10 research outputs found
Recommendations for reporting ion mobility mass spectrometry measurements
© 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. Here we present a guide to ion mobility mass spectrometry experiments, which covers both linear and nonlinear methods: what is measured, how the measurements are done, and how to report the results, including the uncertainties of mobility and collision cross section values. The guide aims to clarify some possibly confusing concepts, and the reporting recommendations should help researchers, authors and reviewers to contribute comprehensive reports, so that the ion mobility data can be reused more confidently. Starting from the concept of the definition of the measurand, we emphasize that (i) mobility values (K0) depend intrinsically on ion structure, the nature of the bath gas, temperature, and E/N; (ii) ion mobility does not measure molecular surfaces directly, but collision cross section (CCS) values are derived from mobility values using a physical model; (iii) methods relying on calibration are empirical (and thus may provide method-dependent results) only if the gas nature, temperature or E/N cannot match those of the primary method. Our analysis highlights the urgency of a community effort toward establishing primary standards and reference materials for ion mobility, and provides recommendations to do so. © 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc
Urban water supply systems - The repair option
Faced with a neglected, malfunctioning, inefficient or broken down water supply system there is a temptation to overlook the option in favour of replacement. Considerable savings can be achieved through well conceived repairs or improvements. Additionally the efficiency and treatment capacity of existing works can be often significantly improved by introducing new management or operational techÂniques
Comprehensive Tandem-Mass-Spectrometry Coverage of Complex Samples Enabled by Data-Set-Dependent Acquisition
Tandem
mass spectrometry (MS/MS) is an invaluable experimental
tool for providing analytical data supporting the identification of
small molecules and peptides in mass-spectrometry-based âomicsâ
experiments. Data-dependent MS/MS (DDA) is a real-time MS/MS-acquisition
strategy that is responsive to the signals detected in a given sample.
However, in analysis of even moderately complex samples with state-of-the-art
instrumentation, the speed of MS/MS acquisition is insufficient to
offer comprehensive MS/MS coverage of all detected molecules. Data-independent
approaches (DIA) offer greater MS/MS coverage, typically at the expense
of selectivity or sensitivity. This report describes data-set-dependent
MS/MS (DsDA), a novel integration of MS1-data processing and target
prioritization to enable comprehensive MS/MS sampling during the initial
MS-level experiment. This approach is guided by the premise that in
omics experiments, individual injections are typically made as part
of a larger set of samples, and feedback between data processing and
data acquisition can allow approximately real-time optimization of
MS/MS-acquisition parameters and nearly complete MS/MS-sampling coverage.
Using a combination of R, Proteowizard, XCMS, and WRENS software,
this concept was implemented on a liquid-chromatograph-coupled quadrupole
time-of-flight mass spectrometer. The results illustrate comprehensive
MS/MS coverage for a set of complex small-molecule samples and demonstrate
a strong improvement on traditional DDA
Comprehensive Tandem-Mass-Spectrometry Coverage of Complex Samples Enabled by Data-Set-Dependent Acquisition
Tandem
mass spectrometry (MS/MS) is an invaluable experimental
tool for providing analytical data supporting the identification of
small molecules and peptides in mass-spectrometry-based âomicsâ
experiments. Data-dependent MS/MS (DDA) is a real-time MS/MS-acquisition
strategy that is responsive to the signals detected in a given sample.
However, in analysis of even moderately complex samples with state-of-the-art
instrumentation, the speed of MS/MS acquisition is insufficient to
offer comprehensive MS/MS coverage of all detected molecules. Data-independent
approaches (DIA) offer greater MS/MS coverage, typically at the expense
of selectivity or sensitivity. This report describes data-set-dependent
MS/MS (DsDA), a novel integration of MS1-data processing and target
prioritization to enable comprehensive MS/MS sampling during the initial
MS-level experiment. This approach is guided by the premise that in
omics experiments, individual injections are typically made as part
of a larger set of samples, and feedback between data processing and
data acquisition can allow approximately real-time optimization of
MS/MS-acquisition parameters and nearly complete MS/MS-sampling coverage.
Using a combination of R, Proteowizard, XCMS, and WRENS software,
this concept was implemented on a liquid-chromatograph-coupled quadrupole
time-of-flight mass spectrometer. The results illustrate comprehensive
MS/MS coverage for a set of complex small-molecule samples and demonstrate
a strong improvement on traditional DDA
Comprehensive Tandem-Mass-Spectrometry Coverage of Complex Samples Enabled by Data-Set-Dependent Acquisition
Tandem
mass spectrometry (MS/MS) is an invaluable experimental
tool for providing analytical data supporting the identification of
small molecules and peptides in mass-spectrometry-based âomicsâ
experiments. Data-dependent MS/MS (DDA) is a real-time MS/MS-acquisition
strategy that is responsive to the signals detected in a given sample.
However, in analysis of even moderately complex samples with state-of-the-art
instrumentation, the speed of MS/MS acquisition is insufficient to
offer comprehensive MS/MS coverage of all detected molecules. Data-independent
approaches (DIA) offer greater MS/MS coverage, typically at the expense
of selectivity or sensitivity. This report describes data-set-dependent
MS/MS (DsDA), a novel integration of MS1-data processing and target
prioritization to enable comprehensive MS/MS sampling during the initial
MS-level experiment. This approach is guided by the premise that in
omics experiments, individual injections are typically made as part
of a larger set of samples, and feedback between data processing and
data acquisition can allow approximately real-time optimization of
MS/MS-acquisition parameters and nearly complete MS/MS-sampling coverage.
Using a combination of R, Proteowizard, XCMS, and WRENS software,
this concept was implemented on a liquid-chromatograph-coupled quadrupole
time-of-flight mass spectrometer. The results illustrate comprehensive
MS/MS coverage for a set of complex small-molecule samples and demonstrate
a strong improvement on traditional DDA
Comprehensive Tandem-Mass-Spectrometry Coverage of Complex Samples Enabled by Data-Set-Dependent Acquisition
Tandem
mass spectrometry (MS/MS) is an invaluable experimental
tool for providing analytical data supporting the identification of
small molecules and peptides in mass-spectrometry-based âomicsâ
experiments. Data-dependent MS/MS (DDA) is a real-time MS/MS-acquisition
strategy that is responsive to the signals detected in a given sample.
However, in analysis of even moderately complex samples with state-of-the-art
instrumentation, the speed of MS/MS acquisition is insufficient to
offer comprehensive MS/MS coverage of all detected molecules. Data-independent
approaches (DIA) offer greater MS/MS coverage, typically at the expense
of selectivity or sensitivity. This report describes data-set-dependent
MS/MS (DsDA), a novel integration of MS1-data processing and target
prioritization to enable comprehensive MS/MS sampling during the initial
MS-level experiment. This approach is guided by the premise that in
omics experiments, individual injections are typically made as part
of a larger set of samples, and feedback between data processing and
data acquisition can allow approximately real-time optimization of
MS/MS-acquisition parameters and nearly complete MS/MS-sampling coverage.
Using a combination of R, Proteowizard, XCMS, and WRENS software,
this concept was implemented on a liquid-chromatograph-coupled quadrupole
time-of-flight mass spectrometer. The results illustrate comprehensive
MS/MS coverage for a set of complex small-molecule samples and demonstrate
a strong improvement on traditional DDA
Energy-Resolved Ion Mobility Spectrometry: Composite Breakdown Curves for Distinguishing Isomeric Product Ions
Identification of lipopeptides (LpAA)
synthesized
from bacteria involves the study of structural characterization. Twenty LpAA have been characterized using commercial tandem high-resolution
mass spectrometers in negative electrospray, employing nonresonant
excitation in âRF onlyâ collision cells and generally
behave identically. However, [LpAA-H]â (AA = Asp or Glu) shows surprising fragmentation pathways, yielding
a complementary fatty acid carboxylate and dehydrated amino acid fragment
anions. In this study, the dissociation mechanisms of [C12Glu-H]â were determinate using energy-resolved mass spectrometry
(ERMS). Product ion breakdown profiles are, generally, unimodal with
full width at half-maximum (fwhm) increasing as product ion m/z ratios decrease, except for the two
product ions of interest (fatty acid carboxylate and dehydrated glutamate)
characterized by broad and composite profiles. Such behavior was already
shown for other ions using a custom-built guided ion beam mass spectrometer.
In this study, we investigate the meaning of these particular profiles
from an ERMS breakdown, using fragmentation mechanisms depending on
the collision energy. ERMS on line with ion mobility spectrometry
(IMS), here called ER-IMS, provides a way to probe such questions.
Broad or composite profiles imply that the corresponding product ions
may be generated by two (or more) pathways, resulting in common or
isomeric product ion structures. ER-IMS analysis indicates that the
fatty acid carboxylate product ion is produced with a common structure
through different pathways, while dehydrated glutamate has two isomeric
forms depending on the mechanism involved. Drift time values correlate
with the calculated collision cross section that confirms the product
ion structures and fragmentation mechanisms
Assigning Structures to Gas-Phase Peptide Cations and Cation-Radicals. An Infrared Multiphoton Dissociation, Ion Mobility, Electron Transfer, and Computational Study of a Histidine Peptide Ion
Infrared multiphoton dissociation (IRMPD) spectroscopy,
using a
free-electron laser, and ion mobility measurements, using both drift-cell
and traveling-wave instruments, were used to investigate the structure
of gas-phase peptide (AAHAL + 2H)<sup>2+</sup> ions produced by electrospray
ionization. The experimental data from the IRMPD spectra and collisional
cross section (Ω) measurements were consistent with the respective
infrared spectra and Ω calculated for the lowest-energy peptide
ion conformer obtained by extensive molecular dynamics searches and
combined density functional theory and <i>ab initio</i> geometry
optimizations and energy calculations. Traveling-wave ion mobility
measurements were employed to obtain the Ω of charge-reduced
peptide cation-radicals, (AAHAL + 2H)<sup>+â</sup>, and the <b><i>c</i><sub>3</sub></b>, <b><i>c</i><sub>4</sub></b>, <i><b>z</b></i><sub><b>3</b></sub>, and <b><i>z</i><sub>4</sub></b> fragments
from electron-transfer dissociation (ETD) of (AAHAL + 2H)<sup>2+</sup>. The experimental Ω for the ETD charge-reduced and fragment
ions were consistent with the values calculated for fully optimized
ion structures and indicated that the ions retained specific hydrogen
bonding motifs from the precursor ion. In particular, the Ω
for the doubly protonated ions and charge-reduced cation-radicals
were nearly identical, indicating negligible unfolding and small secondary
structure changes upon electron transfer. The experimental Ω
for the (AAHAL + 2H)<sup>+â</sup> cation-radicals were compatible
with both zwitterionic and histidine radical structures formed by
electron attachment to different sites in the precursor ion, but did
not allow their distinction. The best agreement with the experimental
Ω was found for ion structures fully optimized with M06-2X/6-31+GÂ(d,p)
and using both projection approximation and trajectory methods to
calculate the theoretical Ω values
Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization
A novel data-independent
acquisition (DIA) method incorporating
a scanning quadrupole in front of a collision cell and orthogonal
acceleration time-of-flight mass analyzer is described. The method
has been characterized for the qualitative and quantitative label-free
proteomic analysis of complex biological samples. The principle of
the scanning quadrupole DIA method is discussed, and analytical instrument
characteristics, such as the quadrupole transmission width, scan/integration
time, and chromatographic separation, have been optimized in relation
to sample complexity for a number of different model proteomes of
varying complexity and dynamic range including human plasma, cell
lines, and bacteria. In addition, the technological merits over existing
DIA approaches are described and contrasted. The qualitative and semiquantitative
performance of the method is illustrated for the analysis of relatively
simple protein digest mixtures and a well-characterized human cell
line sample using untargeted and targeted search strategies. Finally,
the results from a human cell line were compared against publicly
available data that used similar chromatographic conditions but were
acquired with DDA technology and alternative mass analyzer systems.
Qualitative comparison showed excellent concordance of results with
>90% overlap of the detected proteins
Scanning Quadrupole Data-Independent Acquisition, Part B: Application to the Analysis of the Calcineurin-Interacting Proteins during Treatment of <i>Aspergillus fumigatus</i> with Azole and Echinocandin Antifungal Drugs
Calcineurin is a critical cell-signaling
protein that orchestrates
growth, stress response, virulence, and antifungal drug resistance
in several fungal pathogens. Blocking calcineurin signaling increases
the efficacy of several currently available antifungals and suppresses
drug resistance. We demonstrate the application of a novel scanning
quadrupole DIA method for the analysis of changes in the proteins
coimmunoprecipitated with calcineurin during therapeutic antifungal
drug treatments of the deadly human fungal pathogen <i>Aspergillus
fumigatus.</i> Our experimental design afforded an assessment
of the precision of the method as demonstrated by peptide- and protein-centric
analysis from eight replicates of the study pool QC samples. Two distinct
classes of clinically relevant antifungal drugs that are guideline
recommended for the treatment of invasive âaspergillosisâ
caused by <i>Aspergillus fumigatus</i>, the azoles (voriconazole)
and the echinocandins (caspofungin and micafungin), which specifically
target the fungal plasma membrane and the fungal cell wall, respectively,
were chosen to distinguish variations occurring in the proteins coimmunoprecipitated
with calcineurin. Novel potential interactors were identified in response
to the different drug treatments that are indicative of the possible
role for calcineurin in regulating these effectors. Notably, treatment
with voriconazole showed increased immunoprecipitation of key proteins
involved in membrane ergosterol biosynthesis with calcineurin. In
contrast, echinocandin (caspofungin or micafungin) treatments caused
increased immunoprecipitation of proteins involved in cell-wall biosynthesis
and septation. Furthermore, abundant coimmunoprecipitation of ribosomal
proteins with calcineurin occurred exclusively in echinocandins treatment,
indicating reprogramming of cellular growth mechanisms during different
antifungal drug treatments. While variations in the observed calcineurin
immunoprecipitated proteins may also be due to changes in their expression
levels under different drug treatments, this study suggests an important
role for calcineurin-dependent cellular mechanisms in response to
antifungal treatment of <i>A.</i> fumigatus that warrants
future studies