Automation of data collection for matrix-assisted laser desorption/ionization mass spectrometry using a correlative analysis algorithm

Biomedical application of MALDI mass spectrometry for small-molecule analysis

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is an emerging analytical tool for the analysis of molecules with molar masses below 1,000 Da; that is, small molecules. This technique offers rapid analysis, high sensitivity, low sample consumption, a relative high tolerance towards salts and buffers, and the possibility to store sample on the target plate. The successful application of the technique is, however, hampered by low molecular weight (LMW) matrix-derived interference signals and by poor reproducibility of signal intensities during quantitative analyses. In this review, we focus on the biomedical application of MALDI-MS for the analysis of small molecules and discuss its favorable properties and its challenges as well as strategies to improve the performance of the technique. Furthermore, practical aspects and applications are presented.

Ionic (liquid) matrices for matrix-assisted laser desorption/ionization mass spectrometry-applications and perspectives

A large number of matrix substances have been used for various applications in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). The majority of matrices applied in ultraviolet-MALDI MS are crystalline, low molecular weight compounds. A problem encountered with many of these matrices is the formation of hot spots, which lead to inhomogeneous samples, thus leading to increased measurement times and hampering the application of MALDI MS for quantitative purposes. Recently, ionic (liquid) matrices (ILM or IM) have been introduced as a potential alternative to the classical crystalline matrices. ILM are equimolar mixtures of conventional MALDI matrix compounds such as 2,5-dihydroxybenzoic acid (DHB), alpha-cyano-4-hydroxycinnamic acid (CCA) or sinapinic acid (SA) together with organic bases [e.g., pyridine (Py), tributylamine (TBA) or N,N-dimethylethylenediamine (DMED)]. The present article presents a first overview of this new class of matrices. Characteristic properties of ILM, their influence on mass spectrometric parameters such as sensitivity, resolution and adduct formation and their application in the fields of proteome analysis, the measurement of low molecular weight compounds, the use of MALDI MS for quantitative purposes and in MALDI imaging will be presented. Scopes and limitations for the application of ILM are discussed.

Mathematical tools in analytical mass spectrometry

Over the last few decades, mass spectrometry has become a powerful tool for exploring various aspects of molecular processes occurring in biological systems. Such exploration is leading to a greater understanding of various complex life processes; unraveling these processes poses the greatest challenge to contemporary bioscience. With due respect to sample preparation, data analysis is rapidly becoming a major obstacle to the conversion of experimental knowledge into valid conclusions. It is interesting to note that many problems related to mass spectrometry can be solved using techniques from computer science, graph theory and discrete mathematics. The aim of this manuscript is to recollect several essays that demonstrate the power and the need to apply such skills to mass spectrometry data interpretation. Special attention is paid to situations where traditional chemical analysis reaches its limits but mathematical reasoning can still allow us to reach valid conclusions.

Quantification of Peptides for the Monitoring of Protease-Catalyzed Reactions by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Using Ionic Liquid Matrixes

Ionic liquid matrixes (ILM) have been shown to allow very homogeneous sample preparations, facilitating relative quantifications using internal standards in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). In the present work, the ability to perform quantifications of peptides without using internal standards in these matrixes was investigated. Linear correlations between peptide amount and signal intensities could be observed when increased molar matrix-to-analyte ratios were applied. The dynamic range of linearity was approximately 1 order of magnitude. The method was applied successfully to monitor the time-dependent evolution of substrates and products in trypsin-catalyzed digests of single peptides and peptide mixtures. Thus, ionic liquid matrixes allow quantitative MALDI-MS without the need for internal standards, making the method a suitable tool for the fast screening of new enzymes or the search for substrates or inhibitors.

Enhancement of sensitivity and resolution of surface-enhanced laser desorption/ionization time-of-flight mass spectrometric records for serum peptides using time-series analysis techniques

BACKGROUND

Measurement of peptide/protein concentrations in biological samples for biomarker discovery commonly uses high-sensitivity mass spectrometers with a surface-processing procedure to concentrate the important peptides. These time-of-flight (TOF) instruments typically have low mass resolution and considerable electronic noise associated with their detectors. The net result is unnecessary overlapping of peaks, apparent mass jitter, and difficulty in distinguishing mass peaks from background noise. Many of these effects can be reduced by processing the signal using standard time-series background subtraction, calibration, and filtering techniques.

METHODS

Surface-enhanced laser desorption/ionization (SELDI) spectra were acquired on a PBS II instrument from blank, hydrophobic, and IMAC-Cu ProteinChip arrays (Ciphergen Biosystems, Inc.) incubated with calibration peptide mixtures or pooled serum. TOF data were recorded after single and multiple laser shots at different positions. Correlative analysis was used for time-series calibration. Target filters were used to suppress noise and enhance resolution after baseline removal and noise rescaling.

RESULTS

The developed algorithms compensated for the electronic noise attributable to detector overload, removed the baseline caused by charge accumulation, detected and corrected mass peak jitter, enhanced signal amplitude at higher masses, and improved the resolution by using a deconvolution filter.

CONCLUSIONS

These time-series techniques, when applied to SELDI-TOF data before any peak identification procedure, can improve the data to make the peak identification process simpler and more robust. These improvements may be applicable to most TOF instrumentation that uses analog (rather than counting) detectors.

A sensitive method for detection of sulfamethazine and N4-acetylsulfamethazine residues in environmental samples using solid phase immunoextraction coupled with MALDI-TOF MS

Sulfamethazine (SMT) and its major metabolite, N(4)-acetylsulfamethazine (NA-SMT), were each recovered from spiked water (0.1 ppb) and 10% (w/v) aqueous suspensions of soil (1 ppb) or composted manure (1 ppb), by using a three-stage solid phase immunoextraction (SPIE) system, followed by detection with matrix-assisted laser/desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Sulfonamide recovery rates are reported for separate stages of the SPIE system and for trace-level sulfonamide SPIE extraction from the environmental samples. SPIE MALDI-TOF MS is a rapid and definitive technique with potentially better efficiency relative to other established trace-level sulfonamide analytical methods. SPIE MALDI-TOF MS required 1.5 h per batch (8-24 samples/batch) for sample enrichment, 5 min per batch for probe preparation, and 5 min per sample to acquire and process the spectrum. This is the first time MALDI-TOF MS has been reported as a potential means of detecting trace-level drug residues in complex environmental samples.

Covariance mapping in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

A novel method for acquisition and numerical analysis of matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectral data is described. The digitized ion current transient from each consecutive laser shot is first acquired and stored independently. Subsequently, statistical correlation parameters between all stored transients are computed. We illustrate the uses of this event-by-event analysis method for studies of sample surface heterogeneity as well as for elucidating the mechanisms of ion formation in MALDI. Other potential applications of the method are also outlined.