Biomedical subjects

Navdeep Jaitly

Publications and source records attributed to Navdeep Jaitly.

5 recordsLinked to original sources

PubMed2006

Mass measurement accuracy in analyses of highly complex mixtures based upon multidimensional recalibration.

Mass spectrometry combined with a range of on-line separation techniques has become a powerful tool for characterization of complex mixtures, including protein digests in proteomics studies. Accurate mass measurements can be compromised due to variations that occur in the course of an on-line separation, e.g., due to excessive space charge in an ion trap, temperature changes, or other sources of instrument "drift". We have developed a multidimensional recalibration approach that utilizes existing information on the likely mixture composition, taking into account variable conditions of mass measurements, and that corrects the mass calibration for sets of individual peaks binned by, for example, the total ion count for the mass spectrum, the individual peak abundance, m/z value, and liquid chromatography separation time. The multidimensional recalibration approach uses a statistical matching of measured masses in such measurements, often exceeding 105, to a significant number of putative known species likely to be present in the mixture (i.e., having known accurate masses), to identify a subset of the detected species that serve as effective calibrants. The recalibration procedure involves optimization of the mass accuracy distribution (histogram), to provide a more confident distinction between true and false identifications. We report the mass accuracy improvement obtained for data acquired using a TOF and several FTICR mass spectrometers. We show that the multidimensional recalibration better compensates for systematic mass measurement errors and also significantly reduces the mass error spread: i.e., both the accuracy and precision of mass measurements are improved. The mass measurement improvement is found to be virtually independent of the initial instrument calibration, allowing, for example, less frequent calibration. We show that this recalibration can provide sub-ppm mass measurement accuracy for measurements of a complex fungal proteome tryptic digest and provide improved confidence or numbers of peptide identifications.

Calibration↗

PubMed2006

Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline.

Liquid chromatography coupled to mass spectrometry (LC-MS) and tandem mass spectrometry (LC-MS/MS) has become a standard technique for analyzing complex peptide mixtures to determine composition and relative abundance. Several high-throughput proteomics techniques attempt to combine complementary results from multiple LC-MS and LC-MS/MS analyses to provide more comprehensive and accurate results. To effectively collate and use results from these techniques, variations in mass and elution time measurements between related analyses need to be corrected using algorithms designed to align the various types of data: LC-MS/MS versus LC-MS/MS, LC-MS versus LC-MS/MS, and LC-MS versus LC-MS. Described herein are new algorithms referred to collectively as liquid chromatography-based mass spectrometric warping and alignment of retention times of peptides (LCMSWARP), which use a dynamic elution time warping approach similar to traditional algorithms that correct for variations in LC elution times using piecewise linear functions. LCMSWARP is compared to the equivalent approach based upon linear transformation of elution times. LCMSWARP additionally corrects for temporal drift in mass measurement accuracies. We also describe the alignment of LC-MS results and demonstrate their application to the alignment of analyses from different chromatographic systems, showing the suitability of the present approach for more complex transformations.

Algorithms↗

PubMed2006

Proteomic approaches to bacterial differentiation.

Mass spectrometry-based proteomics has been used extensively to explore the proteomes of various organisms, and this technology is now being applied to the characterization of bacterial species. Predominantly, two methods emerge as leaders in this application. Intact protein profiling creates fingerprints of bacterial species which can be used for differentiation and tracking over time. Peptide-centric approaches, analyzed after enzymatic digestion, enable high-throughput proteome characterization in addition to species determination from the identification of peptides distinctive to a species. Highlighted herein is an application of a peptide-centric approach to the identification and quantitation of species-specific peptide identifiers using an in silico exploration and an experimental mass spectrometry-based method. The application to microbial communities is addressed with an in silico analysis of an artificial complex community of 25 microorganisms.

Bacteria↗

PubMed2006

PRISM: a data management system for high-throughput proteomics.

Advanced proteomic research efforts involving areas such as systems biology or biomarker discovery are enabled by the use of high level informatics tools that allow the effective analysis of large quantities of differing types of data originating from various studies. Performing such analyses on a large scale is not feasible without a computational platform that performs data processing and management tasks. Such a platform must be able to provide high-throughput operation while having sufficient flexibility to accommodate evolving data analysis tools and methodologies. The Proteomics Research Information Storage and Management system (PRISM) provides a platform that serves the needs of the accurate mass and time tag approach developed at Pacific Northwest National Laboratory. PRISM incorporates a diverse set of analysis tools and allows a wide range of operations to be incorporated by using a state machine that is accessible to independent, distributed computational nodes. The system has scaled well as data volume has increased over several years, while allowing adaptability for incorporating new and improved data analysis tools for more effective proteomics research.

Chromatography, Liquid↗

PubMed2005

Unusual aggregates from the oxidation of alkene self-assembled monolayers: a previously unrecognized mechanism for SAM ozonolysis?

Self-assembled monolayers (SAMs) of vinyl-terminated 3- and 8-carbon compounds were generated on Si substrates and reacted at room temperature with approximately 1 ppm gaseous O(3). A combination of atomic force microscopy (AFM), scanning electron microscopy (SEM), Auger electron spectroscopy (AES) and time-of-flight secondary ion mass spectrometry (TOF-SIMS) was used to study the surface composition and morphology after oxidation. A distribution of large ( approximately 0.1-10 microm) organic aggregates was formed, while the surrounding substrate became depleted of carbon compared to the unreacted SAM. This highly unusual result establishes that the mechanism of ozonolysis of alkene SAMs must have a channel that is unique compared to that in the gas phase or in solution, and may involve polymerization induced by the Criegee intermediate (CI). Oxidation at 60% RH led to the formation of a number of smaller aggregates, suggesting water intercepted the CI in competition with aggregate formation. The uptake of water, measured using transmission FTIR, was not increased upon oxidation of these films. In conjunction with literature reports of polymer formation from VOC-NO(x) photooxidations, these results suggest that formation of aggregates and polymers in the atmosphere is much more widespread than previously thought. The implications for the ozonolysis of alkenes on surfaces, for the transformation of organics in the atmosphere, and for the reactions and stability of unsaturated SAMs, are discussed.

Alkenes↗