AMS Clinic4

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This page is a repository of information for planning the 4th AMS Clinic and the 1st Aerodyne CIMS Meeting and Clinic (March 2012). A shorcut to this page is

Data analysis in dessert form.

Dates and Location

The 4th AMS Instrument and Data Analysis Clinic and 1st Aerodyne CIMS Meeting and Clinic will take place in the Spring of 2012 at the University of Colorado-Boulder. They are organized by the Jimenez Group and Aerodyne, and also sponsored by CIRES.

  • The location will be the Ekeley Building in the CU Campus in Boulder. The location is linked here in Google Maps and here in the CU online map. The Northeast door of the building will be the only door open on Sunday. The room is Ekeley E1B20, just to the left after entering the building. It is the same location as last year.
  • All AMS days will start at 9 am and go till 5-6 pm, with a break for lunch and additional coffee breaks.

The schedule for the meetings will be:

  • Sun March 25: AMS Hardware tutorial & Q&A (starting 9am, with an AMS in the room)
  • Mon March 26: AMS: Quantification, unit resolution issues, PToF, w/ TOF, Quad, ACSM
  • Tue March 27: AMS: High resolution issues (PIKA). Music jam at Donna Sueper's house.
  • Wed March 28: AMS: PMF, including errors & discussion of user cases. (CIMS users may be interested to sit in) & ARI dinner: Sign up required for dinner
  • Thu March 29: CIMS: 1st day. The series of presentations may run late.
  • Fri March 30: CIMS: 2nd day.
  • Sat March 31: CIMS: 3rd day
  • Sun April 1: CIMS: small group CIMS meetings as needed / hiking or skiing for interested folks

AMS only users may want to come Sun-Wed, or a subset of those days, while CIMS-only users will come Wed-Sun, or a subset of those days. Pls fill this Doodle Poll with the dates you are planning to attend. (Mark them with "(yes)" if tentative). This is the OFFICIAL attendee list for the meeting, which is important to plan for meeting rooms, lunches, coffee breaks, etc.

  • Feedback from the 2012 Clinic is available here

Detailed program of 4th AMS Clinic

The people who should attend the AMS Clinic are those who are directly doing (or are VERY involved in directly supervising) AMS data analysis of field or lab data. The clinic will be much less useful for PIs who are not directly involved in data analysis, or for people who are just starting to learn about the AMS but haven't done serious data analysis yet. Attendees are expected to bring to the Clinic datasets in which they are currently working, and be ready to use them as a basis for discussion with the group.

As planned, this is "out of phase" with the AMS Users Meeting and the heavy Fall meeting season (AAAR, EAC, AMS Users Meeting, AGU...).

There is no registration fee, but please let us know if you are coming to plan food, coffee, tables, power, internet, name tags, hotel room block, etc.

Feedback from past Clinics has been very positive overall, and we try to learn every time how to make the Clinic more useful and interesting to the users. You you can see the details for 2009, 2010, and 2011.

Information from previous AMS clinics (including presentations) are linked here: 1st AMS Clinic, 2nd AMS Clinic, and 3rd AMS Clinic.

Pictures from the 4th AMS Clinic can be found here.

Presentations from the 4th AMS Clinic are linked below:

Sun, Hardware day

  • Matt Coggon, Caltech: "We had some interesting problems with the AMS come up during our field mission, particularly with the chopper. I just want to summarize how we went about troubleshooting the problem" pptx with a video of servo jitters, PDF w/o videos
  • Sonya Collier, Davis: "We seem to be having an issue with our chopper. When doing the 'top hat' test we only get 'half a top hat'. I will bring a screen shot."
  • Sonya Collier, Davis: "We have a USB error when trying to communicate between the pump box and the pump diagnostics software. We already have taken various steps according to John Jayne and Ed Fortner's recommendations but the problem is not completely solved yet" pptx, PDF
  • Zhaoheng Gong, Shenzen Univ.: When a pump generates an error, where in the pump control software (shown on the LCD) can we go to check what error it is?
  • Ping Tang, UC-Riverside: "Our AMS has a noisy W-mode baseline. After I bypassed CH2, the baseline looks better, but the noise is still there. We did several tests with Joel, but the problem haven't solved yet"
  • Yu Jun Leong, Rice U: "Turbo pump failure – We have faced frequent failure with our turbo pumps, and the latest failure was dramatic – fins were ripped out and went through the metal screen. Our group would like to know if we are doing anything wrong with the pump settings, to reduce costly repairs in the future." pptx, PDF, Pics from pptx: pic1, pic2, pic3, pic4, pic5, pic6
  • Yu Jun Leong, Rice U: "V-mode tuning/frag panel – We have observed unsatisfactory performance with V-mode data, presumably due to tuning/settings on our HR-ToF-AMS. W-mode data appears to be better. I would really appreciate some guidance on improving our V-mode data." pptx, PDF
  • Link to download PumpControl software
  • Link to read about and download Speedfan, software to monitor temperatures inside your computer

Mon, quantification, unit resolution with TOF, quad, ACSM

  • Christine Loza, Caltech: "I'd like to talk about airbeam corrections when you deliberately vary the N2 concentration (for example, sampling from a chamber that has 0-10% Ar during an experiment" pptx, PDF
  • Roya Bahreini, NOAA and Jill Craven, Caltech: What to measure and how to calculate AMS mass concentration uncertainty (and how to report it) for field campaigns. Roya's Auxiliary Material of her 2008 Houston paper is a great summary with numbers and references, but how to get all of those numbers exactly has been sometimes unclear to me. pptx, PDF
  • Anna Ripoll, IDAEA-CSIC: ACSM naphthalene calibration method, and would it be applicable to the AMS
  • Florian Rubach, Juelich: "I've been trying to optimize the Zeppelin-AMS settings for PToF timing as well as for averaging and saving. I think I found some good settings, but I would like discuss this and hear some opinions." pptx, PDF
  • Matt Coggon, Caltech: "I don't have a full understanding of how PToF is calculated. I've been making up some image plots for people so that they can average the distributions according to their instruments time stamp. However, if I give them an image based on the saved AMS time stamp, the distributions averaged to other instrument time stamps are messy. If I give them an image based on a 5 min squirell average, the averaged distributions are nicer. I realize that this is an "average of an average", but I'm interested in learning how squirrel fundamentally calculates PToF distributions." pptx, PDF
  • Brett Palm, Colorado: m/z calibration at high organic concentrations pptx, PDF
  • Patrick Hayes, Colorado: multi-instrument intercomparisons during CalNex-LA (afternoon only)
  • Patrick Hayes, Colorado: Effect of NaNO3 on the AMS data during CalNex-LA
  • Jurgita Ovadnevaite, Galway: various ACSM issues
  • Joel Corbin, ETH Zurich: SP laser affecting mz28; identification of radio interference in data

Tue, High-resolution analysis

  • Intro and Clicker Questions from Jose PDF
  • Clicker Questions from Donna & Manjula ppt PDF
  • Jill Craven, Caltech: General issues that cropped up during PIKA analysis, interpretation of high m/z ions PDF
  • Paola Massoli, Aerodyne: 1)Adding new ions into PIKA to account for marine organic aerosol ion fragments, and 2)Precautions for deciding when N containing ions peaks in fits are real or not ppt, PDF and excel file containing the exact masses of halide clusters (with metals) that users might find useful.
  • Jurgita Ovadnevaite, Galway: sea salt detection with the AMS
  • Matt Coggon, Caltech: "I've been working on data from a field mission and I've found that masses at m/z 42 and m/z 99 are important in cloud processed ship emissions. I have an idea (based on HiRes data) what these ions are, but I'm interested in trying to figure out if anyone has any idea what compounds might fragment to generate these masses"
  • Lea Hildebrandt, UT-Austin: Organic H2O/CO2 ratio (frag table correction) for chamber experiments I have been analyzing
  • Sonya Collier, Davis: "During a recent field campaign in Los Angeles, measuring vehicle emissions, we ran the HR-ToF-AMS at very high sampling fequency (10 second averaging, 4 Open, 2 Closed, 6 PTOF). The data is noisy but passable. However, in the PIKA peak fitting window I've noticed various instances where the peaks in the closed panel are shifted with respect to the open and diff panels. Its not always consistent. There are also some strange overall shifts despite processing the data with a fair m/z calibration. Qi suspects it is due to the unequal open and closed times."
  • Zhaoheng Gong, Shenzen Univ.: How should we do baseline fitting (especially for PIKA) when a dataset has a low signal to noise ratio? Can we just set the baseline to a specific value for each m/z? Is this scientificly acceptable? Is it technically possible? pptx, PDF
  • Zhaoheng Gong, Shenzen Univ.: What's the syntax for HR frag table? Donna gave out a ppt showing this on the 2011 user meeting, yet it's a pity that one slide is missing.
  • Ed Fortner, Aerodyne: "The topic of my problem is figuring out how to fit the midcarbon clusters at mz 150-500 and PAHs at mz 150-500 in HR (this is for a SPAMS). This requires first a good mzcal and typically I do my mz cals in closed using most of the default species. I knew I needed to change this for BC at high masses so I am trying to look at open and include masses like C60 (mz720) and other such high masses in the fit. Problem is as my fit at high mz gets better my fit at low mz gets worse. I am working through this hour by hour so things may be better and I may have a more specific question at the clinic but that is where I'm at at the moment."
  • Shunsuke Nakao, UC-Riverside: "1. What modifications are required for chamber-SOA application? E.g., no ammonium sulfate/nitrate; how should we change frag-table? Is there any tutorial on that? 2. Should we take HEPA filter measurement? How often should we do it? Should we use Licor measurement to adjust CO2?"
  • Jose and Michael, Colorado: update on high-resolution MS database
  • Link to Pete DeCarlo's 2009 AMS Users Mtg presentation about V, W, VW ions
  • Link to open source mass spec tool:
  • Informal pizza and music event at Donna's house 7pm, 875 Roxwood Lane #A Boulder CO, 80303. Boulder yellow cab number is 303-777-7777. We'll order pizza as needed, some drinks provided, but bring your own if you've a favorite.

Wed, PMF

  • Ingrid Ulbrich, Colorado: brief demo of new 2D PET version, discussion of beta testing and plans for full release (Ingrid will only attend on Wed) pptx, PDF
  • Jill Craven, Caltech: PMF of smog chamber experiments PDF
  • Manuel Hutterli, Tofwerk: New Tofwerk autotuning/diagnostics software (30-45 min, incl. questions & discussion)
  • Samara Carbone, FMI: PMF analysis with ACSM data
  • Samara Carbone, FMI: SNR and classification of weak and bad variables for ACSM and ToF-AMS PDF
  • Florian Rubach, Juelich: "I would love to know how to do vector-matrix based 3D-PMF (and as a first step, make ME2 do what I want it to do), but I just haven't managed to understand how the scripting language works. This means I basically don't have anything to show but I would be eager to learn."
  • Link to the AMS Global Database:
  • Link to Dr. Ulbrich's Intermediate Igor Programming Course at CU-Boulder
  • Meeting photo after lunch on library steps.

Details of 1st CIMS Meeting and Clinic

  • This first meeting of ToF-CIMS users is being held Thursday, March 29 through Saturday, March 31 2012, immediately following the AMS Clinic. AMS users are invited to attend any portion of the ToF-CIMS meeting and vice versa. All details related to that meeting are on the ToF-CIMS website.


  • The list of attendees is kept on this Doodle Poll. This Poll will be the official list of attendees, so please remember to update it if your plans change. If you would like to attend but are not sure yet, please enter the "(Yes)" option (it'll show up in yellow in the poll) and update the entries later when your plans become solid either way.

Lodging and Travel

  • General information on Boulder is here
  • You will most likely travel via Denver International Airport
  • You can use the Supershuttle service between the airport and the hotel and back (once in Boulder, you can walk to and from the meeting)
  • A map with three local hotels that have offered to give us a discounted rate can be found here
  • A map with all the hotels in Boulder is here.
  • If you are looking for someone to share a room with we have created a spreadsheet for coordinating and posting contact information here
  • Millenium (recommended, closest to meeting location)
    • Rate: $104.00 for one King / $104.00 for two doubles / $114 for a triple / $124 for a quad (we are currently holding 10 rooms)
    • Reservations: register online here
    • Contact p.303.443.3850 / AMS Users (for discounted rate)
    • Reservations can only be made up to February 23, 2012 (for guaranteed rate)
  • Boulder Inn (farther from meeting location, but a little cheaper)
    • Rate: $82.00 for one King bed / $92.00 for two Queen Beds
    • Contact: p.800.233.8469 / AMS (for discounted rate)
    • Reservations can only be made up to February 23, 2012 (for guaranteed rate)
  • Boulder Outlook
    • Rate: $74.00 for standard outside / $84.00 inside by pool / $94 executive (can either be a king or two doubles)
    • Contact: p.800.542.0304 ext. 0 / ask for CU CIRES group rate
  • Quality Inn
    • Rate: $79.00 one queen / $79.00 two queens
    • Contact: 1.888.449.7550 / ask for AMS Conference Rates
  • If you want to find a roommate for the Clinic, please enter your information in this spreadsheet.

Please feel free to contact Michael Lechner (michael.lechner(at) for any further question)