AMS Elemental Analysis

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AMS Elemental Analysis


This wiki is intended to assist users of the Aerodyne High-Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS) with the elemental quantification of organic 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. For concerns about this code or analysis method, please contact,

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: The defaults for the elemental analysis code described below are appropriate for ambient data. Users should modify the settings as needed for laboratory or unusual ambient conditions.

This elemental analysis code is embedded within Pika. The stand-alone ipf was originally created for circumstances such as analyzing PMF factors (this is now a part of the PMF package), but is maintained here for potentially other uses. AMS users may go to for general analysis questions.


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

This ipf must be used within a Pika experiment even if the HR spectra to be analyzed is not Pika generated, because it relies on function within Squirrel and Pika ipfs. Users need at least Igor 6.0; this code was primarily tested using Igor 6.37 and later Igor 7.07.

Version Information and Download Site

The latest version of the APES code is available through the ToF AMS software download site at

Historical info: Version 1.02 was released 27 Jan 2009. Version 1.02 of APES corrects for a possibly significant bug having to do with CO. If CO was included in the HR (Pika) fits, then the calculations in 1.01 are correct. A user can check if CO was included by seeing if CO appears in the ExactMassText text wave. (CO should immediately precede N2 in the ExactMassText wave). If CO was not included the 1.01 version of APES will result in an error. The problem in APES 1.01 is that CO will not be correctly accounted for (the column that would be assigned to CO does not exist). This applies only to CO, and to no other species where the user may need to make adjustments, such as the species CO2, H2O, OH, and O. Version 1.01 of APES was released 11 Nov 2008.

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 non-trivial, especially for ambient data with low concentrations or with higher m/z mass fragments.

HR Data to be Analyzed

The code assumes that all waves reside in the current data folder. Three Igor waves are needed: the high resolution mass spectra (i.e. PMF profile x), the wave indicating the chemical formula for the HR ions and the mass of the HR ions. These three waves should all be the same length.

Calibration Factors: Mathematical Treatments

The APES code will return nans for instances where there are nans in the HR spectra.

AMS chemical fragments do not ionize at equal proportions; 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. The Canagaratna et al 2014 ACP paper corrections are implemented.

Elemental Analysis, Family Results

Users can opt to calculate and display the elemental ratios or the elemental mass spectrum or the family-grouped mass spectrum. The order in which either calculation is performed is irrelevant. Once the analysis has been performed, one can view the table of elemental mass fractions to troubleshoot and verify the correct parsing of the chemical formulas and the grouping of fragments to the organic mass entity.

The grouping for HR ions into families, i.e. CxHy, or family CH is performed using the family designations within the HR data folder. Users may choose to import these family designations from their Pika experiments. If the data folder HR does not exist at the time when one attempt to retrieve information from it, the default families CH, CHO1, CHOgt1, etc, will be created.