scholarly journals FLASHIda: Intelligent data acquisition for top-down proteomics that doubles proteoform level identification count

2021 ◽  
Author(s):  
Kyowon Jeong ◽  
Masa Babovic ◽  
Vladimir Gorshkov ◽  
Jihyung Kim ◽  
Ole Noerregaard Jensen ◽  
...  

Top-down proteomics (TDP) has gained a lot of interest in biomedical application for detailed analysis and structural characterization of proteoforms. Data-dependent acquisition (DDA) of intact proteins is non-trivial due to the diversity and complex signal of proteoforms. Dedicated acquisition methods thus have the potential to greatly improve TDP. We present FLASHIda, an intelligent online data acquisition algorithm for TDP that ensures the real-time selection of high-quality precursors of diverse proteoforms. FLASHIda combines fast charge deconvolution algorithms and machine learning-based quality assessment for optimal precursor selection. In analysis in E. coli lysates, FLASHIda increased the number of unique proteoform level identifications from 800 to 1,500, or generated a near-identical number of identifications in ⅓ of instrument time when compared to standard DDA mode. Furthermore, FLASHIda enabled sensitive mapping of post translational modifications and detection of chemical adducts. As an extension module to the instrument, FLASHIda can be readily adopted for TDP studies of complex samples to enhance proteoform identification rates.

2014 ◽  
Vol 86 (3) ◽  
pp. 1485-1492 ◽  
Author(s):  
Kenneth R. Durbin ◽  
Ryan T. Fellers ◽  
Ioanna Ntai ◽  
Neil L. Kelleher ◽  
Philip D. Compton

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 422.1-422
Author(s):  
M. Volkov ◽  
A. S. B. Kampstra ◽  
K. van Schie ◽  
J. Kwekkeboom ◽  
T. Huizinga ◽  
...  

Background:Rheumatoid arthritis (RA) is characterized by autoantibodies against post-translationally modified proteins (AMPA) such as citrullinated, carbamylated and acetylated proteins. Importantly, these antibodies are highly multireactive, as they often recognize more than one of these post-translational modifications. Despite extensive research, the antigens inducing the breach of tolerance remain unknown, although microbial antigens are often suspected. Various bacteria are known to be capable of acetylation, therefore, it is intriguing to know what mechanisms can underlie the breach of tolerance towards acetylated proteins and development of anti-acetylated protein antibodies (AAPA).Objectives:To investigate whether acetylated proteins of bacterial origin (1) are recognized by human derived AMPA and AMPA expressing B cells; and (2) can induce AMPA development when used to immunize mice.Methods:Acetylated E. coli proteins were acquired with two separate methods (Figure 1A): by culturing E. coli in a condition promoting auto-acetylation (intrinsically acetylated bacterial proteins, IABP), or by directly acetylating lysate-derived proteins via a chemical reaction (extrinsically acetylated BP, EABP). Acetylated ovalbumin (AcOVA) served as positive control for AAPA induction in mice, non-acetylated BP (NABP) and phosphate buffer saline (PBS) served as negative control. Mice were immunized with these proteins and the resulting antibody response was studied by ELISA. Furthermore, EABP/IABP/NABP were investigated for recognition by human-derived AAPA with ELISA and AAPA-expressing B cells with spleen tyrosine kinase (Syk) phosphorylation assay; acetylated human fibrinogen and native fibrinogen served as positive and negative control.Results:Repetitive immunization of mice with EABP resulted in an AMPA response recognizing acetylated, carbamylated and citrullinated proteins. AMPA titers in these mice exceeded the titers in the positive control mice immunized with AcOVA and were substantially higher than in the NABP-immunized mice (Figure 1B). Human-derived monoclonal AAPA recognized EABP and IABP (not shown). B cell activation (measured by Syk phosphorylation) assay indicated that AAPA expressing B cells recognized EABP and (to a lesser extent) IABP, but not NABP (Figure 1C).Conclusion:Acetylated bacterial proteins are potent antigens that can induce cross-reactive AMPA responses in mice and they are recognized by human AAPA. This suggests that acetylated bacterial proteins could possibly be involved in the breach of tolerance in RA.Acknowledgements:We thank Dr. Can Araman and Prof. Chunaram Choudhary for their advice regarding optimization of bacterial auto-acetylation.Disclosure of Interests:None declared


2014 ◽  
Vol 651-653 ◽  
pp. 2296-2300
Author(s):  
Jing Huang ◽  
She Yu Zhou ◽  
Bing Lei Guan

Based on the theory of ultrasonic testing, an online data-acquisition and storage system is designed. The design scheme of hardware and software of the system is introduced in this paper, in which the embedded processor DSP and FPGA is used as its control core and the interface of PCI bus and DSP is designed. Thus a high speed and large-capacity ultrasonic signal can be processed, furthermore the pipelines defects can be analyze and evaluate.


Author(s):  
Dahang Yu ◽  
Zhe Wang ◽  
Kellye A. Cupp-Sutton ◽  
Yanting Guo ◽  
Qiang Kou ◽  
...  

2020 ◽  
Author(s):  
Kevin Jahnke ◽  
Noah Ritzmann ◽  
Julius Fichtler ◽  
Anna Nitschke ◽  
Yannik Dreher ◽  
...  

Abstract Bottom-up and top-down approaches to synthetic biology each employ distinct methodologies with the common aim to harness new types of living systems. Both approaches, however, face their own challenges towards biotechnological and biomedical applications. Here, we realize a strategic merger to convert light into proton gradients for the actuation of synthetic cellular systems. We genetically engineer E. coli to overexpress the light-driven inward-directed proton pump xenorhodopsin and encapsulate them as organelle mimics in artificial cell-sized compartments. Exposing the compartments to light-dark cycles, we can reversibly switch the pH by almost one pH unit and employ these pH gradients to trigger the attachment of DNA structures to the compartment periphery. For this purpose, a DNA triplex motif serves as a nanomechanical switch responding to the pH-trigger of the E. coli. By attaching a polymerized DNA origami plate to the DNA triplex motif, we obtain a cytoskeleton mimic that considerably deforms lipid vesicles in a pH-responsive manner. We foresee that the combination of bottom-up and top down approaches is an efficient way to engineer synthetic cells as potent microreactors.


PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3512 ◽  
Author(s):  
Adam Bajinting ◽  
Ho Leung Ng

Fibroblast growth factor receptors (FGFRs) are a family of receptor tyrosine kinases containing three domains: an extracellular receptor domain, a single transmembrane helix, and an intracellular tyrosine kinase domain. FGFRs are activated by fibroblast growth factors (FGFs) as part of complex signal transduction cascades regulating angiogenesis, skeletal formation, cell differentiation, proliferation, cell survival, and cancer. We have developed the first recombinant expression system in E. coli to produce a construct of human FGFR2 containing its transmembrane and extracellular receptor domains. We demonstrate that the expressed construct is functional in binding heparin and dimerizing. Size exclusion chromatography demonstrates that the purified FGFR2 does not form a complex with FGF1 or adopts an inactive dimer conformation. Progress towards the successful recombinant production of intact FGFRs will facilitate further biochemical experiments and structure determination that will provide insight into how extracellular FGF binding activates intracellular kinase activity.


Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 939
Author(s):  
Flávia Fonseca Bagno ◽  
Lara Carvalho Godói ◽  
Maria Marta Figueiredo ◽  
Sarah Aparecida Rodrigues Sérgio ◽  
Thaís de Fátima Silva Moraes ◽  
...  

Chikungunya virus (CHIKV) is a mosquito-borne pathogen that causes a disease characterized by the acute onset of fever accompanied by arthralgia and intense joint pain. Clinical similarities and cocirculation of this and other arboviruses in many tropical countries highlight the necessity for efficient and accessible diagnostic tools. CHIKV envelope proteins are highly conserved among alphaviruses and, particularly, the envelope 2 glycoprotein (CHIKV-E2) appears to be immunodominant and has a considerable serodiagnosis potential. Here, we investigate how glycosylation of CHIKV-E2 affects antigen/antibody interaction and how this affects the performance of CHIKV-E2-based Indirect ELISA tests. We compare two CHIKV-E2 recombinant antigens produced in different expression systems: prokaryotic-versus eukaryotic-made recombinant proteins. CHIKV-E2 antigens are expressed either in E. coli BL21(DE3)—a prokaryotic system unable to produce post-translational modifications—or in HEK-293T mammalian cells—a eukaryotic system able to add post-translational modifications, including glycosylation sites. Both prokaryotic and eukaryotic recombinant CHIKV-E2 react strongly to anti-CHIKV IgG antibodies, showing accuracy levels that are higher than 90%. However, the glycan-added viral antigen presents better sensitivity and specificity (85 and 98%) than the non-glycosylated antigen (81 and 71%, respectively) in anti-CHIKV IgM ELISA assays.


2019 ◽  
Vol 7 (11) ◽  
pp. 488 ◽  
Author(s):  
Clifton K. Fagerquist ◽  
William J. Zaragoza ◽  
Michelle Q. Carter

Shiga-toxin-producing Escherichia coli (STEC) are a burden on agriculture and a threat to public health. Rapid methods are needed to identify STEC strains and characterize the Shiga toxin (Stx) they produce. We analyzed three STEC strains for Stx expression, using antibiotic induction, matrix-assisted laser desorption/ionization time-of-flight-time-of-flight (MALDI-TOF-TOF) mass spectrometry, and top-down proteomic analysis. E. coli O157:H- strain 493/89 is a clinical isolate linked to an outbreak of hemolytic uremic syndrome (HUS) in Germany in the late 1980s. E. coli O145:H28 strains RM12367-C1 and RM14496-C1 were isolated from an agricultural region in California. The stx operon of the two environmental strains were determined by whole genome sequencing (WGS). STEC strain 493/89 expressed Shiga toxin 2a (Stx2a) as identified by tandem mass spectrometry (MS/MS) of its B-subunit that allowed identification of the type and subtype of the toxin. RM12367-C1 also expressed Stx2a as identified by its B-subunit. RM14496-C1 expressed Shiga toxin 1a (Stx1a) as identified from its B-subunit. The B-subunits of Stx1 and Stx2 both have an intramolecular disulfide bond. MS/MS was obtained on both the disulfide-bond-intact and disulfide-bond-reduced B-subunit, with the latter being used for top-down proteomic identification. Top-down proteomic analysis was consistent with WGS.


2019 ◽  
Vol 35 (18) ◽  
pp. 3489-3490 ◽  
Author(s):  
Diogo B Lima ◽  
André R F Silva ◽  
Mathieu Dupré ◽  
Marlon D M Santos ◽  
Milan A Clasen ◽  
...  

Abstract Motivation We present the first tool for unbiased quality control of top-down proteomics datasets. Our tool can select high-quality top-down proteomics spectra, serve as a gateway for building top-down spectral libraries and, ultimately, improve identification rates. Results We demonstrate that a twofold rate increase for two E. coli top-down proteomics datasets may be achievable. Availability and implementation http://patternlabforproteomics.org/tdgc, freely available for academic use. Supplementary information Supplementary data are available at Bioinformatics online.


Sign in / Sign up

Export Citation Format

Share Document