READ AND REVIEW ANY APPLICABLE MANUFACTURER/VENDOR SAFETY INFORMATION BEFORE DEVELOPING STANDARD OPERATING PROCEDURE AND PERFORMING WORK.

PI Name: Sergey Nizkorodov Date Modified: August 14, 2015

Name of Work Unit: Aerosol Photochemistry Group

Standard Operating Procedure (SOP) for

Proton Transfer Reaction Time of Flight Mass Spectrometer (PTR-ToF-MS)

#1 / Scope of Work/Activity: Describe the experiment purpose/scope.
-  Identify all apparatus that will be used, and associated requirements.
-  List special equipment (X-ray generators, lasers, furnaces, etc.) that will be used for the project.
-  Identify measurement and test equipment, apparatus operating conditions,
Include process flow diagrams, pressures, and required maintenance procedures as appropriate.
The system consists of:
·  PTRMS
·  Computer and monitor
·  Backup battery
·  Standing desk
Test equipment needed:
·  Calibration gas mix (commercial)
#2 / Specific Safety and Environmental Hazards: State the specific hazard and consequences if procedure not followed to person, environment, or property.
There are many ways to break this expensive instrument if not following directions. Also, risk of electrical shock and radiation exposure is possible while servicing the instrument.
#3 / Describe in detail how the hazards will be controlled.
a. Identify the Engineering Controls (e.g. interlocks, shielding), Standard Operating Procedures, or Personal Protective Equipment (e.g. respirators, gloves;) that will be employed to reduce hazards to acceptable levels.
·  Instrument is grounded.
·  Ion source is concealed.
b. Address emergency shutdown procedures.
·  Shut down the instrument with switch in the back (bottom). Also, physically unplugging it is faster in some cases.
#4 / Designated Area: Indicate the designated area for performing this process in the laboratory.
Instrument is mobile. There is no designated area.
#5 / Personal Protective Equipment (PPE): State the personal protective equipment selected and required. Examples: safety spectacles, work gloves, respiratory protection, steel toe shoes.
N/A
#6 / Important Steps to Follow: List the specific sequence staff should follow to avoid hazard.
Refer to the instructions provided at the end of this document.
#7 / Emergency First Aid Procedures:
a.  Describe immediate medical treatment required in case of personnel exposure.
-Complete online incident report form at www.ehs.uci.edu
Electrical shock or exposure to ionizing radiation:
·  Switch off power
·  Seek medical attention immediately
#8 / Training & Competency Requirements: Describe necessary training and demonstration of competency for performing the hazardous operation.
Everyone operating the PTRMS must:
·  Read the manual
·  Read this SOP
#9 / Identify waste stream and disposition of unused stock of chemicals
List concentrations and amounts of hazardous wastes or emissions and control measures.
Additional guidelines regarding hazardous waste at : http://www.ehs.uci.edu/programs/enviro/
N/A.
#10 / Decontamination and spill clean-up procedures
N/A.

As the Principal Investigator, it is your responsibility to ensure that all individuals listed in this protocol is taught correct procedures for the safe handling of hazardous materials involved in this study. It is also your responsibility to assure that your personnel attend Lab Core Safety Training and other applicable safety training courses.

Both PI and all persons associated with the protocol must sign the following acknowledgement:

I have read, asked questions, and understand the hazards of and safe working procedures for the activity/materials described herein.

PI Signature: DATE

Other Personnel:

Name/ Signature DATE

Name/Signature DATE

Name/Signature DATE

Standard Operating Procedure for Proton Transfer Reaction Time of Flight Mass Spectrometer (PTR-ToF-MS)

Last updated on August 14, 2015

*Always check the PTRMS LOG BOOK for any changes in settings values or for important notes

1)  PPE required

·  Gloves, lab glasses, and lab coat have to be worn when servicing the PTRMS components

·  No special PPE is required to operate the PTR-MS

2)  Technical Information to Know Before Operating PTR-MS

  1. H3O+ is the primary ion for this instrument and the proton affinity of VOC measured must be higher than that of water (697 kJ/mol).
  2. Alkanes, in general, cannot be detected
  3. Formaldehyde (718 kJ/mol) will be sensitive to sample inlet relative humidity (needs correction)
  4. Alcohols, organic acids, organic nitro, nitrite, and nitrate compounds, and organic halogenated compounds will fragment to some extent in the PTR. Alchols may lose H2O, acids may lose CO2, nitrogen compounds may lose HNO2, HNO3, etc., and halogenated compounds may lose HX (X = halogen).

iv.  Dont exceed 10% concentration of H3O+ ions for total concentration of measurable analyte ([H3O+] ~ 5 ppm)

  1. O2+ and N2+ modes also available, consult manual if necessary to switch.
  2. Accuracy can be 3-6% if calibrated with standard.
  3. Sensitivity is at ppt level.
  4. Selectivity is low – cannot resolve isobars!
  5. If the m/z 37 signal is too high then the PTR is not too efficient – need to correct.
  6. The sample inlet tube should be open to atmospheric pressure in order for the PTRMS to operate properly!

3)  Turning on the PTR-MS for the first time (e.g. after moving)

  1. Turn on the instrument via the power switch in the back.
  2. Wait > 1 hour both for the turbo pumps to spin up to their full speed (~1000 Hz). Remove the blindplug on the sampling inlet. DO NOT BLINDPLUG INLET WHEN H2O FLOW IS ON!!
  3. To start the PTRMS, open the “PTR Manager” program by double clicking the icon located on the desktop. This program controls the pressures and flows in the PTRMS. Go to the “Control” tab, click on “Operation” and make sure the instrument is on Operation Mode. Check the front of the instrument to see that the Drift pressure is around 2.2 mbar, the Foreline pressure is < 5 mbar, the TOF lens pressure is ~ 1 x10-5 mbar, and the TOF pressure is ~ 1 x10-7 mbar.
  4. Tune the temperature in the Drift Tube and Inlet:
  5. On the PTR Manager program, go to the “Hardware” tab, select “Temperatures”
  6. Open “Drift” and “Inlet”
  7. Hit “Autotune”
  8. You can adjust the temperature after this initial (necessary) autotune step.
  9. The drift temp. can be as high as 120 C. The inlet temp. can be as high as 150 C, but NOT > 20 C higher than drift temp. to avoid condensation in the drift tube!!
  10. When on Operation Mode, the settings should be:
  11. E/N ~135 Td (E/N 120-140 Td is NORMAL operation. If you increase it (by adjusting Drift Voltage), expect more fragmentation! If you decrease it, expect more water clusters!)
  12. Us = 100 V
  13. Uso = 75 V
  14. Udrift= 600 V
  15. Udx = 32 V
  16. Ihc = 4 mA (turned ON) (Keep the source at a low current. You may need to increase the source current if the source is dirty (or you can take out the source and clean it…)
  17. PC inlet = 275 mbar
  18. FC inlet = 100 sccm (Range is 0-200 sccm. Sticky analyte or long inlet line will require a higher sampling rate >100 sccm)
  19. H2O = 6.0 sccm
  20. Tdrift = 60 C
  21. T inlet = 70 C
  22. If not in use, PTRMS should be put on “Standby” or “Idle” modes (Control à Operation à Standby) which both turn off the water, current, and voltages. You can blindplug the inlet if the PTRMS is in either of these modes, but not in Operation.

4)  Turning on the PTR-MS for normal use:

  1. Make sure the inlet of the PTRMS is connected to your chamber (or other container) with a Teflon tube (do not use conductive tubing – it introduces significant contamination in the mass spectrum at high m/z). Be careful not to pull on or kink the small yellow PEEK (a heat-resistant plastic) tube in any way- it is advisable to clamp the tubes in place so that you don’t accidentally pull on the PEEK tube.
  2. Assuming PTRMS is in Standby or idle mode:
  3. Make sure the inlet is not blindpluged!
  4. Turn on Operation mode (on PTR Manager, Control à Operation à Operation)

iii.  DO NOT TURN OFF THE PTR MANAGER PROGRAM THROUGOUT USE.

  1. Open the “TPS Controller” program from the desktop icon. This program controls all the voltages applied in the PTRMS.
  2. Click the “Initialize” button on the top left.
  3. Go to the “Setting Files” tab and click on a file called “UCI_07_05_2015.set” or an updated version.
  4. Click on the “All Voltages” button on the top.
  5. Wait > 30 minutes for the voltages to stabilize.

5)  Program the PTRMS and Start Collecting Data

  1. Click on the “TofDaqRec” yellow icon on the desktop.
  2. Click on the the “DAQ” button on the top toolbar and go to the “Files/Paths” tab.
  3. On the data directory, choose your own folder (or make one)
  4. For the file name, the system has set up a <timestamp>_filename.h5 naming mechanism. It’s best to use this because every time you start/stop the program it generates a new file so the timestamp keeps the filenames unique. Delete all files you are not using (e.g. mass calibration)! Close the DAQ window.

e.  Don’t mess with the timing if you don’t know what you’re doing!!!

  1. You will see two screens: the top one shows the updated and averaged mass spectrum and the bottom one shows the time-dependent traces of selected VOC. In order to select VOC, find them in any of the 5 scroll-down menus. It’s a good idea to choose H318O+ as one of your traces because this monitors the primary ion (you want this trace to be stable).
  2. Click the start button at the top left. Check the “Log scale” box on the bottom of the top window to enhance the intensities of the smaller peaks.

h.  If the program fails to work properly:

i.  Turn off voltages

ii.  Put PTRMS in “standby” mode

iii.  Restart computer

iv.  Follow instructions for “Turning on the PTR-MS for normal use”

  1. Click on “average” box on the right toolbar and click off “combined.” Wait a few minutes and zoom in to the 21 peak using your magnifier tool and check the “peak parameters” box at the bottom of the top screen. If the peak is pretty close to 21.0235 m/z then skip calibration. If not, to do calibration, you have to stop the data acquisition so click “stop.” Highlight the 21 peak and click on “set” button on the right toolbar. Enter in the following values for the respective peaks (after typing in values hit “enter”, then press “close” after each one, and “calibrate” after the last one):
  2. 21.0235 m/z
  3. 29.9980 m/z
  4. 59.0497 m/z
  5. Click “calibrate”
  6. Restart data collection. Delete the file you had created before. You are now collecting data – the program will stop only when the set time runs out (7 hours or so) or you stop it.

6)  Stop the PTRMS

  1. Stop PTRMS data collection and back up data. To turn off the instrument:
  2. Close the TOFDaqRec (your data is saved when you hit stop).
  3. Go to the TPS, click on the “shutdown” button and wait for voltages to reach 0.
  4. If you won’t be using the PTRMS for a couple of days, go to the PTR Manager and click “Control à Operationà Standby” to turn off all current and water flow. If you will be using the instrument the next day, it’s okay to keep it in operation or on standby – but don’t turn off the PTR Manager!
  5. Again…do NOT plug the inlet of the PTRMS when water flow is ON!!!

v.  DO blind plug the inlet while the PTRMS is in “standby” mode!!!

7)  Moving the PTRMS

  1. Make sure the TPS Controller voltages are shut down.
  2. If you are NOT moving it far (within your lab or to a nearby lab)
  3. The PTRMS plugged into a battery. You have 5 minutes to move it somewhere close.
  4. Put the PTR on “Idle.”
  5. Blindplug the sample inlet.
  6. Unplug the battery (NOT THE INSTRUMENT) and move very slowly.
  7. Plug the battery back in and resume normal operation.
  8. If you are moving it far
  9. Shut down the PTR (on PTR Manager, Control à Operation à Shutdown)
  10. Blindplug the sample inlet.
  11. Switch off the power button on the back of the instrument.
  12. Move very slowly and carefully (keep upright).
  13. When you are at the new location, follow instructions in section (2).