Supplementary material to "Applications and limitations of constrained high-resolution peak fitting on low resolving power mass spectra from the ToF-ACSM"

Abstract. The applicability, methods and limitations of constrained peak fitting on mass spectra of low mass resolving power (m∕Δm50 ∼ 500) recorded with a time-of-flight aerosol chemical speciation monitor (ToF-ACSM) are explored. Calibration measurements as well as ambient data are used to exemplify the methods that should be applied to maximise data quality and assess confidence in peak-fitting results. Sensitivity analyses and basic peak fit metrics such as normalised ion separation are employed to demonstrate which peak-fitting analyses commonly performed in high-resolution aerosol mass spectrometry are appropriate to perform on spectra of this resolving power. Information on aerosol sulfate, nitrate, sodium chloride, methanesulfonic acid as well as semi-volatile metal species retrieved from these methods is evaluated. The constants in a commonly used formula for the estimation of the mass concentration of hydrocarbon-like organic aerosol may be refined based on peak-fitting results. Finally, application of a recently published parameterisation for the estimation of carbon oxidation state to ToF-ACSM spectra is validated for a range of organic standards and its use demonstrated for ambient urban data.

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Applications and limitations of constrained high-resolution peak fitting on low resolving power mass spectra from the ToF-ACSM

10.5194/amt-2016-13 ◽

2016 ◽

Author(s):

Hilkka Timonen ◽

Mike Cubison ◽

Minna Aurela ◽

David Brus ◽

Heikki Lihavainen ◽

...

Keyword(s):

High Resolution ◽

Mass Spectra ◽

Resolving Power ◽

Sensitivity Analyses ◽

Metal Species ◽

Aerosol Mass ◽

Aerosol Mass Spectrometry ◽

Peak Fitting ◽

Mass Resolving Power ◽

Low Mass

Abstract. The applicability, methods and limitations of constrained peak-fitting on mass spectra of low mass resolving power (m/dm50 ~ 500) recorded with a time-of-flight aerosol chemical speciation monitor (ToF-ACSM) are explored. Calibration measurements as well as ambient data are used to exemplify the methods that should be applied to maximise data quality and assess confidence in peak-fitting results. Sensitivity analyses and basic peak fit metrics such as normalised ion separation are employed to demonstrate which peak-fitting analyses commonly performed in high-resolution aerosol mass spectrometry are appropriate to perform on spectra of this resolving power. Information on aerosol sulphate, nitrate, sodium chloride, methanesulphonic acid as well as semi-volatile metal species retrieved from these methods is evaluated. The constants in a commonly used formula for the estimation of the mass concentration of hydrocarbon-like organic aerosol may be refined based on peak-fitting results. Finally, application of a recently-published parameterisation for the estimation of carbon oxidation state to ToF-ACSM spectra is validated for a range of organic standards and its use demonstrated for ambient urban data.

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A novel approach for simple statistical analysis of high-resolution mass spectra

Atmospheric Measurement Techniques ◽

10.5194/amt-12-3761-2019 ◽

2019 ◽

Vol 12 (7) ◽

pp. 3761-3776 ◽

Cited By ~ 4

Author(s):

Yanjun Zhang ◽

Otso Peräkylä ◽

Chao Yan ◽

Liine Heikkinen ◽

Mikko Äijälä ◽

...

Keyword(s):

Mass Spectrometry ◽

Data Analysis ◽

High Resolution ◽

Mass Spectra ◽

Routine Data ◽

Well Being ◽

Full Potential ◽

Positive Matrix ◽

Peak Fitting ◽

Novel Approach

Abstract. Recent advancements in atmospheric mass spectrometry provide huge amounts of new information but at the same time present considerable challenges for the data analysts. High-resolution (HR) peak identification and separation can be effort- and time-consuming yet still tricky and inaccurate due to the complexity of overlapping peaks, especially at larger mass-to-charge ratios. This study presents a simple and novel method, mass spectral binning combined with positive matrix factorization (binPMF), to address these problems. Different from unit mass resolution (UMR) analysis or HR peak fitting, which represent the routine data analysis approaches for mass spectrometry datasets, binPMF divides the mass spectra into small bins and takes advantage of the positive matrix factorization's (PMF) strength in separating different sources or processes based on different temporal patterns. In this study, we applied the novel approach to both ambient and synthetic datasets to evaluate its performance. It not only succeeded in separating overlapping ions but was found to be sensitive to subtle variations as well. Being fast and reliable, binPMF has no requirement for a priori peak information and can save much time and effort from conventional HR peak fitting, while still utilizing nearly the full potential of HR mass spectra. In addition, we identify several future improvements and applications for binPMF and believe it will become a powerful approach in the data analysis of mass spectra.

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Supplementary material to "A Novel Approach for Simple Statistical Analysis of High-Resolution Mass Spectra"

10.5194/amt-2019-59-supplement ◽

2019 ◽

Author(s):

Yanjun Zhang ◽

Otso Peräkylä ◽

Chao Yan ◽

Liine Heikkinen ◽

Mikko Äijälä ◽

...

Keyword(s):

Statistical Analysis ◽

High Resolution ◽

Mass Spectra ◽

High Resolution Mass ◽

Novel Approach ◽

Supplementary Material ◽

Simple Statistical Analysis ◽

Resolution Mass

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A Novel Approach for Simple Statistical Analysis of High-Resolution Mass Spectra

10.5194/amt-2019-59 ◽

2019 ◽

Author(s):

Yanjun Zhang ◽

Otso Peräkylä ◽

Chao Yan ◽

Liine Heikkinen ◽

Mikko Äijälä ◽

...

Keyword(s):

Mass Spectrometry ◽

Data Analysis ◽

High Resolution ◽

Mass Spectra ◽

A Priori ◽

Routine Data ◽

Well Being ◽

Full Potential ◽

Peak Fitting ◽

Novel Approach

Abstract. Recent advancements in atmospheric mass spectrometry provide huge amounts of new information, but at the same time present considerable challenges for the data analysts. High-resolution (HR) peak identification and separation can be effort- and time-consuming, yet still tricky and inaccurate due to the complexity of overlapping peaks, especially at larger mass-to-charge ratios. This study presents a simple and novel method, mass spectral binning combined with positive matrix factorization (binPMF) to address these problems. Different from unit mass resolution (UMR) analysis or HR peak fitting, which represent the routine data analysis approaches for mass spectrometry datasets, binPMF divides the mass spectra into small bins and takes advantage of PMF’s strength in separating different sources or processes based on different temporal patterns. In this study, we applied the novel approach to both ambient and synthetic datasets to evaluate its performance. It not only succeeded in separating overlapping ions, but was found to be sensitive to subtle variations as well. Being fast and reliable, binPMF has no requirement for a priori peak information and can save much time and effort from conventional HR peak fitting, while still utilizing nearly the full potential of HR mass spectra. In addition, we identify several future improvements and applications for binPMF, and believe it will become a powerful approach in the data analysis of mass spectra.

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The High Resolution Scanning Transmission Electron Microscope

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100051591 ◽

1974 ◽

Vol 32 ◽

pp. 316-317

Author(s):

A. V. Crewe

Keyword(s):

Electron Microscope ◽

High Resolution ◽

High Vacuum ◽

Scanning Transmission Electron Microscope ◽

Ultra High Vacuum ◽

Resolving Power ◽

Imaging Characteristics ◽

Transmission Electron ◽

Scanning Transmission ◽

The Moment

The high resolution STEM is now a fact of life. I think that we have, in the last few years, demonstrated that this instrument is capable of the same resolving power as a CEM but is sufficiently different in its imaging characteristics to offer some real advantages.It seems possible to prove in a quite general way that only a field emission source can give adequate intensity for the highest resolution^ and at the moment this means operating at ultra high vacuum levels. Our experience, however, is that neither the source nor the vacuum are difficult to manage and indeed are simpler than many other systems and substantially trouble-free.

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An Analysis of Dissociation of Molecules in a High Resolution Electron Microscope

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100072873 ◽

1973 ◽

Vol 31 ◽

pp. 486-487

Author(s):

Mihir Parikh

Keyword(s):

Electron Microscope ◽

High Resolution ◽

Cross Sections ◽

Resolving Power ◽

Peak Intensity ◽

Molecular Film ◽

Resolution Electron ◽

Dissociation Cross Section ◽

High Resolution Electron Microscope ◽

The Stability

It is well known that the resolution of bio-molecules in a high resolution electron microscope depends not just on the physical resolving power of the instrument, but also on the stability of these molecules under the electron beam. Experimentally, the damage to the bio-molecules is commo ly monitored by the decrease in the intensity of the diffraction pattern, or more quantitatively by the decrease in the peaks of an energy loss spectrum. In the latter case the exposure, EC, to decrease the peak intensity from IO to I’O can be related to the molecular dissociation cross-section, σD, by EC = ℓn(IO /I’O) /ℓD. Qu ntitative data on damage cross-sections are just being reported, However, the microscopist needs to know the explicit dependence of damage on: (1) the molecular properties, (2) the density and characteristics of the molecular film and that of the support film, if any, (3) the temperature of the molecular film and (4) certain characteristics of the electron microscope used

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Practical High Resolution Microscopy

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100101256 ◽

1968 ◽

Vol 26 ◽

pp. 302-303

Author(s):

P. A. Marsh ◽

T. Mullens ◽

D. Price

Keyword(s):

High Resolution ◽

Magnetic Fields ◽

Low Frequency ◽

Resolving Power ◽

Careful Attention ◽

Electron Microscopes ◽

The Relationship ◽

High Resolution Microscopy ◽

New Facilities

It is possible to exceed the guaranteed resolution on most electron microscopes by careful attention to microscope parameters essential for high resolution work. While our experience is related to a Philips EM-200, we hope that some of these comments will apply to all electron microscopes.The first considerations are vibration and magnetic fields. These are usually measured at the pre-installation survey and must be within specifications. It has been our experience, however, that these factors can be greatly influenced by the new facilities and therefore must be rechecked after the installation is completed. The relationship between the resolving power of an EM-200 and the maximum tolerable low frequency interference fields in milli-Oerstedt is 10 Å - 1.9, 8 Å - 1.4, 6 Å - 0.8.

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A Super-High-Resolution HVEM (H-1500) Newly Installed in NIRIM

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100179464 ◽

1990 ◽

Vol 48 (1) ◽

pp. 142-143

Author(s):

S. Horiuchi ◽

Y. Matsui

Keyword(s):

Magnetic Field ◽

High Resolution ◽

Chromatic Aberration ◽

Inorganic Materials ◽

Electron Gun ◽

Resolving Power ◽

National Budget ◽

Voltage Electron ◽

Specimen Holder ◽

The Magnetic Field

A new high-voltage electron microscope (H-1500) specially aiming at super-high-resolution (1.0 Å point-to-point resolution) is now installed in National Institute for Research in Inorganic Materials ( NIRIM ), in collaboration with Hitachi Ltd. The national budget of about 1 billion yen including that for a new building has been spent for the construction in the last two years (1988-1989). Here we introduce some essential characteristics of the microscope.(1) According to the analysis on the magnetic field in an electron lens, based on the finite-element-method, the spherical as well as chromatic aberration coefficients ( Cs and Cc ). which enables us to reach the resolving power of 1.0Å. have been estimated as a function of the accelerating As a result of the calculaton. it was noted that more than 1250 kV is needed even when we apply the highest level of the technology and materials available at present. On the other hand, we must consider the protection against the leakage of X-ray. We have then decided to set the conventional accelerating voltage at 1300 kV. However. the maximum accessible voltage is 1500 kV, which is practically important to realize higher voltage stabillity. At 1300 kV it is expected that Cs= 1.7 mm and Cc=3.4 mm with the attachment of the specimen holder, which tilts bi-axially in an angle of 35° ( Fig.1 ). In order to minimize the value of Cc a small tank is additionally placed inside the generator tank, which must serve to seal the magnetic field around the acceleration tube. An electron gun with LaB6 tip is used.

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Exploring the Active Compounds of Traditional Mongolian Medicine Agsirga in Intervention of Novel Coronavirus (2019-nCoV) Based on HPLC-Q-Exactive-MS/MS and Molecular Docking Method

10.26434/chemrxiv.11955273 ◽

2020 ◽

Author(s):

Jie Cheng ◽

Yuchen Tang ◽

Baoquan Bao ◽

Ping Zhang

Keyword(s):

Mass Spectrometry ◽

Molecular Docking ◽

High Resolution ◽

Mass Spectra ◽

High Resolution Mass Spectrometry ◽

Structural Formula ◽

Active Compounds ◽

High Resolution Mass ◽

Q Exactive ◽

Resolution Mass

<a></a><a></a><a></a><a>Objective</a>: To screen all compounds of Agsirga based on the HPLC-Q-Exactive high-resolution mass spectrometry and find potential inhibitors that can respond to 2019-nCoV from active compounds of Agsirga by molecular docking technology. Methods: HPLC-Q-Exactive high-resolution mass spectrometry was adopted to identify the complex components of Mongolian medicine Agsirga, and separated by the high-resolution mass spectrometry Q-Exactive detector. Then the Orbitrap detector was used in tandem high-resolution mass spectrometry, and the related molecular and structural formula were found by using the chemsipider database and related literature, combined with precise molecular formulas (errors ≤ 5 × 10−6) , retention time, primary mass spectra, and secondary mass spectra information, The fragmentation regularities of mass spectra of these compounds were deduced. Taking ACE2 as the receptor and deduced compounds as the ligand, all of them were pretreated by discover studio, autodock and Chem3D. The molecular docking between the active ingredients and the target protein was studied by using AutoDock molecular docking software. The interaction between ligand and receptor is applied to provide a choice for screening anti-2019-nCoV drugs. Result: Based on the fragmentation patterns of the reference compounds and consulting literature, a total of 96 major alkaloids and stilbenes were screened and identified in Agsirga by the HPLC-Q-Exactive-MS/MS method. Combining with molecular docking, a conclusion was got that there are potential active substances in Mongolian medicine Agsirga which can block the binding of ACE2 and 2019-nCoV at the molecular level.

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