AMS Elemental Analysis
AMS Elemental Analysis
Contents
Introduction
This wiki is intended to assist users of the Aerodyne Inc. high resolution time of flight aerosol mass spectrometer (HR - ToF AMS) with the elemental quantification of aerosol signal. The material in this wiki assumes that users will have a good working knowledge of the analysis for UMR (Unit Mass Resolution) data using Squirrel and for High Resolution analysis using Pika.
A Message to Contributors
We want to encourage active participation by all users in the evolution of the information contained within this wiki and welcome the addition of content that is beneficial to the community as a whole. However, please DO NOT delete any content from this page!! Rather than deleting content, please feel free to voice your concerns by posting a comment to the discussion page where others can contribute (please be sure to include a topic to be referenced in responses).
Analysis Method
An essential primer on the analysis method was given by Jose Jimenez at the 2008 AMS User's meeting in Manchester, UK. The pdf can be found at: http://cires.colorado.edu/jimenez-group/UsrMtgs/UsersMtg9/2008-09_AUM_Jose_Elemental.pdf
APES code
An Igor procedure file (.ipf) has been created and is available for free to all AMS users. This code is named APES (Analytic Procedure for Elemental Separation) and is based on the work done in A.C. Aiken, P.F. DeCarlo, and J.L. Jimenez, Analytical Chemistry, 79, 8350-8358, doi:10.1021/ac071150w, 2007 and Aiken, A.C., et al. Environmental Science and Technology, 42, 4478–4485, doi: 10.1021/es703009q, 2008
Version Information and Download Site
The latest version is 1.01 dated Nov 11, 2008. This version and all previous versions are available at the ToF AMS software download site at http://cires.colorado.edu/jimenez-group/ToFAMSResources/ToFSoftware/index.html#APES
Before you begin
The elemental analysis code (APES) assumes that the high resolution (HR) sticks used for input are both quantitative and inclusive of all measured HR fragments. Generating a complete and quantitative set of HR AMS sticks is quite difficult, especially for ambient data with low concentrations and at higher mass fragments.
Step 0: HR data to be analyzed
The user can select either Pika calculated sticks or user-defined sticks. When APES is used with Pika sticks the data set HRDiffSticks, the wave containing the chemical formulas for those HR sticks, and the todo wave and all the associated Squirrel/Pika infrastructure is used. When the 'User identified' option is chosen the user selects the names of the waves needed for the calculations: the HR sticks, the wave with the chemical formulas of the fragments and the chemical mass of the fragments, and if needed the names of the family mask waves (step 1E).
Step 1A, 1B: Mathematical treatments
HR results from Pika can include nans (Not a Number) and small negative (~ -1e-6ish) values. The APES code needs to know how to handle these values. Default options are to set the nans and negatives to zeros. Users should be aware that nan HR stick results from Pika should be investigated before this option is employed to ensure the validity of APES results. The APES code will return nans for instances where there are nans in the HR stick matrix and the user chooses not to change nans to zeros.
AMS chemical fragments do not ionize at equal rates; calibration factors are needed. Default calibration factors are as given in the Aiken et. al. Anal. Chem. paper with the exception of the S/C factor which has not been found. It is given a default value of 1.
Step 1C - 1G The definition of organic mass (OM)
OM is defined as the sum of the masses of all HR species which have at least one carbon atom. While this definition seems intuitive and straight-forward, the application of this definition for AMS data requires user input.
In the case of CO2, the Pika generated HR stick may reflect gas-phase and aerosol loadings. CO2 is often one of the larges components of OM, so it is critical to correctly partition this fragment. The frag checks in squirrel will inform this accurate partitioning. User choices are entered in section 1B of the panel.
In the case of CO, it may be difficult in Pika to accurately resolve this HR peak with its neighbor N2. User choices are entered in section 1C of the panel.
A portion of the non-carbon containing water fragments of H2O, OH and O should often be included in the definition of OM. For example organic acids often fragment into H2O, OH and O. Users are able to specify the amount of these three fragments which contribute to OM in step 1D of the panel. The default for this option is given as indicated in Aikin et al Anal Chem paper, Table S-3.
Users can include entire inorganic families of HR fragments to the total OM by using the checkboxes in step 1E. This option is intended for laboratory studies, when the organic aerosol is composed of a known compound. For example if laboratory generated aerosol contains only organic nitrates, the user may want to include all variations of NO fragments, which is the NO family.
Users can include additional individual HR fragments by entering the names of the HR fragments in step 1F. This list of HR fragments should be separated by commas; spaces will be ignored. This option is especially useful for the analysis of laboratory standards where all fragments should be more easily identified as originating from an organic molecule. When the OH family is checked, the partitioning of the water fragments H2O, OH and O will proceed as indicated in step 1D. The remaining HR fragments in the OH family (H3O, etc) will be included in OM as an other non-carbon containing fragment.
Users can exclude HR fragments which may be due to air or other interferring species that would otherwise be included in the OM grouping by entering the name of the HR fragment(s) in 1F. This list of HR fragments should be separated by commas, spaces will be ignored.
In summary, the defaults for the elemental analysis are appropriate for ambient data. Users should modify the settings as needed for laboratory or unusual ambient conditions.
