the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
A searchable database and mass spectral comparison tool for aerosol mass spectrometry (AMS) and aerosol chemical speciation monitor (ACSM)
Sohyeon Jeon
Michael J. Walker
Donna T. Sueper
Douglas A. Day
Anne V. Handschy
Jose L. Jimenez
Brent J. Williams
Abstract. The Aerodyne Aerosol Mass Spectrometer (AMS) and Aerosol Chemical Speciation Monitor (ACSM) are the most widely applied tools for in-situ chemical analysis of the non-refractory bulk composition of fine atmospheric particles. The mass spectra (MS) of many AMS and ACSM observations from field and laboratory studies have been reported in peer-reviewed literature and many of these MS have been submitted to an open-access website. With the increased reporting of such data sets, the database interface requires revisions to meet new demands and applications. One major limitation of the web-based database is the inability to automatically search the database and compare previous MS with the researcher’s own data. In this study, a searchable database tool for the AMS and ACSM mass spectral dataset was built to improve the efficiency of data analysis using Igor Pro, consistent with existing AMS and ACSM software. The database tool incorporates the published MS and sample information uploaded on the website. This tool allows the comparison of a target mass spectrum with the reference MS in the database, calculating match similarity, and provides a range of MS comparison plots, reweighting, and mass spectrum filtering options. The aim of this work is to help AMS users efficiently analyze their own data for possible source or atmospheric processing features by comparison to previous studies, enhancing information gained from past and current global research on atmospheric aerosol.
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Sohyeon Jeon et al.
Status: final response (author comments only)
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RC1: 'Comment on egusphere-2023-1129', Anonymous Referee #1, 18 Jul 2023
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2023/egusphere-2023-1129/egusphere-2023-1129-RC1-supplement.pdf
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RC2: 'Comment on egusphere-2023-1129', Anonymous Referee #2, 25 Aug 2023
General comments:
The manuscript by Joen et al. describes a new software tool (AMS MS Comparison Tool) that can be used to compare measured (or deconvoluted) mass spectra measured by AMS or ACSM with the large existing set of mass spectra on the AMS database. This database up to now was a more or less a loose collection of mass spectra collecterd over about 20 years by the Jimenez group.
This new software tool is very useful to AMS and ACSM users because it greatly facilitates the comparison and identification of measured organic mass spectra with known source spectra and standards, and with established PMF factor results. I downloaded the software tool and played around with the existing mass spectra for quite a while.The manuscript describes the application of the tool, but also illustrates some of the uncertainties that arise when interpreting PMF results of AMS or ACSM data. For example, a factor identified as BBOA (biomass burning OA) shows high scores in the correlation not only with other BBOA spectra, but with HOA, SOA, or COA from the data base. This is important, since up now it is likely that users would have searched the data base only for other BBOA spectra and would have taken the high correlation as a proof that the factor is indeed BBOA. Now the tool atomatically searches the whole database and will offer other, perhaps unexpected interpretations of PMF factors.
The software tool also allows for a weighting of the mass spectra. This introduces additional uncertainty and I wonder if it is necessary. The user can vary the weighting until the result matches with the desired (or expected) results. I am not sure if this is a valid approach.Â
I wonder if it is possible to optimize this weighting by taking different source spectra from the data base (e.g. all BBOA spectra, all diesel exhaust spectra) and adjust the weighting factors until best scores between als MS from the same source are reached. Then, these weighting factors can be used as default or recommended settings. This should reduce the degree of free and subjective choice of the user.Overall, I recommend the mansucript to be published, after the comment above and the following minor points have been addressed:
Minor comments:
This software tool should also be accessible through the ToFAMS Software Page
https://cires1.colorado.edu/jimenez-group/ToFAMSResources/ToFSoftware/index.htmlIs there any interaction with Datalystica (the SoFi tool by Canonaco and coworkers)? I have the feeling this is more and more used by AMS/ACSM users for their PMF analysis.
Does the AMS MS Comparison Tool regularly check for updates or changes in the database? Does "Download the newest version of DB" load new data from the database or does it load the updated Igor procedures only?
I noticed that some URL are not given or are not valid anymore. Also, group identification and persons doing the measurements need updates (at least in our case).
Should/can users update their entries in the data base to keep it up to date? Or can this be done via the AMS MS Comparison Tool?Last but not least: You need a good acrynom (such as SPARROW, SQURREL, PIKA etc).
Specific comments:
lines 68-74: BBOA and COA are also primary OA. HOA as surrogate for POA is too simple.Â
line 123: "Igor-Pro"Â
line 148: Is the uncentered correlation coefficient also the default setting in PMF analysis? (both PET and SoFi).
lines 155-165: Is there an option to reweight only selected m/z values? e.g., only downweight mz 44?
Citation: https://doi.org/10.5194/egusphere-2023-1129-RC2 -
RC3: 'Comment on egusphere-2023-1129', Anonymous Referee #3, 27 Aug 2023
The software in the manuscript is a very good idea and easy for conducting comparison between different studies. There are many merits of this software including its searchable, scaling factor on mass or intensity, and adjustable on UMR or HR. The manuscript also present examples on test and operation on the software with the real MS, and give the user guider in the SI. I agree for publication on AMT after minor revision as follows.
- My major confusion is that if you have HR MS, why is not directly compare with other HR MS other than comparison with family ions (line 290-298). The family ions is shown the exact composition of fragments. In addition, the case in the manuscript is also not presented the HR MS comparison which in my image, is more precise than UMR MS.
- The high correlation of BBOA with OOA factors (line 306-308) is also not accept by me. Maybe this is not a good case which BBOA is not good separated which included many CHO ions.
Citation: https://doi.org/10.5194/egusphere-2023-1129-RC3 -
RC4: 'Comment on egusphere-2023-1129', Anonymous Referee #4, 28 Aug 2023
Sohyeon Jeon et al. are presenting here a very useful tool for AMS/ACSM mass spectra comparison using a publicly available and expandable database. This paper is surely worth for publication within AMT, after minor revisions and further adding, probably including the following ones :
- The reason why the Cosine score 'only', among other possible methods, has been chosen shall be clarified.
- Similar databases using such comparison tools already exist for other types of datasets. In particular, cf. SPECIEUROPE mainly for PM source profiles obtained from receptor models applied to chemical species (https://publications.jrc.ec.europa.eu/repository/handle/JRC96463), which could be mentioned here, and possibly seen as a source of inspiration for further development.Â
- As different fragmentation tables may be used to retrieve OA mass spectra from AMS/ACSM measurements, information on the used fragmentation table should be stated as a metadata for each mass spectra archived in this new database.Â
- The meaning of the y-label used in every figures (i.e., 'fraction of signal' vs. 'relative abundance') should be better explained (e.g., in the paragraph starting line 130 ?).
- The authors might also consider any interest in keeping the exact same ranges for each y-axis in Figure 7 (??).
- (How) could we imagine to store and compare mass spectra associated with some kind of uncertainties for each m/z ? (e.g., for deconvoluted mass spectra obtained from bootstrap analyses).Â
- What about mass spectra obtained from measurements achieved with the new ToF-ACSM:X instrument ?Â
Citation: https://doi.org/10.5194/egusphere-2023-1129-RC4
Sohyeon Jeon et al.
Sohyeon Jeon et al.
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