1and has been initially targeted for the analysis of peptides and proteins present on or near the surface of tissue sections 2 . Imaging MS brings a new tool to bear on the problem of unraveling and understanding the molecular complexities of cells. It joins techniques such as immunochemistry and fluorescence microscopy for the study of the spatial arrangement of molecules within biological tissues. Many previous experiments using MS to image samples have focused on the measurement of the distribution of elements and small molecules in biological specimens, including tissue slices and individual cells 3‐5 . An extensive review on imaging by MS can be found in the article by Pacholski and Winograd 6

Imaging mass spectrometry: a new technology for the analysis of protein expression in mammalian tissues.

A low-temperature plasma (LTP) probe has been developed for ambient desorption ionization. An ac electric field is used to induce a dielectric barrier discharge through use of a specially designed electrode configuration. The low-temperature plasma is extracted from the probe where it interacts directly with the sample being analyzed, desorbing and ionizing surface molecules in the ambient environment. This allows experiments to be performed without damage to the sample or underlying substrate and, in the case of biological analysis on skin surfaces, without electrical shock or perceptible heating. Positive or negative ions are produced from a wide range of chemical compounds in the pure state and as mixtures in the gaseous, solution, or condensed phases, using He, Ar, N2, or ambient air as the discharge gas. Limited fragmentation occurs, although it is greater in the cases of the molecular than the atomic discharge gases. The effectiveness of the LTP probe has been demonstrated by recording characteristi...

Low-temperature plasma probe for ambient desorption ionization.

Peptide sequencing via tandem mass spectrometry (MS/MS) is one of the most powerful tools in proteomics for identifying proteins. Because complete genome sequences are accumulating rapidly, the recent trend in interpretation of MS/MS spectra has been database search. However, de novo MS/MS spectral interpretation remains an open problem typically involving manual interpretation by expert mass spectrometrists. We have developed a new algorithm, SHERENGA, for de novo interpretation that automatically learns fragment ion types and intensity thresholds from a collection of test spectra generated from any type of mass spectrometer. The test data are used to construct optimal path scoring in the graph representations of MS/MS spectra. A ranked list of high scoring paths corresponds to potential peptide sequences. SHERENGA is most useful for interpreting sequences of peptides resulting from unknown proteins and for validating the results of database search algorithms in fully automated, high-throughput peptide s...

/pdf/de-novo-peptide-sequencing-via-tandem-mass-spectrometry-31ezuvwzul.pdf

De Novo Peptide Sequencing via Tandem Mass Spectrometry

A novel method for on-tissue identification of proteins in spatially discrete regions is described using tryptic digestion followed by matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) with MS/MS analysis. IMS is first used to reveal the protein and peptide spatial distribution in a tissue section and then a serial section is robotically spotted with small volumes of trypsin solution to carry out in situ protease digestion. After hydrolysis, 2,5-Dihydroxybenzoic acid (DHB) matrix solution is applied to the digested spots, with subsequent analysis by IMS to reveal the spatial distribution of the various tryptic fragments. Sequence determination of the tryptic fragments is performed using on-tissue MALDI MS/MS analysis directly from the individual digest spots. This protocol enables protein identification directly from tissue while preserving the spatial integrity of the tissue sample. The procedure is demonstrated with the identification of several proteins in the coronal sections of a rat brain.

Identification of proteins directly from tissue: in situ tryptic digestions coupled with imaging mass spectrometry.

http://www.proteomic-basics.eu/2004/spengler_2.pdf

Scanning microprobe matrix-assisted laser desorption ionization (SMALDI) mass spectrometry: Instrumentation for sub-micrometer resolved LDI and MALDI surface analysis

Mass spectrometry (MS) was employed to detect and structurally characterize peptides in two functionally related neurons, named VD1 and RPD2, which form a network involved in the modulation of heartbeat in Lymnaea. Matrix-assisted laser desorption/ionization MS, directly applied to single neurons VD1 and RPD2, showed overlapping yet distinct mass profiles, with a subset of putative peptides specifically present in neuron VD1. Direct tandem MS of a single VD1 neuron revealed the primary structures of the VD1-specific peptides, which were identified as members of the family of small cardioactive peptides. Based on the tandem MS data, a degenerate oligonucleotide was made for use in a polymerase chain reaction strategy to isolate the cDNA encoding the precursor to the small cardioactive peptides from a brain-specific cDNA library. The calculated masses of the mature, posttranslationally modified peptides, as predicted from the corresponding cDNA, agreed with the measured masses of the actual peptides, as det...

Direct mass spectrometric peptide profiling and sequencing of single neurons reveals differential peptide patterns in a small neuronal network

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Direct mass spectrometric peptide profiling and sequencing of single neurons reveals differential peptide patterns in a small neuronal network