Direct analysis of lipids on thin layer plates by matrix-assisted secondary ion mass spectrometry

A simple and rapid method for the analysis of lipids on a thin layer chromatography (TLC) plate by matrix-assisted secondary ion mass spectrometry (SI-MS) is reported. Analysis was performed without elution of the sample from the TLC plate. Mass spectra obtained by this method are free from interference due to the TLC plate absorbent and reagents used for the detection of the spots. About 1 micrograms of lipids applied on a TLC plate can be analyzed by this method. On scanning the plate, mass chromatograms of each lipid were obtained based on its migration distance along the plate.     

Data mining in proteomic mass spectrometry

Data mining application to proteomic data from mass spectrometry has gained much interest in recent years. Advances made in proteomics and mass spectrometry have resulted in considerable amount of data that cannot be easily visualized or interpreted. Mass spectral proteomic datasets are typically high dimensional but with small sample size. Consequently, advanced artificial intelligence and machine learning algorithms are increasingly being used for knowledge discovery from such datasets. Their overall goal is to extract useful information that leads to the identification of protein biomarker candidates. Such biomarkers could potentially have diagnostic value as tools for early detection, diagnosis, and prognosis of many diseases. The purpose of this review is to focus on the current trends in mining mass spectral proteomic data. Special emphasis is placed on the critical steps involved in the analysis of surface-enhanced laser desorption/ionization mass spectrometry proteomic data. Examples are drawn from previously published studies and relevant data mining terminology and techniques are exlained.     

Sample classification from protein mass spectrometry, by 'peak probability contrasts'

MOTIVATION: Early cancer detection has always been a major research focus in solid tumor oncology. Early tumor detection can theoretically result in lower stage tumors, more treatable diseases and ultimately higher cure rates with less treatment-related morbidities. Protein mass spectrometry is a potentially powerful tool for early cancer detection. We propose a novel method for sample classification from protein mass spectrometry data. When applied to spectra from both diseased and healthy patients, the 'peak probability contrast' technique provides a list of all common peaks among the spectra, their statistical significance and their relative importance in discriminating between the two groups. We illustrate the method on matrix-assisted laser desorption and ionization mass spectrometry data from a study of ovarian cancers. RESULTS: Compared to other statistical approaches for class prediction, the peak probability contrast method performs as well or better than several methods that require the full spectra, rather than just labelled peaks. It is also much more interpretable biologically. The peak probability contrast method is a potentially useful tool for sample classification from protein mass spectrometry data.     

Characterisation of sphingolipids in the human lens by thin layer chromatography–desorption electrospray ionisation mass spectrometry

The lipidome of the human lens is unique in that cholesterol and dihydrosphingomyelin are the dominant classes. Moreover, the lens lipidome is not static with dramatic changes in several sphingolipid classes associated with both aging and cataract. Accordingly, there is a clear need to expand knowledge of the molecular species that constitute the human lens sphingolipidome. In this study, human lens lipids have been extracted and separated by thin-layer chromatography (TLC). Direct analysis of the TLC plates by desorption electrospray ionisation–mass spectrometry (DESI–MS) allowed the detection over 30 species from 11 classes of sphingolipids. Significantly, novel classes of lens lipids including sulfatides, dihydrosulfatides, lactosylceramide sulfates and dihydrolactosylceramide sulfates were identified.     

Sub-femtomole peptide detection in ion mobility-time-of-flight mass spectrometry measurements

Sensitivity and detection limit enhancements are obtained for peptides by performing high repetition rate (150 Hz) matrix-assisted laser desorption/ionization (MALDI) coupled with ion mobility-time-of-flight mass spectrometry. Absolute limits of detection (3sigma) for model peptides are on the order of 0.1 fmol of peptide deposited and represent a factor of 40-60 improvement over data obtained using typical low repetition (20 Hz) MALDI. This increase in sensitivity is demonstrated for two-dimensional MALDI-IM-TOFMS peptide mass mapping of bovine hemoglobin.     

Stationary phase thickness determines the quality of thin-layer chromatography/matrix-assisted laser desorption and ionization mass spectra of lipids

Normal phase thin-layer chromatography (NP TLC) is an established method of (phospho)lipid analysis. The determination of the fatty acyl composition is, however, a more challenging task by NP TLC. The direct coupling of TLC separation with mass spectrometric detection (e.g., matrix-assisted laser desorption/ionization mass spectrometry, MALDI MS), however, enables a detailed characterization of complex lipid mixtures. Here we show that the thickness of the silica gel layer has a considerable effect on the quality of the mass spectra recorded directly from the TLC plate. In particular, the intensity of the matrix background signals can be reduced if “thinner” TLC layers are used.     

Free-radical fragmentation of galactocerebrosides: a MALDI-TOF mass spectrometry study

Analysis of final products of radiation-induced transformations of galactocerebrosides (GalCer) in aqueous dispersions has been performed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and its combination of thin-layer chromatography (TLC). Ceramides were found to be the main products of GalCer gamma-radiolysis. From experimental results obtained in this study, as well as from the data available in the literature, an inference is made that the formation of ceramides occurs owing to fragmentation of radicals with an unpaired electron of the C2 atom of the carbohydrate moiety, formed from the starting compounds.     

Direct analysis of glycolipids on thin-layer plates by matrix-assisted secondary ion mass spectrometry: application for glycolipid storage disorders

The lipids accumulated in organs of patients with Gaucher's, Tay-Sachs, and Fabry's disease were identified by means of the combination of thin-layer chromatography and matrix-assisted secondary ion mass spectrometry. The total lipid extract of each lipidosis tissue was chromatographed on a TLC plate and then analyzed directly by mass spectrometry without elution of the sample from the TLC plate. The amount of material needed to obtain an adequate spectrum is in the order of a few micrograms of lipids per band for both positive and negative ion detection. By scanning the plates, mass spectral and chromatographic information can be obtained simultaneously, which was shown to be useful for the qualitative identification of the components on the plates.     

Molecular mass spectrometry imaging in biomedical and life science research

This review describes the current state of mass spectrometry imaging (MSI) in life sciences. A brief overview of mass spectrometry principles is presented followed by a thorough introduction to the MSI workflows, principles and areas of application. Three major desorption-ionization techniques used in MSI, namely, secondary ion mass spectrometry (SIMS), matrix-assisted laser desorption ionization (MALDI), and desorption electrospray ionization (DESI) are described, and biomedical and life science imaging applications of each ionization technique are reviewed. A separate section is devoted to data handling and current challenges and future perspectives are briefly discussed at the end.     

The use of mass spectrometry in genomics

Recent advances in the development of electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) now permit the near routine analysis of oligonucleotides and intact nucleic acids. These developments have led to the use of mass spectrometry (MS) as a detection platform for genomics studies. Among the various uses of mass spectrometry in genomics, applications focused on the characterization of single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) are particularly well-suited to MALDI or ESI-based analysis. It is predicted that continued developments in methodology and instrumentation will further improve the capabilities of mass spectrometry for nucleic acid analysis.     

Combined experimental and statistical strategy for mass spectrometry based serum protein profiling for diagnosis of breast cancer: a case-control study

Serum protein profiling by mass spectrometry is a promising method for early detection of cancer. We have implemented a combined strategy based on matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) and statistical data analysis for serum protein profiling and applied it in a well-described breast cancer case-control study. A rigorous sample collection protocol ensured high quality specimen and reduced bias from preanalytical factors. Preoperative serum samples obtained from 48 breast cancer patients and 28 controls were used to generate MALDI MS protein profiles. A total of nine mass spectrometric protein profiles were obtained for each serum sample. A total of 533 common peaks were defined and represented a 'reference protein profile'. Among these 533 common peaks, we identified 72 peaks exhibiting statistically significant intensity differences ( p < 0.01) between cases and controls. A diagnostic rule based on these 72 mass values was constructed and exhibited a cross-validated sensitivity and specificity of approximately 85% for the detection of breast cancer. With this method, it was possible to distinguish early stage cancers from controls without major loss of sensitivity and specificity. We conclude that optimized serum sample handling and mass spectrometry data acquisition strategies in combination with statistical analysis provide a viable platform for serum protein profiling in cancer diagnosis.     

Electrohydrodynamic ionization mass spectrometry of biochemical materials

Electrohydrodynamic ionization mass spectrometry has been applied to a range of biochemical materials dissolved in glycerol with NaI as electrolyte. Sugars (glucose, sucrose, raffinose), nucleosides (adenosine, thymidine, uridine), a tripeptide (glutathione) and an aminocyclitol antibiotic (neomycin) have been analyzed. Unambiguous analysis of a multicomponent solution has been demonstrated. All samples yielded several quasimolecular ions involving either proton or cation attachment to clusters of sample and/or solvent molecules. Unlike other techniques such as field desorption, electrohydrodynamic ionization is not observed to cause fragmentation of sample molecules. The mass spectrometer was operated so as to analyze only those ion clusters which had not undergone decomposition processes; under these conditions, most materials are ionized with similar efficiencies if the total abundance of all characteristic quasimolecular ions is considered. Information regarding the amino acid sequence of glutathione was obtained by thermal pretreatment of the glycerol solution before mass analysis. Positive and negative ion spectra give complementary information which can resolve potential ambiguities regarding the exact composition of quasimolecular ions. Electrohydrodynamic ionization mass spectrometry should be applicable to materials which cannot be ionized by other methods.     

生物质谱技术在糖蛋白结构分析中的应用

生物质谱包括基质辅助激光解吸附飞行时间质谱及电喷雾质谱被广泛应用于生物样品如多肽、蛋白质及核酸的分析,由于这种具有软电离方式的质谱具有极高的灵敏度及准确度,目前也被成功地用于糖蛋白的结构分析,与普通的化学方法相比,质谱法快速、简单,结合网上数据库检索、凝集素亲和提取、二维凝胶电泳以及靶上直接酶切等新方法,可以提供糖蛋白的一级结构乃至高级结构的信息。     

Negative mode nanostructure-initiator mass spectrometry for detection of phosphorylated metabolites

The chemical complexity of the metabolome requires the development of new detection methods to enlarge the range of compounds detectable in a biological sample. Recently, a novel matrix-free laser desorption/ionization method called nanostructure-initiator mass spectrometry (NIMS) [Northen et al., Nature 449(7165):1033–1036, 2007] was reported. Here we investigate NIMS in negative ion mode for the detection of endogenous metabolites, namely small phosphorylated molecules. 3-Aminopropyldimethylethoxysilane was found to be suitable as initiator for the analytes studied and a limit of detection in the tens of femtomoles was reached. The detection of different endogenous cell metabolites in a yeast cell extract is demonstrated.     

Detection of tetrodotoxin by thin-layer chromatography/fast atom bombardment mass spectrometry

A new method for detection of tetrodotoxin (TTX) by thin-layer chromatography/fast atom bombardment (FAB) mass spectrometry was developed. TTX and/or related substances were separated by TLC on LHP-K high-performance precoated plates, with a solvent system of pyridine:ethyl acetate:acetic acid:water (15:5:3:4). The plates were subjected to positive FAB mass spectrometry, under scanning within a mass range from m/z 100 to 500. TTX was identified by selected ion-monitored chromatograms at m/z 320 (M + H)+ and 302 (M + H - H2O)+, along with full scan positive ion FAB mass spectrometry. The limit of detection for TTX was about 0.1 micrograms. TTX was also detected by cellulose acetate membrane electrophoresis/FAB mass spectrometry.     

On-probe sample pretreatment for direct analysis of lipids in gram-positive bacterial cells by matrix-assisted laser desorption ionization mass spectrometry

On-probe sample pretreatment using trifluoroacetic acid as an additional reagent enabled the direct detection of phospholipids in whole bacteria by means of matrix-assisted laser desorption ionization mass spectrometry for not only gram-negative organisms but also gram-positive ones with a thicker peptidoglycan layer.     

Genotyping single-nucleotide polymorphisms by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry

In recent years matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI) has emerged as a very powerful method for genotyping single nucleotide polymorphisms. The accuracy, speed of data accumulation, and data structure are the major features of MALDI. Several SNP genotyping methods have been implemented with a high degree of automation and are being applied for large-scale association studies. Most methods for SNP genotyping using MALDI mass spectrometric detection and their potential application for high-throughput are reviewed here.     

Integration of surface plasmon resonance with mass spectrometry: automated ligand fishing and sample preparation for MALDI MS using a Biacore 3000 biosensor.

Integrating surface plasmon resonance analysis with mass spectrometry allows detection and characterization of molecular interactions to be complemented with identification of interaction partners. We have developed a procedure for Biacore 3000 that automatically performs all steps from ligand fishing and recovery to sample preparation for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry including on-target digestion. In the model system used in this study a signal transduction protein, calmodulin, was selectively captured from brain extract by one of its interaction partners immobilized on a sensor chip. The bound material was eluted, deposited directly onto a MALDI target, and analyzed by mass spectrometry both as an intact protein and after on-target tryptic digestion. The procedure with direct deposition of recovered material on the MALDI target reduces sample losses and, in combination with automatic sample processing, increases the throughput of surface plasmon resonance mass spectrometry analysis.     

Molecular imaging of thin mammalian tissue sections by mass spectrometry

Imaging of tissue sections by mass spectrometry provides a detailed molecular picture containing information on both the abundance and distribution of many constituent compounds. Mass spectra are acquired directly from fresh frozen tissue sections using matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS); sample preparation and data collection mode determine the spatial resolution or surface area of the section represented in each mass spectrum. Statistical analyses of the individual ion signatures yield biomarkers whose abundances correlate to cell development processes, tumorigenesis and/or drug treatment. In an alternate mode, the generation of intensity maps for individual ions provides a visual representation of the distribution of each species throughout the section at spatial resolutions as small as 50 microm. The availability of this molecular information is likely to be of great value to clinicians and should lead to improved therapeutic efficacy in the future.     

Imaging mass spectrometry for lipidomics

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a powerful tool that enables the simultaneous detection and identification of biomolecules in analytes. MALDI-imaging mass spectrometry (MALDI-IMS) is a two-dimensional MALDI-MS technique used to visualize the spatial distribution of biomolecules without extraction, purification, separation, or labeling of biological samples. This technique can reveal the distribution of hundreds of ion signals in a single measurement and also helps in understanding the cellular profile of the biological system. MALDI-IMS has already revealed the characteristic distribution of several kinds of lipids in various tissues. The versatility of MALDI-IMS has opened a new frontier in several fields, especially in lipidomics. In this review, we describe the methodology and applications of MALDI-IMS to biological samples.