A Customizable Flow Injection System for Automated, High Throughput, and Time Sensitive Ion Mobility Spectrometry and Mass Spectrometry Measurements.

To better understand disease conditions and environmental perturbations, multiomic studies combining proteomic, lipidomic, and metabolomic analyses are vastly increasing in popularity. In a multiomic study, a single sample is typically extracted in multiple ways, and various analyses are performed using different instruments, most often based upon mass spectrometry (MS). Thus, one sample becomes many measurements, making high throughput and reproducible evaluations a necessity.

Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry.

Ion mobility spectrometry in conjunction with liquid chromatography separations and mass spectrometry offers a range of new possibilities for analyzing complex biological samples. To fully utilize the information obtained from these three measurement dimensions, informatics tools based on the accurate mass and time tag methodology were modified to incorporate ion mobility spectrometry drift times for peptides observed in human serum. In this work a reference human serum database was created for 12,139 peptides and populated with the monoisotopic mass, liquid chromatography normalized elution time, and ion mobility spectrometry drift time(s) for each.

GlyQ-IQ: glycomics quintavariate-informed quantification with high-performance computing and GlycoGrid 4D visualization.

Glycomics quintavariate-informed quantification (GlyQ-IQ) is a biologically guided glycomics analysis tool for identifying N-glycans in liquid chromatography-mass spectrometry (LC-MS) data. Glycomics LC-MS data sets have convoluted extracted ion chromatograms that are challenging to deconvolve with existing software tools. LC deconvolution into constituent pieces is critical in glycomics data sets because chromatographic peaks correspond to different intact glycan structural isomers.

Signatures for mass spectrometry data quality.

Ensuring data quality and proper instrument functionality is a prerequisite for scientific investigation. Manual quality assurance is time-consuming and subjective. Metrics for describing liquid chromatography mass spectrometry (LC-MS) data have been developed; however, the wide variety of LC-MS instruments and configurations precludes applying a simple cutoff.

Advancing the high throughput identification of liver fibrosis protein signatures using multiplexed ion mobility spectrometry.

Rapid diagnosis of disease states using less invasive, safer, and more clinically acceptable approaches than presently employed is a crucial direction for the field of medicine. While MS-based proteomics approaches have attempted to meet these objectives, challenges such as the enormous dynamic range of protein concentrations in clinically relevant biofluid samples coupled with the need to address human biodiversity have slowed their employment. Herein, we report on the use of a new instrumental platform that addresses these challenges by coupling technical advances in rapid gas phase multiplexed ion mobility spectrometry separations with liquid chromatography and MS to dramatically increase measurement sensitivity and throughput, further enabling future high throughput MS-based clinical applications.

LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets.

Motivation: The addition of ion mobility spectrometry to liquid chromatography-mass spectrometry experiments requires new, or updated, software tools to facilitate data processing.

Results: We introduce a command line software application LC-IMS-MS Feature Finder that searches for molecular ion signatures in multidimensional liquid chromatography-ion mobility spectrometry-mass spectrometry (LC-IMS-MS) data by clustering deisotoped peaks with similar monoisotopic mass, charge state, LC elution time and ion mobility drift time values. The software application includes an algorithm for detecting and quantifying co-eluting chemical species, including species that exist in multiple conformations that may have been separated in the IMS dimension.

MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis.

Background: MultiAlign is a free software tool that aligns multiple liquid chromatography-mass spectrometry datasets to one another by clustering mass and chromatographic elution features across datasets. Applicable to both label-free proteomics and metabolomics comparative analyses, the software can be operated in several modes. For example, clustered features can be matched to a reference database to identify analytes, used to generate abundance profiles, linked to tandem mass spectra based on parent precursor masses, and culled for targeted liquid chromatography-tandem mass spectrometric analysis.

A cabled acoustic telemetry system for detecting and tracking juvenile salmon: part 2. Three-dimensional tracking and passage outcomes.

In Part 1 of this paper, we presented the engineering design and instrumentation of the Juvenile Salmon Acoustic Telemetry System (JSATS) cabled system, a nonproprietary sensing technology developed by the U.S. Army Corps of Engineers, Portland District (Oregon, USA) to meet the needs for monitoring the survival of juvenile salmonids through the hydroelectric facilities within the Federal Columbia River Power System.

A cabled acoustic telemetry system for detecting and tracking juvenile salmon: part 1. Engineering design and instrumentation.

In 2001 the U.S. Army Corps of Engineers, Portland District (OR, USA), started developing the Juvenile Salmon Acoustic Telemetry System, a nonproprietary sensing technology, to meet the needs for monitoring the survival of juvenile salmonids through eight large hydroelectric facilities within the Federal Columbia River Power System (FCRPS).

An LC-IMS-MS platform providing increased dynamic range for high-throughput proteomic studies.

A high-throughput approach and platform using 15 min reversed-phase capillary liquid chromatography (RPLC) separations in conjunction with ion mobility spectrometry-mass spectrometry (IMS-MS) measurements was evaluated for the rapid analysis of complex proteomics samples. To test the separation quality of the short LC gradient, a sample was prepared by spiking 20 reference peptides at varying concentrations from 1 ng/mL to 10 microg/mL into a tryptic digest of mouse blood plasma and analyzed with both a LC-Linear Ion Trap Fourier Transform (FT) MS and LC-IMS-TOF MS. The LC-FT MS detected 13 out of the 20 spiked peptides that had concentrations >or=100 ng/mL.

Selection of the optimum electrospray voltage for gradient elution LC-MS measurements.

Changes in liquid composition during gradient elution liquid chromatography (LC) coupled to mass spectrometry (MS) analyses affect the electrospray operation. To establish methodologies for judicious selection of the electrospray voltage, we monitored in real time the effect of the LC gradient on the spray current. The optimum range of the electrospray voltage decreased as the concentration of organic solvent in the eluent increased during reversed-phase LC analyses.

Analytical characterization of the electrospray ion source in the nanoflow regime.

A detailed characterization of a conventional low-flow electrospray ionization (ESI) source for mass spectrometry (MS) using solution compositions typical of reversed-phase liquid chromatography is reported. Contrary to conventional wisdom, the pulsating regime consistently provided better ESI-MS performance than the cone-jet regime for the interface and experimental conditions studied. This observation is supported by additional measurements showing that a conventional heated capillary interface affords more efficient sampling and transmission for the charged aerosol generated by a pulsating electrospray.

Fully automated four-column capillary LC-MS system for maximizing throughput in proteomic analyses.

We describe a four-column, high-pressure capillary liquid chromatography (LC) system for robust, high-throughput liquid chromatography-mass spectrometry (LC-MS(/MS)) analyses. This system performs multiple LC separations in parallel, but staggers each of them such that the data-rich region of each separation is sampled sequentially. By allowing nearly continuous data acquisition, this design maximizes the use of the mass spectrometer.

High speed method for in situ multispectral image registration.

High speed data registration is required for the study of fluorescence resonance energy transfer in real time as well as fast dynamic intra- and inter-cellular signaling events. Multispectral confocal spinning disk microscopy provides a high resolution method for performing such real time live cell imaging. However, optical distortions and the physical misalignments introduced by the use of multiple acquisition cameras can obscure spatial information contained in the captured images.