans.

"The development of this system will allow us to educate many more undergraduate students at one time in challenging technologies that are increasingly essential for conducting much of today's research," says Mark Bier, director of the Mellon College of Science's Center for Molecular Analysis in the Department of Chemistry at Carnegie Mellon.

"Since the VMSL is carefully designed to allow students great freedom with no risks, we believe it will engage them via the discovery process in a way traditional course experiments rarely can," says Joseph Grabowski, professor of chemistry at the University of Pittsburgh.

According to Bier, who is presenting results of their polymer case study at the ACS meeting, typically only one or two students at a time can use a mass spectrometer. Moreover, in many universities, faculty monopolize this equipment for their studies. VMSL ( allows many more students to learn at the same time, doing so without interrupting ongoing faculty research.

Smaller colleges that cannot afford the instrumentation, which totals about $1 million, could also use the VMSL to introduce their science students to mass spectrometers and cross-disciplinary case studies. In fact, most small colleges do not have the mass spectrometers that make up the VMSL, according to Bier.

The VMSL experiments also are completed quickly, in about three hours. A typical protein identification analysis performed in the laboratory might take two or more days to complete, depending upon the quality of the sample being studied. Moreover, the computer requirements for logging onto VMSL are minimal, ensuring that virtually anyone with Internet access can logon and navigate the site.

The VMSL system incorporates four different kinds of mass spectrometers, each of which is used to study the composition of compounds, such proteins, polymers, or small molecules based on their molecular weight and electric charge. The instruments include a MALDI-TOF (matrix-assisted laser desorption ionization time-of-flight) mass spectrometer, a gas chromatograph quadrupole mass spectrometer, an electrospray ionization ion trap mass spectrometer and a magnetic sector mass spectrometer. (See Figure 1)

The system connects the student to data files stored from one of the four mass spectrometers with one of three VMSL servers, two located at Carnegie Mellon and one at the University of Pittsburgh. An Internet user can logon to the VMSL remotely to select one of four case studies. These include identification of a protein, analysis of an unknown anesthetic, detection of cocaine in a hair sample or determination of a polymer's composition.

A student conducting an analysis first reads background information about the case then goes to the virtual lab to prepare the sample. In the protein case, for instance, the student must first virtually "digest" the protein to create smaller peptides that are introduced into one of the mass spectrometers for analysis. In the polymer case, a student must analyze several polymers so that he/she can choose the proper combination to meet the specifications of a polymer-containing product under design. After preparing the sample and introducing it into the mass spectrometer, the student must set the instrument controls and calibrate it using a known standard compound, or calibrant. The student then acquires the data in the form of a plot called a mass spectrum (see Figure 2) and interprets the data. Problems arise if a student fails to prepare a sample correctly, set the instrument controls properly, or massages the dataset appropriately. For example, failing to do the latter step in the protein identification case study might result in a dataset that appears to contain peptide fragments from several different species, rather than from a single species.

"Our system helps create a 'real-life' experience for students, not a recipe-driven experiment, as is typically encountered in an undergraduate laboratory," adds Bier. "Students may need to go back at any time along their work to modify a step so that they succeed in producing results that can be successfully analyzed and interpreted. One advantage over reality is that the program will correct you from making a bad sample early on, which is not the case in reality, where you can spend hours of time before realizing that you made a mistake."

The VMSL contains four entertaining case studies, such as analyzing an animal blood protein (serum albumin) to eliminate ringers from a species Olympics event. Another case study involves analyzing an unknown anesthetic found in a medical bag thought to belong to a Civil-War era physician.

"We also can use the VMSL to teach aspects of running spectroscopic instrumentation," notes Bier. In the case of MALDI-TOF spectrometer, for instance, a peptide mixture can be acquired several times using a different number of "shots" from an ionizing laser beam. This results in a series of spectra that students can use to learn about signal averaging. Additionally, in any one optimized peptide mass spectrum, students can zoom into one set of spectral peaks and investigate the isotope composition of the molecular ion.

Many students have helped in the development of the VMSL. A major portion of the VMLS computer program is being developed by Chunguang Yang, a research assistant working with Bier. The VMSL runs rapidly on most computers, in part, because a large 250 kilobyte spectrum is compressed into 1-to-5 kilobyte GIF (graphics interchange format) file before transmission from the server to the Internet user's computer (see Figure 3). Hundreds of actual spectra are stored on the VMSL servers for each spectrometer, and any one can be converted into a GIF image and sent to an experimenter, depending upon what experimental instrument parameters are used in an analysis. No additional software is required to run VMSL other than an Internet browser, a program to manipulate molecules in space (CHIME tutorial) and a program to run virtual lab movies (QuickTime, Microsoft Corp.). This user-friendly strategy thus allows the programmers to update the VMSL for all users at once.

Students at Carnegie Mellon have been exposed to the VMSL in both a chemistry and biology class. "Our next step is to expand the use of the VMSL in the classroom and evaluate its effectiveness in preparing students to use the real mass spectrometers to solve real problems," adds Grabowski.


This research is funded by the National Science Foundation. Figures are downloadable by using an Internet browser to download them at

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