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Automated assignment of ionization states in broad-mass matrix-assisted laser desorption/ionization spectra of protein mixtures.

ABSTRACT: A computational technique is presented for the automated assignment of the multiple charge and multimer states (ionization states) in the time-of-flight (TOF) domain for matrix-assisted laser desorption/ionization (MALDI) spectra. Examples of the application of this technique include an improved, automatic calibration over the 2 to 70 kDa mass range and a reduced data redundancy after reconstruction of the molecular spectrum of only singly charged monomers. This method builds on our previously reported enhancement of broad-mass signal detection, and includes two steps: (1) an automated correction of the instrumental acquisition initial time delay, and (2) a recursive TOF detection of multiple charge states and singly charged multimers of molecular [MH](+) ions over the entire record range, based on MALDI methods. The technique is tested using calibration mixtures and pooled serum quality control samples acquired along with clinical study data. The described automated procedure improves the analysis and dimension reduction of MS data for comparative proteomics applications.

SUBMITTER: Malyarenko DI

PROVIDER: S-EPMC4508872 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature

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Automated assignment of ionization states in broad-mass matrix-assisted laser desorption/ionization spectra of protein mixtures.

Malyarenko Dariya I DI Cooke William E WE Bunai Christine L CL Manos Dennis M DM

Rapid communications in mass spectrometry : RCM 20100101 1

A computational technique is presented for the automated assignment of the multiple charge and multimer states (ionization states) in the time-of-flight (TOF) domain for matrix-assisted laser desorption/ionization (MALDI) spectra. Examples of the application of this technique include an improved, automatic calibration over the 2 to 70 kDa mass range and a reduced data redundancy after reconstruction of the molecular spectrum of only singly charged monomers. This method builds on our previously r ...[more]

PMID: 19960505

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Project description:RationaleUnderstanding the mechanisms of matrix-assisted laser desorption/ionization (MALDI) promises improvements in the sensitivity and specificity of many established applications in the field of mass spectrometry. This paper reports a serendipitous observation of a significant ion yield in a post-ionization experiment conducted after the sample had been removed from a standard atmospheric pressure (AP)-MALDI source. This post-ionization is interpreted in terms of collisions of microparticles moving with a hypersonic velocity into a solid surface. Calculations show that the thermal energy released during such collisions is close to that absorbed by the top matrix layer in traditional MALDI. The microparticles, containing both the matrix and analytes, could be detached from a film produced inside the inlet capillary during the sample ablation and accelerated by the flow rushing through the capillary. These observations contribute some new perspective to ion formation in both laser and laser-less matrix-assisted ionization.MethodsAn AP-MALDI ion source hyphenated with a three-stage high-pressure ion funnel system was utilized for peptide mass analysis. After the laser had been turned off and the MALDI sample removed, ions were detected during a gradual reduction of the background pressure in the first funnel. The constant-rate pressure reduction led to the reproducible appearance of different singly and doubly charged peptide peaks in mass spectra taken a few seconds after the end of the MALDI analysis of a dried-droplet spot.ResultsThe ion yield as well as the mass range of ions observed with a significant delay after a completion of the primary MALDI analysis depended primarily on the background pressure inside the first funnel. The production of ions in this post-ionization step was exclusively observed during the pressure drop. A lower matrix background and significant increase in relative yield of double-protonated ions are reported.ConclusionsThe observations were partially consistent with a model of the supersonic jet from the inlet capillary accelerating detached particles to kinetic energies suitable for matrix-assisted hypersonic-velocity impact ionization.

Dataset Information

Automated assignment of ionization states in broad-mass matrix-assisted laser desorption/ionization spectra of protein mixtures.

Publications

Automated assignment of ionization states in broad-mass matrix-assisted laser desorption/ionization spectra of protein mixtures.

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