Difference between revisions of "AMS Elemental Analysis"

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== Introduction ==
 
== Introduction ==
  
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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 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 donna.sueper@colorado.edu, jose.jimenez@colorado.edu and allison.aiken@colorado.edu.
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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 donna.sueper@colorado.edu, jose.jimenez@colorado.edu.
  
 
== A Message to Contributors ==
 
== A Message to Contributors ==
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http://cires.colorado.edu/jimenez-group/UsrMtgs/UsersMtg9/2008-09_AUM_Jose_Elemental.pdf
 
http://cires.colorado.edu/jimenez-group/UsrMtgs/UsersMtg9/2008-09_AUM_Jose_Elemental.pdf
 
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.
 
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.
 +
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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 http://cires1.colorado.edu/jimenez-group/wiki/index.php/ToF-AMS_Analysis_Software for general analysis questions.
  
 
== APES Code ==  
 
== APES Code ==  
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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
 
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
  
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This ipf can be used within a Pika experiment or used as a stand-alone ipf for the analysis of any HR spectra.
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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 ===
 
=== Version Information and Download Site ===
  
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The latest version is 1.01 and is dated Nov 11, 2008.  This version and all previous versions are available at the ToF AMS software download site at  
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The latest version of the APES code is available through the ToF AMS software download site at  
 +
 
 
http://cires.colorado.edu/jimenez-group/ToFAMSResources/ToFSoftware/index.html#APES
 
http://cires.colorado.edu/jimenez-group/ToFAMSResources/ToFSoftware/index.html#APES
 +
 +
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 ===
 
=== Before You Begin ===
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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.
 
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.
  
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=== Step 0: HR Data to be Analyzed ===
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=== HR Data to be Analyzed ===
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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 chosen' option is selected the user identifies 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).  The code assumes that all waves reside in the root folder.
 
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=== Step 1A, 1B: Mathematical Treatments ===
 
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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.
 
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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.
 
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=== Step 1C - 1G The Definition of Organic Mass (OM) ===
 
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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.
 
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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 1C of the panel.  If the HR stick for CO2 is already correctly partitioned and reflects only the aerosol loading, then the user may enter 0 (ppm)for the estimate of the gas phase CO2 and the entire stick value will be used in the analysis.
 
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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 1D of the panel.
 
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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 1E of the panel. The default for this option is given as indicated in Aikin et al Anal Chem paper, Table S-3.
 
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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.
 
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The concept of families of HR fragments was introduced into Pika as a way of grouping similar fragments.  In Pika, once the user selects the fragments to fit mask waves (waves with 1s and nans or 1s and 0s) are automatically created which indicate the truth/false of whether an ion belongs to a family.  Every ion belongs to one and only one family.  The Pika code tries to decipher the chemical formula to determine a fragment's family status.  If the chemical formula is strange or not formatted properly the fragment may default to belong to the 'other' family.
 
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Users can include additional individual HR fragments by entering the names of the HR fragments in step 1G. 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.
 
  
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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 1G. This list of HR fragments should be separated by commas, spaces will be ignored.
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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.
  
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=== Step 2 Elemental Analysis ===
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=== Calibration Factors: Mathematical Treatments ===
  
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Users can opt to calculate and display the elemental ratios (Step 2A) or the elemental mass spectrum (Step 2B).  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.
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The APES code will return nans for instances where there are nans in the HR spectra.
  
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== Step 2A ==
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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.
  
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When this button is pressed the code will sum the the elemental loadings and apply the calibration factors.  If the Pika HR sticks are used, the results will be displayed as a time series (runs not in the chosen todo wave will have values of Nans).  If user defined HR sticks were used, a simple table of all the ratios will be displayed.
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=== Elemental Analysis, Family Results ===
  
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== Step 2B ==
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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.
  
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When this button is pressed the code will find the elemental loadings and display the results as a mass spectrum. The elemental alibration factors are not applied in this analysis.
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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.

Latest revision as of 15:06, 1 February 2018

AMS Elemental Analysis

Introduction

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 donna.sueper@colorado.edu, jose.jimenez@colorado.edu.

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 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 http://cires1.colorado.edu/jimenez-group/wiki/index.php/ToF-AMS_Analysis_Software for general analysis questions.

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

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

http://cires.colorado.edu/jimenez-group/ToFAMSResources/ToFSoftware/index.html#APES

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.

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