56 research outputs found
ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry
ProSight PTM 2.0 (http://prosightptm2.scs.uiuc.edu) is the next generation of the ProSight PTM web-based system for the identification and characterization of proteins using top down tandem mass spectrometry. It introduces an entirely new data-driven interface, integrated Sequence Gazer for protein characterization, support for fixed modifications, terminal modifications and improved support for multiple precursor ions (multiplexing). Furthermore, it supports data import and export for local analysis and collaboration
Phocine distemper Virus: Current knowledge and future directions
Phocine distemper virus (PDV) was first recognized in 1988 following a massive epidemic in harbor and grey seals in north-western Europe. Since then, the epidemiology of infection in North Atlantic and Arctic pinnipeds has been investigated. In the western North Atlantic endemic infection in harp and grey seals predates the European epidemic, with relatively small, localized mortality events occurring primarily in harbor seals. By contrast, PDV seems not to have become established in European harbor seals following the 1988 epidemic and a second event of similar magnitude and extent occurred in 2002. PDV is a distinct species within the Morbillivirus genus with minor sequence variation between outbreaks over time. There is now mounting evidence of PDV-like viruses in the North Pacific/Western Arctic with serological and molecular evidence of infection in pinnipeds and sea otters. However, despite the absence of associated mortality in the region, there is concern that the virus may infect the large Pacific harbor seal and northern elephant seal populations or the endangered Hawaiian monk seals. Here, we review the current state of knowledge on PDV with particular focus on developments in diagnostics, pathogenesis, immune response, vaccine development, phylogenetics and modeling over the past 20 years
A population-based study of tumor gene expression and risk of breast cancer death among lymph node-negative patients
INTRODUCTION: The Oncotype DX assay was recently reported to predict risk for distant recurrence among a clinical trial population of tamoxifen-treated patients with lymph node-negative, estrogen receptor (ER)-positive breast cancer. To confirm and extend these findings, we evaluated the performance of this 21-gene assay among node-negative patients from a community hospital setting. METHODS: A case-control study was conducted among 4,964 Kaiser Permanente patients diagnosed with node-negative invasive breast cancer from 1985 to 1994 and not treated with adjuvant chemotherapy. Cases (n = 220) were patients who died from breast cancer. Controls (n = 570) were breast cancer patients who were individually matched to cases with respect to age, race, adjuvant tamoxifen, medical facility and diagnosis year, and were alive at the date of death of their matched case. Using an RT-PCR assay, archived tumor tissues were analyzed for expression levels of 16 cancer-related and five reference genes, and a summary risk score (the Recurrence Score) was calculated for each patient. Conditional logistic regression methods were used to estimate the association between risk of breast cancer death and Recurrence Score. RESULTS: After adjusting for tumor size and grade, the Recurrence Score was associated with risk of breast cancer death in ER-positive, tamoxifen-treated and -untreated patients (P = 0.003 and P = 0.03, respectively). At 10 years, the risks for breast cancer death in ER-positive, tamoxifen-treated patients were 2.8% (95% confidence interval [CI] 1.7ā3.9%), 10.7% (95% CI 6.3ā14.9%), and 15.5% (95% CI 7.6ā22.8%) for those in the low, intermediate and high risk Recurrence Score groups, respectively. They were 6.2% (95% CI 4.5ā7.9%), 17.8% (95% CI 11.8ā23.3%), and 19.9% (95% CI 14.2ā25.2%) for ER-positive patients not treated with tamoxifen. In both the tamoxifen-treated and -untreated groups, approximately 50% of patients had low risk Recurrence Score values. CONCLUSION: In this large, population-based study of lymph node-negative patients not treated with chemotherapy, the Recurrence Score was strongly associated with risk of breast cancer death among ER-positive, tamoxifen-treated and -untreated patients
Race and Equality in the Academy: Rethinking Higher Education Actors and the Struggle for Equality in the Post-World War II Period
Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial
Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients received corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.86-1.47; pā=ā0.40). There was no significant effect of DMF on any secondary outcome
Proteoform-selective imaging of tissues using mass spectrometry
Unraveling the complexity of biological systems relies on the development of new approaches for spatially resolved proteoform-specific analysis of the proteome. Herein, we employ nanospray desorption electrospray ionization mass spectrometry imaging (nano-DESI MSI) for the proteoform-selective imaging of biological tissues. Nano-DESI generates multiply charged protein ions, which is advantageous for their structural characterization using tandem mass spectrometry (MS/MS) directly on the tissue. Proof-of-concept experiments demonstrate that nano-DESI MSI combined with on-tissue top-down proteomics is ideally suited for the proteoform-selective imaging of tissue sections. Using rat brain tissue as a model system, we provide the first evidence of differential proteoform expression in different regions of the brain
The CāScore: A Bayesian Framework to Sharply Improve Proteoform Scoring in High-Throughput Top Down Proteomics
The
automated processing of data generated by top down proteomics
would benefit from improved scoring for protein identification and
characterization of highly related protein forms (proteoforms). Here
we propose the āC-scoreā (short for Characterization
Score), a Bayesian approach to the proteoform identification and characterization
problem, implemented within a framework to allow the infusion of expert
knowledge into generative models that take advantage of known properties
of proteins and top down analytical systems (e.g., fragmentation propensities,
āoff-by-1 Daā discontinuous errors, and intelligent
weighting for site-specific modifications). The performance of the
scoring system based on the initial generative models was compared
to the current probability-based scoring system used within both ProSightPC
and ProSightPTM on a manually curated set of 295 human proteoforms.
The current implementation of the C-score framework generated a marked
improvement over the existing scoring system as measured by the area
under the curve on the resulting ROC chart (AUC of 0.99 versus 0.78)
Fragmentation of Integral Membrane Proteins in the Gas Phase
Integral membrane proteins (IMPs)
are of great biophysical and
clinical interest because of the key role they play in many cellular
processes. Here, a comprehensive top down study of 152 IMPs and 277
soluble proteins from human H1299 cells including 11ā087 fragments
obtained from collisionally activated dissociation (CAD), 6452 from
higher-energy collisional dissociation (HCD), and 2981 from electron
transfer dissociation (ETD) shows their great utility and complementarity
for the identification and characterization of IMPs. A central finding
is that ETD is ā¼2-fold more likely to cleave in soluble regions
than threshold fragmentation methods, whereas the reverse is observed
in transmembrane domains with an observed ā¼4-fold bias toward
CAD and HCD. The location of charges just prior to dissociation is
consistent with this directed fragmentation: protons remain localized
on basic residues during ETD but easily mobilize along the backbone
during collisional activation. The fragmentation driven by these protons,
which is most often observed in transmembrane domains, both is of
higher yield and occurs over a greater number of backbone cleavage
sites. Further, while threshold dissociation events in transmembrane
domains are on average 10.1 (CAD) and 9.2 (HCD) residues distant from
the nearest charge site (R, K, H, N-terminus), fragmentation is strongly
influenced by the N- or C-terminal position relative to that site:
the ratio of observed b- to y-fragments is ā¼1:3 if the cleavage
occurs >7 residues N-terminal and ā¼3:1 if it occurs >7
residues
C-terminal to the nearest basic site. Threshold dissociation products
driven by a mobilized proton appear to be strongly dependent on not
only relative position of a charge site but also N- or C-terminal
directionality of proton movement
'Iter Dalekarlicum'
Mass spectrometry based proteomics generally seeks to
identify
and fully characterize protein species with high accuracy and throughput.
Recent improvements in protein separation have greatly expanded the
capacity of top-down proteomics (TDP) to identify a large number of
intact proteins. To date, TDP has been most tightly associated with
Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry.
Here, we couple the improved separations to a Fourier-transform instrument
based not on ICR but using the Orbitrap Elite mass analyzer. Application
of this platform to H1299 human lung cancer cells resulted in the
unambiguous identification of 690 unique proteins and over 2000 proteoforms
identified from proteins with intact masses <50 kDa. This is an
early demonstration of high throughput TDP (>500 identifications)
in an Orbitrap mass spectrometer and exemplifies an accessible platform
for whole protein mass spectrometry
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