Swapan K. Chowdhury

Bio: Swapan K. Chowdhury is an academic researcher from Rockefeller University. The author has contributed to research in topics: Mass spectrometry & Electrospray ionization. The author has an hindex of 24, co-authored 48 publications receiving 3030 citations. Previous affiliations of Swapan K. Chowdhury include University of Toronto & ExxonMobil.

Probing conformational changes in proteins by mass spectrometry

Abstract: Mass spectrometry has found wide application for the elucidation of the primary structures of proteins. However, with the exception of topographical studies of membrane-bound proteins, mass spectrometry has not previously been utilized to obtain information concerning in three-dimensional conformation of proteins. In the present communication, the authors describe the first use of mass spectrometry for probing conformational changes in proteins in a manner analogous to that employed in techniques like optical rotary dispersion, circular dichroism, and spectrophotometry.

Electrospray ionization mass spectrometer with new features

Abstract: An electrospray ion source is designed for ready and simple plugging into commercial mass analyzers for mass spectrometric analysis of organic molecules. The electrospray is carried out is the ambient air and the ions and other charged species enter the mass analyuzer through a long metal capillary tube and three stages of differential pumping. The use of the long tube allows (a) convenient injection of the ions into the mass analyzer (b) optimization of the spray by direct visualization in the air (c) efficient and controlled heat transfer to the droplets and (d) efficient pumping of the region between the capillary exit and the skinner. Desolvation of the solvated ions is carried out using a combination of controlled heat transfer to the charged droplets during the transit through the tube and collisional activation in a region of reduced pressure. Desolvation with this system does not involve use of a strong countercurrent flow of heated gas. The system also may be used to obtain the collisional activated fragmentation spectra of molecule ions. The use of a metal capillary tube avoids complications from charging that arise from the use of dielectric capilliary tubes.

Electrospray ionization: a new tool for the analysis of ionic transition-metal complexes

Abstract: Ionic transition-metal complexes have been difficult to analyze by mass spectrometry because of their low volatility, high thermal lability, and their tendency to undergo reduction during the ionization process. The authors have succeeded in generating, by electrospray ionization, intense beams of intact gas-phase cations from ionic transition-metal complexes, such as (Ru{sup II}(bpy){sub 3})Cl{sub 2} (where bpy = 2,2{prime}-bipyridyl) (I) and (Ru{sup II}(phen){sub 3})Cl{sub 2} (where phen = 1,10-phenanthroline) (II). In contrast to infrared laser desorption multiphoton ionization, fast atom bombardment, and field desorption, the cations observed from these complexes with electrospray ionization do not undergo reduction by electron or hydrogen transfer.

Use of a single-quadrupole mass spectrometer for collision-induced dissociation studies of multiply charged peptide ions produced by electrospray ionization.

Abstract: The feasibility of obtaining the collision-induced dissociation (CID) spectra of multiply charged peptide ions produced by electrospray ionization in a simple and inexpensive single-quadrupole mass spectrometer is demonstrated. Collisional activation was carried out in the high-pressure region between the capillary exit and the skimmer entrance to the mass analyzer. The CID of multiply charged peptide ions is very efficient, and the observed fragment ion intensities are typically 1-5% of the parent ion intensity prior to CID. About 70 pmol of the peptide is consumed in obtaining each CID spectrum. Spectra obtained by CID of multiply charged ions from bradykinin, angiotensin II, two peptides with features similar to tryptic peptides, and a synthetic analogue of a component of TGF-alpha containing two disulfide bonds are shown. The influence of the primary structure of the peptide on the observed fragmentation pathways is discussed. Although the present single-quadrupole configuration is simple and effective, the inability to choose a particular parent ion for collisional activation makes it less powerful than the triple-quadrupole configuration for mixtures of peptides and peptide samples that yield more than one charge state in the normal mass spectrum. However, it has the potential for inexpensively obtaining sequence information of proteins at high sensitivity by analyzing the pure tryptic peptides obtained by on-line or off-line chromatographic separation of tryptic digests.

Ion Suppression in Mass Spectrometry

Abstract: Background: Mass spectrometry (MS) is being introduced into a large number of clinical laboratories. It provides specificity because of its ability to monitor selected mass ions, sensitivity because of the enhanced signal-to-noise ratio, and speed because it can help avoid the need for intensive sample cleanup and long analysis times. However, MS is not without problems related to interference, especially through ion suppression effects. Ion suppression results from the presence of less volatile compounds that can change the efficiency of droplet formation or droplet evaporation, which in turn affects the amount of charged ion in the gas phase that ultimately reaches the detector. Content: This review discusses materials shown to cause ion suppression, including salts, ion-pairing agents, endogenous compounds, drugs, metabolites, and proteins. Experimental protocols for examining ion suppression, which should include, at a minimum, signal recovery studies using specimen extracts with added analyte, are also discussed, and a more comprehensive approach is presented that uses postcolumn infusion of the analyte to evaluate protracted ionization effects. Finally, this review presents options for minimizing or correcting ion suppression, which include enhanced specimen cleanup, chromatographic changes, reagent modifications, and effective internal standardization. Summary: Whenever mass spectrometric assays are developed, ion suppression studies should be performed using expected physiologic concentrations of the analyte under investigation.

Mass Spectrometry in Proteomics

Abstract: 4. Automated Interpretation of CID Spectra 282 5. Accurate Mass Tags 282 C. Protein Identification in Complex Mixtures 282 D. Analysis of Protein Expression 284 III. Proteomes and Post-Translational Modifications 285 A. Proteomes 285 1. The Analytical Challenge 285 2. Analysis of Protein−Protein Complexes 286 B. Post-Translational Modifications 286 1. Background 286 2. Detection and Purification of Phosphoproteins 288

Aromatic rings in chemical and biological recognition: energetics and structures.

Abstract: This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.

Atomic and molecular electron affinities: photoelectron experiments and theoretical computations.

Abstract: I. Introduction and Scope 231A. Definitions of Atomic Electron Affinities 233B. Definitions of Molecular Electron Affinities 233II. Experimental Photoelectron Electron Affinities 235A. Historical Background 235B. The Photoeffect 236C. Experimental Methods 237D. Time-of-Flight Negative Ion PhotoelectronSpectroscopy239E. Some Thermochemical Uses of ElectronAffinities241F. Layout of Table 10: ExperimentalPhotoelectron Electron Affinities242III. Theoretical Determination of Electron Affinities 242A. Historical Background 2421. Theoretical Predictions of Atomic ElectronAffinities2422. Theoretical Predictions of MolecularElectron Affinities243B. Present Status of Theoretical Electron AffinityPredictions243C. Basis Sets and Theoretical Electron Affinities 244D. Density Functional Theory (DFT) andElectron Affinities245E. Layout of Tables 8 and 9: Theoretical DFTElectron Affinities247F. Details of Density Functional MethodsEmployed in Tables 8 and 9247IV. Discussion and Observations 248A. Statistical Analysis of DFT Results ThroughComparisons to Experiment and OtherTheoretical Methods248B. Theoretical EAs for Species with UnknownExperimental EAs251C. On the Applicability of DFT to Anions and theFuture of DFT EA Predictions251D. Specific Theoretical Successes 251E. Interesting Problems 2521. C