5.10: TA Notes

This page is directed toward laboratory teaching assistants, but is deliberately left open for students to read.

TA Notes

After completing this module your students will be able to...

• Explain the principles of gas-liquid partitioning.
• Predict relative retention on a GC column based on molecular structure.
• Program a GCMS method and operate the instrument to collect useful data.
• Interpret fragmentation patterns of Electron Ionization Mass Spectra.
• Use the mass spectra data library to identify the components in a mixture.
• Determine the response factor of an analyte.

Quantitate an analyte using an internal standard.

Pre-Semester Preparations

Do the following during the TA training and orientation week(s)

1. Check that the materials listed below are available and sufficient for all students to use them. If they are running low, please create more or inform the instructor. 

   • 4 ppm doxepin in methanol. This solution is stored in the refrigerator. Please keep the stock flask cold and take out a small amount for use during the lab. Please seal the flask with parafilm after each use and return it to the refrigerator.

   • Methanol, mass spectrometry grade. The MS grade methanol is stored in a flammable cabinet near the windows, and poured into a working container for students to use. Avoid contamination!

   •  Calibration standards: Calibration standards contain 4 ppm doxepin and various concentrations of cocaine. Instructions for their preparation are below. Usually, these are prepared once at the beginning of the semester and used by all students during the semester. The standards should last the entire semester if treated carefully.

     Preparation of calibration standards

     Cocaine standard solution is purchased as 1 mL of a 1.0 mg/mL solution. This is the same as 1000 ppm.

     To make a series of calibration standards, 5 mL each: First create 5 mL of a 100 ppm solution of cocaine in 10 mL of methanol. This requires a 10x dilution of the standard. So use 0.5 mL of standard and dilute to 5 mL. 

     \(\frac{0.5 \; mL \times 1000 \text{ ppm cocaine}}{5 \; mL} = 100 \text{ ppm cocaine working solution}\)

     You will need the 100 ppm cocaine working solution and a 4 ppm doxepin solution. Create the standards using the table below. Add cocaine and doxepin to a 5 mL volumetric flask, then dilute to the volumetric mark with MS-grade methanol. The final concentration of doxepin in each solution is 0.6 ppm.

     Concentration of Cocaine	Vol. of 100 ppm cocaine solution	Vol. of 4 ppm doxepin (mL)
     20 ppm cocaine	1000 \(\mu L\)	750 \(\mu L\)
     15 ppm cocaine	750 \(\mu L\)	750 \(\mu L\)
     10 ppm cocaine	500 \(\mu L\)	750 \(\mu L\)
     7.5 ppm cocaine	375 \(\mu L\)	750 \(\mu L\)
     5 ppm cocaine	250 \(\mu L\)	750 \(\mu L\)
     2.5 ppm cocaine	125 \(\mu L\)	750 \(\mu L\)
     1 ppm cocaine	50 \(\mu L\)	750 \(\mu L\)
     0.5 ppm cocaine	25 \(\mu L\)	750 \(\mu L\)
     0.1 ppm cocaine	5 \(\mu L\)	750 \(\mu L\)

2. During the TA training week(s) you should run all standards in triplicate on both GCMS instruments.

   • Take note of the variation that you see in the triplicate data points on each instrument and discuss this with the instructor to confirm the instruments are performing as expected. Determine if the response varies across different days.

   • Confirm that the response to the solutions is as expected, and to identify any potential issues with the calibration standards.

   • Identify the concentration range where the response is linear and nonlinear on each instrument.

3. Complete instrument training with Dr. Haas.

4. Perform the entire experiment as if you were a student (except, you should inject all available standards and measure concentrations for at least three bill extracts).

5. Write and submit a report as if you were a student.

6. Practice grading your and your partner's report using the grading rubric.

Pre-Lab Preparations

When you are on TA duty, arrive at least 20-30 minutes early to prepare and ready the following materials for students.

• Get some doxepin solution out of the refrigerator and put it in a sealed vial for students to use. Do this at least 20 minutes prior to the start of lab time so that the solution can reach room temperature prior to use.
• Refill the MS-grade methanol working container.  Avoid contamination!
• Check that all standards are present and that there is sufficient volume of each.
• Check that the He gas is sufficient. If it is getting low, please inform the instructor and/or change the tank.
• Remind students to sign into lab 
• Check that the student's pre-lab is complete 
• Determine whether students have brought their own currency for analysis, and if not, make arrangements for them to use lab currency.
• Tell students to gather their glassware as soon as they arrive and get set up on a bench space so that they can make solutions. 
• They should clean their glassware (if they are wise!) prior to use. 

Helping your students

During the laboratory session, you are expected to be present and available for the entire 4.5 hours. Your job is to help students to complete the experiment safely and successfully, while upholding expectations and academic standards for the students. 

In this particular laboratory module, you should begin by demonstrating how to inject samples on the GCMS. Start immediately by demonstrating injection with a methanol blank. Then discuss the pre-lab assignment while the methanol blank is running.

Keep students on task during the lab period. Students should set a timer for 12 minutes, and prepare to run the next sample as the instrument equilibrates between runs. During the 12-minute down time, students should prepare their extract sample, then work on creating their data analysis method, then analyze each sample and adding the data to their calibration template while the next sample is running. By the end of the first period, students should have completed one injection of each standard so they have a complete calibration curve (or at least a first try), they should also complete replicate injections of their sample, and replicate injections of at least one calibration point. If all is well, continue replicates for the remaining time. Otherwise, if something is wrong with the instrument or with the standards, discuss the situation with the instructor and plan to re-start during the next period if necessary.

Encourage students to use at least two full lab periods (assuming a 3-period module) to perform lab work. Ideally, data is actively processed during collection and students are able to finalize data collection and begin writing their reports during the third week of lab.

Shut down/ clean up 

15 minutes prior to the end of the period, students should stop lab work and clean up. They are to leave the room in clean condition prior to the end of the period (17:55).

• Remind students when it is time to clean up.
• Turn the instruments into standby by opening the standby method
• Remind students that all glassware should be returned to the storage locations.
• Any samples that are stored should be labeled clearly with the student's name and section.
• Remind students to sign out with the time they leave and get your signature.
• Check the TA checklist for additional items to be completed.