Andreas Römpp

mzML—a Community Standard for Mass Spectrometry Data

Mass spectrometry is a fundamental tool for discovery and analysis in the life sciences. With the rapid advances in mass spectrometry technology and methods, it has become imperative to provide a standard output format for mass spectrometry data that will facilitate data sharing and analysis. Initially, the efforts to develop a standard format for mass spectrometry data resulted in multiple formats, each designed with a different underlying philosophy. To resolve the issues associated with having multiple formats, vendors, researchers, and software developers convened under the banner of the HUPO PSI to develop a single standard. The new data format incorporated many of the desirable technical attributes from the previous data formats, while adding a number of improvements, including features such as a controlled vocabulary with validation tools to ensure consistent usage of the format, improved support for selected reaction monitoring data, and immediately available implementations to facilitate rapid adoption by the community. The resulting standard data format, mzML, is a well tested open-source format for mass spectrometer output files that can be readily utilized by the community and easily adapted for incremental advances in mass spectrometry technology.

Histology by mass spectrometry: label-free tissue characterization obtained from high-accuracy bioanalytical imaging.

Histological examination of biological and medical specimens has gained its universality and undisputed significance through distinct staining techniques and microscopical evaluation. Discrimination of tissue types after specific staining or labeling is an essential prerequisite for histopathological investigation, for example in accurate diagnosis of cancer. Histochemical staining techniques can only be used in a targeted manner for known compounds, and only a limited number of such targets can be visualized from a given sample at the same time. Another limitation of classical histology lies in the fact that a considerable amount of experience is required and that even well-trained pathologists often interpret histologically stained sections differently. Mass spectrometry (MS), on the other hand, offers complex but objective and reproducible information on biological material. Imaging of biological samples by MS gained interest after development of matrix-assisted laser desorption/ionization (MALDI) as a method to desorb and ionize biomolecules, such as peptides, proteins, glycans, or lipids, with a limit of detection in the attomole range. The first proof-of-principle of imaging by MALDI was presented in 1994, and was followed by numerous applications during the last decade. An extensive overview of instrumental developments and methodological approaches in MS imaging has been published recently. MS imaging allows the distribution of analytes to be investigated and displayed across a sample in a semi-quantitative manner and without the need to predefine or label selected substances prior to analysis. MALDI imaging is typically used with spatial resolutions of between 50 and 200 mm. Increasing the resolution into the lowmicrometer range has been demonstrated, but requires a very low limit of detection of the employed mass spectrometer, as the available amount of material per imaged spot is reduced quadratically with reduction of the spot diameter. Identification of molecules during MS imaging experiments is often limited if mass spectrometers with a rather low mass resolving power and accuracy are used. Additional offline bulk analyses of tissue material are typically used to back up imaging results. Imaging selectivity, that is, mass bin width for allocation to image signals, is typically set to onemass unit. Employing MS imaging for obtaining valid histological information requires a number of improvements: 1. The usable spatial resolution has to be high enough to resolve cellular features. 2. Analytical sensitivity has to be high enough to visualize the majority of interesting substances in high-lateralresolution experiments. 3. Mass resolving power and mass accuracy have to be as high as possible when complex biological samples are under investigation. To unequivocally assign a mass signal to an image and to identify substances by accurate mass, signals have to be stable and correct in detected mass values; that is, mass accuracy should be in the low-ppm range. 4. Image assignment to mass signals has to be both highly selective and flexible. To distinguish neighboring mass signals in biological tissue samples, the coding mass bin width must typically be smaller than 0.1 mass units. 5. To clearly identify imaged substances in complex samples, MS data from fragmentation of precursor ions has to be obtainable directly from individual imaged sample spots. 6. Ambient pressure conditions are often necessary, rather than high-vacuum conditions, for example when working under physiological conditions, imaging volatile substances such as drug metabolites, or using volatile matrices. 7. Sample handling and preparation have to be fast and robust. 8. Results have to be achievable in a reasonable timeframe.

Single Cell Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging

Application of mass spectrometry imaging (MS imaging) analysis to single cells was so far restricted either by spatial resolution in the case of matrix-assisted laser desorption/ionization (MALDI) or by mass resolution/mass range in the case of secondary ion mass spectrometry (SIMS). In this study we demonstrate for the first time the combination of high spatial resolution (7 μm pixel), high mass accuracy (<3 ppm rms), and high mass resolution (R = 100,000 at m/z = 200) in the same MS imaging measurement of single cells. HeLa cells were grown directly on indium tin oxide (ITO) coated glass slides. A dedicated sample preparation protocol was developed including fixation with glutaraldehyde and matrix coating with a pneumatic spraying device. Mass spectrometry imaging measurements with 7 μm pixel size were performed with a high resolution atmospheric-pressure matrix-assisted laser desorption/ionization (AP-MALDI) imaging source attached to an Exactive Orbitrap mass spectrometer. Selected ion images were generated with a bin width of Δm/z = ±0.005. Selected ion images and optical fluorescence images of HeLa cells showed excellent correlation. Examples demonstrate that a lower mass resolution and a lower spatial resolution would result in a significant loss of information. High mass accuracy measurements of better than 3 ppm (root-mean-square) under imaging conditions provide confident identification of imaged compounds. Numerous compounds including small metabolites such as adenine, guanine, and cholesterol as well as different lipid classes such as phosphatidylcholine, sphingomyelin, diglycerides, and triglycerides were detected and identified based on a mass spectrum acquired from an individual spot of 7 μm in diameter. These measurements provide molecularly specific images of larger metabolites (phospholipids) in native single cells. The developed method can be used for a wide range of detailed investigations of metabolic changes in single cells.

Controlling the enzymatic activity of a restriction enzyme by light

For many applications it would be desirable to be able to control the activity of proteins by using an external signal. In the present study, we have explored the possibility of modulating the activity of a restriction enzyme with light. By cross-linking two suitably located cysteine residues with a bifunctional azobenzene derivative, which can adopt a cis- or trans-configuration when illuminated by UV or blue light, respectively, enzymatic activity can be controlled in a reversible manner. To determine which residues when cross-linked show the largest “photoswitch effect,” i.e., difference in activity when illuminated with UV vs. blue light, > 30 variants of a single-chain version of the restriction endonuclease PvuII were produced, modified with azobenzene, and tested for DNA cleavage activity. In general, introducing single cross-links in the enzyme leads to only small effects, whereas with multiple cross-links and additional mutations larger effects are observed. Some of the modified variants, which carry the cross-links close to the catalytic center, can be modulated in their DNA cleavage activity by a factor of up to 16 by illumination with UV (azobenzene in cis) and blue light (azobenzene in trans), respectively. The change in activity is achieved in seconds, is fully reversible, and, in the case analyzed, is due to a change in Vmax rather than Km.

Protein identification by accurate mass matrix-assisted laser desorption/ionization imaging of tryptic peptides

The spatial distribution of proteins in tissue sections can be used to identify potential markers for pathological processes. Tissue sections are often subjected to enzymatic digestion before matrix-assisted laser desorption/ionization (MALDI) imaging. This study is targeted at improving the on-tissue identification of tryptic peptides by accurate mass measurements and complementary off-line liquid chromatography coupled to electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) analysis. Two adjacent mouse brain sections were analyzed in parallel. The first section was spotted with trypsin and analyzed by MALDI imaging. Direct on-tissue MS/MS experiments of this section resulted in the identification of 14 peptides (originating from 4 proteins). The second tissue section was homogenized, fractionated by ultracentrifugation and digested with trypsin prior to LC/ESI-MS/MS analysis. The number of identified peptides was increased to 153 (corresponding to 106 proteins) by matching imaged mass peaks to peptides which were identified in these LC/ESI-MS/MS experiments. All results (including MALDI imaging data) were based on accurate mass measurements (RMS <2 ppm) and allow a confident identification of tryptic peptides. Measurements based on lower accuracy would have led to ambiguous or misleading results. MS images of identified peptides were generated with a bin width (mass range used for image generation) of Δm/z = 0.01. The application of accurate mass measurements and additional LC/MS measurements increased both the quality and the number of peptide identifications. The advantages of this approach for the analysis of biological tissue sections are demonstrated and discussed in detail. Results indicate that accurate mass measurements are needed for confident identification and specific image generation of tryptic peptides in tissue sections.

High‐resolution matrix‐assisted laser desorption/ionization imaging of tryptic peptides from tissue

RATIONALE The analysis of proteins by mass spectrometry imaging is an important biomedical application as spatial distributions can be used to identify markers for pathological processes. The direct detection and identification of proteins on tissue can be hindered by a number of factors including limited mass range and fragmentation efficiency as well as incompatibility with formalin-fixed samples. METHODS To overcome some of these limitations, on-tissue digestion of proteins was followed by detection of the resulting peptides. Trypsin was applied by a spraying device. Matrix-assisted laser desorption/ionization (MALDI) imaging experiments were performed with a home-built atmospheric-pressure imaging source attached to a LTQ Orbitrap mass spectrometer. The mass accuracy under imaging conditions was better than 3 ppm RMS. This allowed for confident identification of tryptic peptides by comparison with liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) measurements of an adjacent mouse brain section. RESULTS A spatial resolution of 50 µm was obtained for tryptic peptides on tissue. Several tryptic peptides of myelin showed matching spatial distributions, and numerous tryptic peptides of other proteins were identified. MS images were generated with a bin size (mass range used for image generation) of Δm/z = 0.01 u. Examples demonstrate that MS images with lower selectivity can result in misleading information about the spatial distribution of tryptic peptides. CONCLUSIONS The presented method combines a significantly improved spatial resolution for tryptic peptides with low-ppm mass accuracy in a single experiment and thus provides highly reliable and specific information.

Proteomics study of silver nanoparticles toxicity on Oryza sativa L.

The increasing use of silver nanoparticles, (AgNPs), will inevitably result in their release into the environment and thereby cause the exposure to plants. It was claimed that using AgNPs is a safe and efficient method to preserve and treat agents of disease in agriculture. This study tries to understand the protein populations and sub-populations and follow up environmental AgNPs stresses. To accomplish these, the action of homemade spherical AgNPs colloidal suspension against Oryza sativa L. was investigated by a proteomic approach (2-DE and NanoLC/FT-ICR MS identification). Twenty-eight responsive (decrement/increment in abundance) proteins were identified. Proteomic results revealed that an exposure of O. sativa L., root with different concentrations of AgNPs resulted in an accumulation of protein precursors, indicative of the dissipation of a proton motive force. The identified proteins are involved in oxidative stress tolerance, Ca(2+) regulation and signaling, transcription and protein degradation, cell wall and DNA/RNA/protein direct damage, cell division and apoptosis. The expression pattern of these proteins and their possible involvement in the nontoxicity mechanisms were discussed.

Petroleum crude oil analysis using low‐temperature plasma mass spectrometry

RATIONALE The analysis of crude oil is a challenging task due to sample complexity. In mass spectrometry, several ionization techniques can be used to perform this task. Herein, we report the use of an atmospheric pressure low-temperature plasma (LTP) probe to desorb and ionize compounds of petroleum crude oil from different sources and residual fuel oil standard reference materials (SRMs). LTP is used to perform rapid screening of low molecular weight and relatively volatile components enabling characterization and differentiation of crude oil samples relying solely on mass spectrometric data. METHODS Crude oil samples were analyzed without sample preparation or dilution directly from sampling surfaces of different materials such as polytetrafluorethylene, glass and polyethylene. Analyses were performed using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) with high mass accuracy and high resolving power of 400,000 at m/z 400 to estimate the elemental composition of the ions produced by LTP. Principal components analysis (PCA) was performed on the LTP data for statistical analysis. RESULTS LTP was found to generate positive ions of lower mass compounds of low to moderate polarity. Three-dimensional PCA plots efficiently differentiated between SRMs and Azerbaijan crude oil samples. Standards of alkanes, nitrogen heterocycles, sulfur heterocycles, hydrocarbon polycyclic aromatics and saturated acids were investigated for their behavior in LTP ionization. Alkanes were found to form oxidized products to some extent. The LTP probe worked particularly well in the characterization of sulfur compounds. CONCLUSIONS LTP ionization of crude oils was found to advantageously complement analysis by electrospray ionization. The LTP probe in combination with miniaturized mass spectrometers has the potential to provide direct composition analysis and source identification of crude oil contaminations in the future.

Natural products in Glycyrrhiza glabra (licorice) rhizome imaged at the cellular level by atmospheric pressure matrix‐assisted laser desorption/ionization tandem mass spectrometry imaging

The rhizome of Glycyrrhiza glabra (licorice) was analyzed by high-resolution mass spectrometry imaging and tandem mass spectrometry imaging. An atmospheric pressure matrix-assisted laser desorption/ionization imaging ion source was combined with an orbital trapping mass spectrometer in order to obtain high-resolution imaging in mass and space. Sections of the rhizome were imaged with a spatial resolution of 10 μm in the positive ion mode, and a large number of secondary metabolites were localized and identified based on their accurate mass and MS/MS fragmentation patterns. Major tissue-specific metabolites, including free flavonoids, flavonoid glycosides and saponins, were successfully detected and visualized in images, showing their distributions at the cellular level. The analytical power of the technique was tested in the imaging of two isobaric licorice saponins with a mass difference of only 0.02 Da. With a mass resolving power of 140 000 and a bin width of 5 ppm in the image processing, the two compounds were well resolved in full-scan mode, and appeared with different distributions in the tissue sections. The identities of the compounds and their distributions were validated in a subsequent MS/MS imaging experiment, thereby confirming their identities and excluding possible analyte interference. The use of high spatial resolution, high mass resolution and tandem mass spectrometry in imaging experiments provides significant information about the biosynthetic pathway of flavonoids and saponins in legume species, combing the spatially resolved chemical information with morphological details at the microscopic level. Furthermore, the technique offers a scheme capable of high-throughput profiling of metabolites in plant tissues.

Examples of Fourier transform ion cyclotron resonance mass spectrometry developments: from ion physics to remote access biochemical mass spectrometry.

The application of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) for high-resolution biomolecular analysis has increased greatly after 30 years of innovation since its conception in 1974. FT-ICR-MS can now be used routinely for the analysis of complex organic mixtures such as biological or petrochemical samples. Many of these new possibilities have been the results of many different instrumental developments. This paper provides a mini review of selected instrumental developments that now allow these measurements. The development of soft ionization techniques such as electrospray ionization and matrix-assisted laser desorption and ionization was crucial for the analysis of biological macromolecules. Improved ion transport optics led to an increase in sensitivity. New ICR cell designs complement the capabilities of FT-ICR-MS by allowing a more thorough study of the mechanism and kinetics of ion reactions in the gas-phase. A selected example of electron capture dissociation (ECD) employs these developments to investigate the role of peptide conformation in ECD. Improved electronics and software allow faster and more flexible experiments. All these improvements led to an increase in speed and sensitivity that are necessary to couple FT-MS to fast separation techniques such as nano-high performance liquid chromatography. The modern FT-ICR-MS instruments can be incorporated in virtual organizations allowing remote access to unique infrastructure. This concept of remote experimentation opens new possibilities for scientific collaborations between expert scientists at different locations and allows the efficient use of this expensive instrumentation