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Accurate and Robust Trypan Blue-Based Cell Viability Measurement Using Neural Networks

July 19, 2021

Author(s)

Adele Peskin, Steven Lund, Chenyi Ling, Laura Pierce, Sumona Sarkar, Firdavs Kurbanov, Michael Halter, Joe Chalfoun, John T. Elliott

Trypan blue dye exclusion-based cell viability measurements are highly dependent upon image quality and consistency. In order to make measurements repeatable, one must be able to reliably capture images at a consistent focal plane, and with signal-to-noise

Microbial interactions with silicate glasses

July 17, 2021

Author(s)

Jamie Weaver, Carolyn Pearce, Robert Koestler, Bruce Arey, Albert Kruger, Paula DePriest, Andrew Plymale

Glass alteration in the presence of microorganisms has been a topic of research for over 150 years. Researchers from a variety of disciplines, including material science, biology, chemistry, geology, physics, and cultural heritage materials preservation

MS_Piano: A Software Tool for Annotating Peaks in CID Tandem Mass Spectra of Peptides and N-Glycopeptides

July 15, 2021

Author(s)

Xiaoyu (Sara) Yang, Pedatsur Neta, Yuri Mirokhin, Dmitrii V. Tchekhovskoi, Concepcion Remoroza, Meghan Burke Harris, Yuxue Liang, Sanford Markey, Stephen E. Stein

Annotating product ion peaks in tandem mass spectra is essential for evaluating spectral quality and validating peptide identification. This task is more complex for glycopeptides and is crucial for the confident determination of glycosylation sites in

Site-Specific Glycan-Conjugated NISTmAb Antibody Drug Conjugate Standards

July 6, 2021

Author(s)

Brian Agnew, Shanhua Lin, Robert Aggeler, John E. Schiel, Trina Mouchahoir

Antibody drug conjugates (ADCs) represent a rapidly growing modality for the treatment of numerous oncology indications. The complexity of analytical characterization method development is increased due to the potential for synthetic intermediates and

Universal Spectrum Identifier for mass spectra

July 2, 2021

Author(s)

Eric Deutsch, Yasset Perez-Riverol, Jeremy Carver, Shin Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Pierre-Alain Binz, Benjamin Pullman, Zhi Sun, Jim Shofstahl, Wout Bittremeieux, Tytus Mak, Joshua Klein, Yunping Zhu, Henry Lam, Juan Antonio Vizcaino, Nuno Bandeira

Mass spectra provide the ultimate evidence to support the findings of mass spectrometry proteomics studies in publications, and it is therefore crucial to be able to trace the conclusions back to the spectra. The Universal Spectrum Identifier (USI)

Early Time-Point Cell Morphology Classifiers Successfully Predict Human Bone Marrow Stromal Cell Differentiation Modulated by Fiber Density in Nanofiber Scaffolds

July 1, 2021

Author(s)

Desu Chen, Joy Dunkers, Wolfgang Losert, Sumona Sarkar

Nanofiber scaffolds can induce osteogenic differentiation and cell morphology alterations of human bone marrow stromal cells (hBMSCs) without introduction of chemical cues. In this study, we investigate the predictive power of day 1 cell morphology

Comprehensive Analysis of Tryptic Peptides Arising from Disulfide Linkages in NISTmAb and Their Use for Developing a Mass Spectral Library

June 22, 2021

Author(s)

Qian Dong, Xinjian Yan, Yuxue Liang, Sanford Markey, Sergey L. Sheetlin, Concepcion Remoroza, William E. Wallace, Stephen Stein

This work presents methods for identifying and then creating a mass spectral library for disulfide-linked peptides originating from the NISTmAb. Analysis involved both partially- reduced and non-reduced proteins under neutral and weakly basic conditions

Dataset from HDX-MS Studies of IgG1 Glycoforms and Their Interactions with the FcgR1a (CD64) Receptor

June 17, 2021

Author(s)

Kyle Anderson, Kerry Scott, Ioannis Karageorgos, Elyssia Gallagher, Venkata Tayi, Michael Butler, Jeffrey W. Hudgens

This database gives hydrogen-deuterium exchange mass spectrometry (HDX-MS) data from measurements of three purified IgG1 glycoform samples, predominantly G0F, G2F, and SAF, in isolation and in complexation with the high-affinity receptor, FcγR1a (CD64)

Recommendations for the Use of In silico Approaches for Next Generation Sequencing Bioinformatic Pipeline Validation: A Report of the Association for Molecular Pathology

May 24, 2021

Author(s)

Eric Duncavage, Justin Zook

In silico approaches for next generation sequencing (NGS) data modeling have utility in the clinical laboratory as a tool for clinical assay validation. In silico NGS data can take a variety of forms including pure simulated data or manipulated data files

The mutation spectrum shapes the spectrum of adaptive substitutions

May 20, 2021

Author(s)

Alejandro Cano, Hana Rozhonova, Arlin B. Stoltzfus, David McCandlish, Joshua Payne

Evolutionary adaptation can be conceived as a series of substitutions representing mutation-fixation events. The changes that are more likely will appear more frequently in the aggregate spectrum of adaptive substitutions. Recent studies establish that

Outcomes from a Cell Viability Pre-Conference Workshop: Fit-For-Purpose Considerations for Cell Viability Measurements in Cell and Gene Therapy

May 14, 2021

Author(s)

Laura Pierce, Sumona Sarkar, Leo Chan, Bo Lin, Jean Qiu

Fit-for-purpose cell viability measurement methods are urgently needed for the characterization and testing of cell and gene therapy products and their manufacturing processes. A recent Cell Viability Workshop held at the virtual Cell Therapy Analytical

A Simple Approach for Reconstruction of Non-uniformly Sampled Psuedo-3D NMR Data for Accurate Measurement of Spin Relaxation Parameters

May 7, 2021

Author(s)

Kyle East, Frank Delaglio, George Lisi

We present a simple approach to reconstruction of NUS 2D spectral series as used in relaxation analysis. The approach treats this data as an ordinary 3D time-domain measurement whose imaginary part in the pseudo-dimension is zero, with familiar 3D NUS

Cautionary Note on Contamination of Reagents Used for Molecular Detection of SARS-CoV-2

May 3, 2021

Author(s)

Peter Vallone, James Huggett, Vladimir Benes, Jeremy Garson, Kathryn Harris, Mikael Kubista, Timothy McHugh, Jacob Moran-Gilad, Tania Nolan, Michael Pfaffl, Marc Salit, Greg Shipley, Jo Vandesompele

Reverse transcription (RT)-PCR, the principal diagnostic method applied in the world-wide struggle against COVID-19, is capable of detecting a single molecule of a viral genome. Correctly designed and practiced RT-PCR assays for SARS-CoV-2 should not cross