Ultraviolet Photodissociation and Activated Electron Photodetachment Mass Spectrometry for Top-Down Sequencing of Modified Oligoribonucleotides.

With the increased development of new RNA-based therapeutics, the need for robust analytical methods for confirming sequences and mapping modifications has accelerated. Characterizing modified ribonucleic acids using mass spectrometry is challenging because diagnostic fragmentation may be suppressed for modified nucleotides, thus hampering complete sequence coverage and the confident localization of modifications. Ultraviolet photodissociation (UVPD) has shown great potential for the characterization of nucleic acids due to extensive backbone fragmentation.

Use of PASEF for Accelerated Protein Sequence Confirmation and De Novo Sequencing with High Data Quality.

Biopharmaceutical sequences can be well confirmed by multiple protease digests-e.g., trypsin, elastase, and chymotrypsin-followed by LC-MS/MS data analysis.

The lysosomal endopeptidases Cathepsin D and L are selective and effective proteases for the middle-down characterization of antibodies.

Mass spectrometry is gaining momentum as a method of choice to de novo sequence antibodies (Abs). Adequate sequence coverage of the hypervariable regions remains one of the toughest identification challenges by either bottom-up or top-down workflows. Methods that efficiently generate mid-size Ab fragments would further facilitate top-down MS and decrease data complexity.

Peak Filtering, Peak Annotation, and Wildcard Search for Glycoproteomics.

Glycopeptides in peptide or digested protein samples pose a number of analytical and bioinformatics challenges beyond those posed by unmodified peptides or peptides with smaller posttranslational modifications. Exact structural elucidation of glycans is generally beyond the capability of a single mass spectrometry experiment, so a reasonable level of identification for tandem mass spectrometry, taken by several glycopeptide software tools, is that of peptide sequence and glycan composition, meaning the number of monosaccharides of each distinct mass, e.g.

Parsimonious Charge Deconvolution for Native Mass Spectrometry.

Charge deconvolution infers the mass from mass over charge (m/z) measurements in electrospray ionization mass spectra. When applied over a wide input m/z or broad target mass range, charge-deconvolution algorithms can produce artifacts, such as false masses at one-half or one-third of the correct mass. Indeed, a maximum entropy term in the objective function of MaxEnt, the most commonly used charge deconvolution algorithm, favors a deconvolved spectrum with many peaks over one with fewer peaks.

Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery.

Applications of antibody de novo sequencing in the biopharmaceutical industry range from the discovery of new antibody drug candidates to identifying reagents for research and determining the primary structure of innovator products for biosimilar development. When murine, phage display, or patient-derived monoclonal antibodies against a target of interest are available, but the cDNA or the original cell line is not, de novo protein sequencing is required to humanize and recombinantly express these antibodies, followed by in vitro and in vivo testing for functional validation. Availability of fully automated software tools for monoclonal antibody de novo sequencing enables efficient and routine analysis.

mzML--a community standard for mass spectrometry data.

Mass spectrometry is a fundamental tool for discovery and analysis in the life sciences. With the rapid advances in mass spectrometry technology and methods, it has become imperative to provide a standard output format for mass spectrometry data that will facilitate data sharing and analysis. Initially, the efforts to develop a standard format for mass spectrometry data resulted in multiple formats, each designed with a different underlying philosophy.

Nonlinear fitting method for determining local false discovery rates from decoy database searches.

False discovery rate (FDR) analyses of protein and peptide identification results using decoy database searching conventionally report aggregate or global FDRs for a whole set of identifications, which are often not very informative about the error rates of individual members in the set. We describe a nonlinear curve fitting method for calculating the local FDR, which estimates the chance that an individual protein (or peptide) is incorrect, and present a simple tool that implements this analysis. The goal of this method is to offer a simple extension to the now commonplace decoy database searching, providing additional valuable information.

The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra.

The Paragon Algorithm, a novel database search engine for the identification of peptides from tandem mass spectrometry data, is presented. Sequence Temperature Values are computed using a sequence tag algorithm, allowing the degree of implication by an MS/MS spectrum of each region of a database to be determined on a continuum. Counter to conventional approaches, features such as modifications, substitutions, and cleavage events are modeled with probabilities rather than by discrete user-controlled settings to consider or not consider a feature.

Accommodative stimulus response curve of emmetropes and myopes.

Introduction: Myopes are suspected to be poorer at responding to accommodative stimuli than emmetropes, and this may worsen the degree of their myopia. The study aims to compare the abilities of young adult emmetropes and myopes in responding to accommodative stimuli, as indicated by their Accommodation Stimulus Response Curves (ASRCs) in a predominantly Chinese population.

Materials And Methods: Seventeen emmetropes and 33 myopes aged between 16 and 23 years (mean, 18.

Efficacy of measuring visual performance of LASIK patients under photopic and mesopic conditions.

Introduction: The aim of the study was to compare the visual performance of LASIK eyes measured using high-contrast logMAR letter charts under bright (photopic) and dim (mesopic) conditions.

Materials And Methods: A total of 46 subjects (35 +/- 8 years of age) undergoing LASIK procedures were recruited for the study. The best spectacle-corrected visual acuity (BSCVA) of each subject was measured using the high-contrast ETDRS logMAR chart under photopic and mesopic conditions at 3 visits: preoperative (Pre), 1 month postoperative (Post1) and 3 months postoperative (Post3).

Discovering known and unanticipated protein modifications using MS/MS database searching.

We present an MS/MS database search algorithm with the following novel features: (1) a novel protein database structure containing extensive preindexing and (2) zone modification searching, which enables the rapid discovery of protein modifications of known (i.e., user-specified) and unanticipated delta masses.

Visual experience during cataract surgery: a nation-wide survey on the knowledge of optometry students.

Purpose: Many patients experience a variety of visual sensations during cataract surgery under local anaesthesia. Up to 16.2% of patients are frightened by their intraoperative visual experience.

Repeatability of IOLMaster biometry in children.

Aims: This study compares the repeatability of IOLMaster (Zeiss, Oberkochen, Germany) axial dimension measurements and conventional ultrasonography in children.

Methods: A series of IOLMaster (partial coherence interferometry, optical pachometry) and Echoscan (US 800, Nidek, Tokyo, Japan) (ultrasound) measurements were taken on 179 Chinese children (mean age, 10.6 +/- 0.