scholarly journals Author Correction: Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis

2021 ◽  
Author(s):  
Rebeca Kawahara ◽  
Anastasia Chernykh ◽  
Kathirvel Alagesan ◽  
Marshall Bern ◽  
Weiqian Cao ◽  
...  
Keyword(s):  
High Performance ◽  
Search Strategies ◽  
Community Evaluation ◽  
Glycopeptide Analysis

scholarly journals Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis

2021 ◽  
Author(s):  
Rebeca Kawahara ◽  
Anastasia Chernykh ◽  
Kathirvel Alagesan ◽  
Marshall Bern ◽  
Weiqian Cao ◽  
...  
Keyword(s):  
Data Analysis ◽  
High Performance ◽  
Mass Spectra ◽  
Search Strategies ◽  
High Coverage ◽  
Tandem Mass Spectra ◽  
Software Packages ◽  
Community Evaluation ◽  
Key Variables ◽  
Glycopeptide Analysis

AbstractGlycoproteomics is a powerful yet analytically challenging research tool. Software packages aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but their relative performance remains untested. Conducted through the HUPO Human Glycoproteomics Initiative, this community study, comprising both developers and users of glycoproteomics software, evaluates solutions for system-wide glycopeptide analysis. The same mass spectrometrybased glycoproteomics datasets from human serum were shared with participants and the relative team performance for N- and O-glycopeptide data analysis was comprehensively established by orthogonal performance tests. Although the results were variable, several high-performance glycoproteomics informatics strategies were identified. Deep analysis of the data revealed key performance-associated search parameters and led to recommendations for improved ‘high-coverage’ and ‘high-accuracy’ glycoproteomics search solutions. This study concludes that diverse software packages for comprehensive glycopeptide data analysis exist, points to several high-performance search strategies and specifies key variables that will guide future software developments and assist informatics decision-making in glycoproteomics.

scholarly journals Community Evaluation of Glycoproteomics Informatics Solutions Reveals High-Performance Search Strategies of Glycopeptide Data

2021 ◽  
Author(s):  
Rebeca Kawahara ◽  
Kathirvel Alagesan ◽  
Marshall Bern ◽  
Weiqian Cao ◽  
Robert J Chalkley ◽  
...  
Keyword(s):  
Data Analysis ◽  
Team Performance ◽  
High Performance ◽  
Serum Proteins ◽  
Search Strategies ◽  
Tandem Mass Spectra ◽  
Community Evaluation ◽  
Key Variables ◽  
The Many ◽  
Human Proteome Project

AbstractGlycoproteome profiling (glycoproteomics) remains a considerable analytical challenge that hinders rapid progress in glycobiology. The complex tandem mass spectra generated from glycopeptide mixtures require sophisticated analysis pipelines for structural determination. Diverse informatics solutions aiding the process have appeared, but their relative strengths and weaknesses remain untested. Conducted through the Human Proteome Project – Human Glycoproteomics Initiative, this community study comprising both developers and expert users of glycoproteomics software is the first to evaluate the relative performance of current informatics solutions for comprehensive glycopeptide analysis. High-quality LC-MS/MS-based glycoproteomics datasets of N- and O-glycopeptides from serum proteins were shared with all teams. The relative team performance for efficient glycopeptide data analysis was systematically established through multiple orthogonal performance tests. Excitingly, several high-performance glycoproteomics informatics solutions and tools displaying a considerable performance potential were identified. While the study illustrated that significant informatics challenges remain in the analysis of glycopeptide data as indicated by a high discrepancy between the reported glycopeptides, a substantial list of commonly reported high-confidence glycopeptides could be extracted from the team reports. Further, the team performance profiles were correlated to the many study variables, which revealed important performance-associated search settings and search output variables, some intuitive others unexpected. This study concludes that diverse informatics solutions for comprehensive glycopeptide data analysis exist within the community, points to several high-performance search strategies, and specifies key variables that may guide future software developments and assist the experimental decision-making of practitioners in glycoproteomics.

Discovery of High-Performance Organic Non-Linear Optical Molecules by Systematic ‘Smart Material’ Design Strategies

2010 ◽  
Vol 123-125 ◽  
pp. 959-962 ◽  
Author(s):  
Jacqueline M. Cole ◽  
Ze F. Weng
Keyword(s):  
High Performance ◽  
Chemical Space ◽  
Active Material ◽  
Material Design ◽  
Search Strategies ◽  
Search Method ◽  
Smart Material ◽  
Non Linear ◽  
Nlo Materials ◽  
Linear Optical

This paper presents the discovery of a range of high-performance organic non-linear optical (NLO) materials, that arises from ‘smart material’ design and systematic search strategies. This systematization circumvents the previous use of iterative discovery methods, which can only ever afford incremental improvements to currently known NLO materials, and they have no capacity to reveal entirely new classes of suitable NLO materials. This new approach employs data-mining, using the world’s repository of all published organic crystal structures as a representative set of chemical space. Two independent search strategies are implemented, each predicting the best organic NLO materials. The first search method relies on the concept of ‘molecular lego’, taking particular types of molecular fragments that are known to be important constituents of an NLO active material (the ‘lego’), and searching for these through chemical space, with the assistance of graph theory algorithms and systematic enumeration and classification. The second search method uses quantum- mechanical calculations to evaluate the molecular hyperpolarizability, β, of every organic molecule in the aforementioned database. Since β affords the intrinsic measure of NLO output, all organic molecules listed in descending order of  values reflects a ranked list of their NLO potential. The NLO properties of selected materials that are highly-ranked in these two lists were then tested experimentally, using Hyper-Rayleigh Scattering (HRS). The predictions are shown to be borne out by such experiments: HRS results show β0 (static hyperpolarizability) values that are up to 10 x greater than those for the industrial reference Disperse Red 1. Due to the commercial potential of these results, four new classes of NLO materials identified by this study have recently been patented.

A High Performance Energy Analyzer for Use in Electron Scanning Microscopy

1969 ◽  
Vol 27 ◽  
pp. 14-15
Author(s):  
A. V. Crewe ◽  
M. Isaacson ◽  
D. Johnson
Keyword(s):  
High Performance ◽  
Vertical Plane ◽  
Median Plane ◽  
Electron Gun ◽  
Uniform Field ◽  
Loss Mechanism ◽  
Electron Scanning Microscopy ◽  
Sector Type ◽  
Double Focusing ◽  
Electron Energy Loss

A double focusing magnetic spectrometer has been constructed for use with a field emission electron gun scanning microscope in order to study the electron energy loss mechanism in thin specimens. It is of the uniform field sector type with curved pole pieces. The shape of the pole pieces is determined by requiring that all particles be focused to a point at the image slit (point 1). The resultant shape gives perfect focusing in the median plane (Fig. 1) and first order focusing in the vertical plane (Fig. 2).

Vacuum System to Minimize the Specimen Contamination of High-Performance EM

1977 ◽  
Vol 35 ◽  
pp. 68-69
Author(s):  
N. Yoshimura ◽  
K. Shirota ◽  
T. Etoh
Keyword(s):  
Electron Microscope ◽  
High Speed ◽  
High Performance ◽  
High Vacuum ◽  
Vacuum System ◽  
Pump System ◽  
Pumping System ◽  
Diffusion Pump ◽  
Almost All ◽  
Cascade Type

One of the most important requirements for a high-performance EM, especially an analytical EM using a fine beam probe, is to prevent specimen contamination by providing a clean high vacuum in the vicinity of the specimen. However, in almost all commercial EMs, the pressure in the vicinity of the specimen under observation is usually more than ten times higher than the pressure measured at the punping line. The EM column inevitably requires the use of greased Viton O-rings for fine movement, and specimens and films need to be exchanged frequently and several attachments may also be exchanged. For these reasons, a high speed pumping system, as well as a clean vacuum system, is now required. A newly developed electron microscope, the JEM-100CX features clean high vacuum in the vicinity of the specimen, realized by the use of a CASCADE type diffusion pump system which has been essentially improved over its predeces- sorD employed on the JEM-100C.

Use of the Magnetostatic Analogue In Electromagnetic Lens Engineering

1970 ◽  
Vol 28 ◽  
pp. 360-361
Author(s):  
John W. Coleman
Keyword(s):  
Boundary Conditions ◽  
High Performance ◽  
Force Fields ◽  
Optical Design ◽  
Direct Conversion ◽  
Design Engineering ◽  
Design Data ◽  
Scalar Potentials ◽  
Geometric Elements ◽  
At Will

In the design engineering of high performance electromagnetic lenses, the direct conversion of electron optical design data into drawings for reliable hardware is oftentimes difficult, especially in terms of how to mount parts to each other, how to tolerance dimensions, and how to specify finishes. An answer to this is in the use of magnetostatic analytics, corresponding to boundary conditions for the optical design. With such models, the magnetostatic force on a test pole along the axis may be examined, and in this way one may obtain priority listings for holding dimensions, relieving stresses, etc..The development of magnetostatic models most easily proceeds from the derivation of scalar potentials of separate geometric elements. These potentials can then be conbined at will because of the superposition characteristic of conservative force fields.

Prospects for convergent beam electron diffraction with a 200kV cold field-emission transmission electron microscope

1991 ◽  
Vol 49 ◽  
pp. 466-467
Author(s):  
J W Steeds ◽  
R Vincent
Keyword(s):  
Field Emission ◽  
High Performance ◽  
Small Diameter ◽  
Convergent Beam Electron Diffraction ◽  
Zone Axis ◽  
Medium Voltage ◽  
Transmission Electron ◽  
Good Crystallinity ◽  
Special Modification ◽  
Convergent Beam

We review the analytical powers which will become more widely available as medium voltage (200-300kV) TEMs with facilities for CBED on a nanometre scale come onto the market. Of course, high performance cold field emission STEMs have now been in operation for about twenty years, but it is only in relatively few laboratories that special modification has permitted the performance of CBED experiments. Most notable amongst these pioneering projects is the work in Arizona by Cowley and Spence and, more recently, that in Cambridge by Rodenburg and McMullan.There are a large number of potential advantages of a high intensity, small diameter, focussed probe. We discuss first the advantages for probes larger than the projected unit cell of the crystal under investigation. In this situation we are able to perform CBED on local regions of good crystallinity. Zone axis patterns often contain information which is very sensitive to thickness changes as small as 5nm. In conventional CBED, with a lOnm source, it is very likely that the information will be degraded by thickness averaging within the illuminated area.

Current State of Biological High-Resolution Scanning Electron Microscopy

1988 ◽  
Vol 46 ◽  
pp. 180-181 ◽  
Author(s):  
Klaus-Ruediger Peters
Keyword(s):  
High Performance ◽  
Low Voltage ◽  
Backscattered Electrons ◽  
Lens Position ◽  
Low Voltage Operation ◽  
Signal Collection ◽  
Probe Size ◽  
Electron Microscopes ◽  
Scanning Electron Microscopes ◽  
Scanning Electron

A new generation of high performance field emission scanning electron microscopes (FSEM) is now commercially available (JEOL 890, Hitachi S 900, ISI OS 130-F) characterized by an "in lens" position of the specimen where probe diameters are reduced and signal collection improved. Additionally, low voltage operation is extended to 1 kV. Compared to the first generation of FSEM (JE0L JSM 30, Hitachi S 800), which utilized a specimen position below the final lens, specimen size had to be reduced but useful magnification could be impressively increased in both low (1-4 kV) and high (5-40 kV) voltage operation, i.e. from 50,000 to 200,000 and 250,000 to 1,000,000 x respectively.At high accelerating voltage and magnification, contrasts on biological specimens are well characterized1 and are produced by the entering probe electrons in the outmost surface layer within -vl nm depth. Backscattered electrons produce only a background signal. Under these conditions (FIG. 1) image quality is similar to conventional TEM (FIG. 2) and only limited at magnifications >1,000,000 x by probe size (0.5 nm) or non-localization effects (%0.5 nm).

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