17 research outputs found
Advances in structure elucidation of small molecules using mass spectrometry
The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules
Congruent strategies for carbohydrate sequencing. 3. OSCAR: An algorithm for assigning oligosaccharide topology from MSn data
This is the third in a sequence of reports devoted to the development of congruent strategies for carbohydrate sequencing. Two previous reports outlined the strategies for observing structural detail from MSn data and introduced tools that compile, search, and compare fragment spectra in a bottom-up approach to oligosaccharide sequencing. In this third report, we. introduce the operational details of an algorithm that we define as the Oligosaccharide Subtree Constraint Algorithm (OSCAR). This algorithm assimilates analyst-selected MSn ion fragmentation pathways into oligosaccharide topology (branching and linkage) using what may be considered a top-down sequencing strategy. Guided by a series of logical constraints, this de novo algorithm provides molecular topology without presumed biosynthetic constraints or external comparisons. In this introductory study, OSCAR is applied to a series of permethylated oligomers and isomeric glycans, and topologies are assigned in a few hundredths of a second
Congruent Strategies for Carbohydrate Sequencing. 3. OSCAR: An Algorithm for Assigning Oligosaccharide Topology from MS n
Electrospray Ionization (ESI) Fragmentations and Dimethyldioxirane Reactivities of Three Diverse Lactams Having Full, Half, and Zero Resonance Energies
Three
lactams having, respectively, ∼20, ∼10, and
0 kcal/mol of resonance energy have been subjected to electrospray
ionization mass spectrometry (ESI/MS) as well as to attempted reaction
with dimethyldioxirane (DMDO). The ESI/MS for all three lactams are
consistent with fragmentation from the N-protonated, rather than the
O-protonated tautomer. Each exhibits a unique fragmentation pathway.
DFT calculations are employed to provide insights concerning these
pathways. <i>N</i>-Ethyl-2-pyrrolidinone and 1-azabicyclo[3.3.1]nonan-2-one,
the full- and half-resonance lactams, are unreactive with DMDO. The
“Kirby lactam” (3,5,7-trimethyl-1-azaadamantan-2-one)
has zero resonance energy and reacts rapidly with DMDO to generate
a mixture of reaction products. The structure assigned to one of these
is the 2,2-dihydroxy-<i>N</i>-oxide, thought to be stabilized
by intramolecular hydrogen bonding and buttressing by the methyl substituents.
A reasonable pathway to this derivative might involve formation of
an extremely labile <i>N</i>-oxide, in a purely formal sense,
an example of the hitherto-unknown amide <i>N</i>-oxides,
followed by hydration with traces of moisture
Protein and Site Specificity of Fucosylation in Liver-Secreted Glycoproteins
Chronic liver diseases are a serious
health problem worldwide.
One of the frequently reported glycan alterations in liver disease
is aberrant fucosylation, which was suggested as a marker for noninvasive
serologic monitoring. We present a case study that compares site specific
glycoforms of four proteins including haptoglobin, complement factor
H, kininogen-1, and hemopexin isolated from the same patient. Our
exoglycosidase-assisted LC–MS/MS analysis confirms the high
degree of fucosylation of some of the proteins but shows that microheterogeneity
is protein- and site-specific. MSn analysis of permethylated detached
glycans confirms the presence of LeY glycoforms on haptoglobin, which
cannot be detected in hemopexin or complement factor H; all three
proteins carry Lewis and H epitopes. Core fucosylation is detectable
in only trace amounts in haptoglobin but with confidence on hemopexin
and complement factor H, where core fucosylation of the bi-antennary
glycans on select glycopeptides reaches 15–20% intensity. These
protein-specific differences in fucosylation, observed in proteins
isolated from the same patient source, suggest that factors other
than up-regulation of enzymatic activity regulate the microheterogeneity
of glycoforms. This has implications for selection of candidate proteins
for disease monitoring and suggests that site-specific glycoforms
have structural determinants, which could lead to functional consequences
for specific subsets of proteins or their domains