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Using negative ion selected ion flow tube mass spectrometry for detection of sea surface emissions

Prof Lucy Carpenter (YDC), Prof Ally Lewis (YDC), Dr Marvin Shaw (YDC)

Project partner(s): Anatune Ltd (CASE)

Contact email:


The development of chemical-ionization mass spectrometry (CIMS) techniques has been essential to the understanding of the chemical composition of the atmosphere (Huey, 2007).   In CIMS the target molecule is ionized via an ion-molecule reaction with a reagent ion and selectively detected with a mass spectrometer.   SIFT-MS is a form of CIMS and has similarities to the commonly used proton-transfer-reactor mass spectrometry (PTR-MS).  We have demonstrated the use of positive ion mode SIFT-MS for detection of a wide variety of volatile organic compounds (VOC) and their oxidation products most recently as part of a field project in Beijing. A new negative ion mode (NI) SIFT-MS is now available, the capabilities of which have yet to be explored for atmospheric composition. A number of atmospherically relevant species that are inaccessible in positive ion mode, including gas-phase inorganic and organic acid and halogenated species, should be detectable using negative-ion chemical-ionization mass spectrometry (Amelynck et al., 2000; Custer et al., 2000; Viidanoja et al., 2000).

A schematic of the NI-SIFT-MS in shown in Figure 1.   Negative reagent ions (O–, O2–, OH–, and NO2- ) are mass-selected by the upstream quadrupole then pass into the flow tube where the reagent ion-analyte reactions take place.   Product ions (along with unreacted reagent ions) are mass-selected by the downstream quadrupole and detected.

Figure 1. Schematic of a commercial Selected Ion Flow Tube-Mass Spectrometry (SIFT-MS) instrument (Hera et al., 2017) 

In this CASE PhD project you will develop the use of negative ion SIFT-MS in atmospheric detection and apply it to studies of sea surface emissions of organic acids and halogens.  Photochemical and ozonolysis reactions at the sea surface have been proposed as novel sources of these gases to the marine atmosphere (Figure 2) at a rate which can lead to aerosol formation and growth, possibly affecting climate (Carpenter et al., 2013; Fu et al. 2015; Rossignol et al., 2016; Mungall et al., 2017).   These are potentially highly significant findings that could transform our understanding of the marine atmosphere and particularly that of marine climate-active secondary organic aerosol. However, these experiments tend to involve highly elevated concentrations of substrates, which can modify not only the product emissions but also the reaction mechanism, and there is a lack of chemical identification required to characterise mechanisms and product yields.   The aim of this work is to develop an understanding of how these laboratory results apply to the atmosphere. Using a photochemical reactor already developed in WACL, you will develop experimental methodologies to examine real-world oceanic emissions from the sea surface microlayer (SML).   These measurements will then be used in a coupled ocean-atmosphere model to assess the role of SML emissions in the oceanic environment.

Figure 2.  Photochemical reactions and products within the sea surface microlayer (SML).Objectives:


Specific goals include:

  • Characterise and optimise the performance of the NI-SIFT-MS for a range of selected organic acids (e.g. HCOOH, HNCO), inorganic acids (HCl, HNO3) and halogenated species (including HOBr, ClNO2 and iodinated species).  Determine the sensitivity, fragmentation patterns, humidity and pressure dependences, and optimum flow rates and pressures.
  • Investigate any secondary ion chemistry arising, e.g. from the reactions of negative reagent ions with atmospheric gases such as CO2
  • Construct calibration sources (e.g. permeation tubes, diffusion cells) to provide standard mixtures of the specific analytes and test the linearity and range of the NI-SIFT-MS
  • Develop an experimental framework to detect gaseous emissions arising from photochemical processing of the sea surface SML under ambient conditions
  • Compare two different mechanisms for production of climate-relevant gases from natural surfactants present in the SML;  ozonolysis and photolysis


The student will work under the supervision of both Prof. Lucy Carpenter and Prof. Ally Lewis (University of York) and will be based at the Wolfson Atmospheric Chemistry Laboratories, part of the Department of Chemistry, University of York.  You will also spend part of your project working in the Cambridge laboratories of our CASE partner, Anatune Ltd.  This project will provide training in a variety of atmospheric measurement, data analysis and modelling techniques.  The student will receive training in the operation of the SIFT-MS by Dr Marvin Shaw who has operated the instruments in a variety of field and laboratory locations.  The student will also receive training in laboratory studies of the sea surface microlayer by a number of experienced researchers in WACL, and in the running and developing of atmospheric chemistry models, interpreting the output and comparing with observations.

The University of York and the wider NERC SPHERES DTP provide comprehensive training programmes for PhD students with a range of courses on both hard and soft skills. The student will also have access to the wider resources of the National Centre for Atmospheric Science (NCAS),  which is affiliated to the Wolfson Atmospheric Chemistry Laboratories (WACL). You will also have access to training provided by NCAS such as the Arran instrumental Summer School, the Earth System Science Summer School (ES4), and future further developments in computations and data analysis.

The student will work in WACL, part of the Department of Chemistry, University of York.  These laboratories were established in 2013 and comprise a state of the art 800 m2 dedicated research building, the first of its kind in the UK. Supported by a large award from the Wolfson Foundation and a private donor, the Laboratories enable experimental and theoretical studies relating to the science of local and global air pollution, stratospheric ozone depletion and climate change. The Laboratories are operated as collaborative venture between the University of York and the National Centre for Atmospheric Science (NCAS), co-locating around 50 researchers from seven academic groups and from NCAS. The Laboratories are also home to independent research fellows, postdoctoral researchers, PhD students and final year undergraduate research projects.

The student will have the opportunity to present their work to the scientific community at national and international meetings and conferences. They will also be encouraged to take part in outreach events organised by both WACL and NCAS in order to disseminate the research beyond the immediate scientific community (e.g. to policymakers and the general public).

We appreciate that this PhD project encompasses several different science and technology areas, and we don’t expect applicants to have experience in many of these fields. The project is very well supported with experienced scientists and training in these new techniques and disciplines is all part of the PhD.

Useful References

Hera, D., V.S. Langford, M. J. McEwan, T. I. McKellar and D. B. Milligan, Negative Reagent Ions for Real Time Detection Using SIFT-MS, Environments, 2017, 4, 16; doi:10.3390/environments4010016

Mungall, E.L. et al., Microlayer source of oxygenated volatile organic compounds in the summertime marine Arctic boundary layer, Proc Natl Acad Sci U S A., 2017, 6203–6208, doi: 10.1073/pnas.1620571114

Rossignol S, Tinel L, Bianco A, Passananti M, Brigante M, Donaldson DJ, George C., Atmospheric photochemistry at a fatty acid-coated air-water interface, Science, 2016, 353(6300):699-702. doi: 10.1126/science.aaf3617.

Viidanoja, J., et al. Laboratory investigations of negative ion molecule reactions of propionic, butyric, glyoxylic, pyruvic, and pinonic acids, Int. J. Mass Spectrom., 2000, 194(1), 53–68, doi:10.1016/S1387-3806(99)00172-4.

Related undergraduate subjects:

  • Atmospheric science
  • Chemical engineering
  • Chemistry
  • Earth system science
  • Engineering
  • Physics