Direct Protein Identification from Nonspecific Peptide Pools by High-Accuracy MS Data Filtering

Intramolecular benzyl cation transfer in the gas-phase fragmentation of protonated benzyl phenyl sulfones

In this study, the gas-phase fragmentations of protonated benzyl phenyl sulfones were investigated by electrospray ionization tandem mass spectrometry (ESI-MSⁿ ). Upon collisional activation, several characteristic fragment ions were observed, and the similar results occurred with different substituted benzyl phenyl sulfones. A mechanism involving an intramolecular benzyl cation transfer and the formation of intermediate ion was proposed and further identified by density functional theory (DFT) calculations. In addition, a reference compound, benzenesulfinic acid benzyl ester, has been synthesized, and its protonated ion has the same gas-phase behavior as compared to the protonated benzyl phenyl sulfone. This work provides access to some insight into the intramolecular benzyl-transfer reactions of benzyl phenyl sulfones in the gas phase and orients the characteristic peaks in collision-induced dissociation spectrometry (CID-MS).

Characterization and diagnostic value of amino acid side chain neutral losses following electron-transfer dissociation

Using a large set of high mass accuracy and resolution ETD tandem mass spectra, we characterized ETD-induced neutral losses. From these data we deduced the chemical formula for 20 of these losses. Many of them have been previously observed in electron-capture dissociation (ECD) spectra, such as losses of the side chains of arginine, aspartic acid, glutamic acid, glutamine, asparagine, leucine, histidine, and carbamidomethylated cysteine residues. With this information, we examined the diagnostic value of these amino acid-specific losses. Among 1285 peptide-spectrum matches, 92.5% have agreement between neutral loss-derived peptide amino acid composition and the peptide sequences. Moreover, we show that peptides can be uniquely identified by using only the accurate precursor mass and amino acid composition based on neutral losses; the median number of sequence candidates from an accurate mass query is reduced from 21 to 8 by adding side chain loss information. Besides increasing confidence in peptide identification, our findings suggest the potential use of these diagnostic losses in ETD spectra to improve false discovery rate estimation and to enhance the performance of scoring functions in database search algorithms.

Characterization of a peptide family from the skin secretion of the Middle East tree frog Hyla savignyi by composition-based de novo sequencing

A new tryptophyllin-like peptide family was found in the skin secretion of the tree frog Hyla savignyi. Peptides were characterized by database-independent sequencing strategies and specific ion fragmentation features were investigated. Skin secretions from specimens of Hyla savignyi were collected by mild electrical stimulation. Peptides were separated by reversed-phase nano-high-performance liquid chromatography (nanoHPLC) and mass spectra were acquired online by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). Peptides were characterized by manual de novo sequencing and by composition-based sequencing (CBS), appearing mostly as C-terminal free acids and as their acid amide analogs. Amide peptides yielded lower intensities of y-type ions after collision-induced dissociation (CID) than their acid analogs. A mechanism of internal b-ion formation (positive ion mode) and of CO(2) elimination (negative ion mode) is proposed. We also exemplified phenomena such as the proline effect and formation of non-direct sequence ions after sequence rearrangements. The occurrence of rearrangement products, of internal ions and of the proline effect made the CID spectra highly complex. CBS analysis nevertheless resulted in successful and highly reliable sequence analysis.

Isolation and sequence analysis of peptides from the skin secretion of the Middle East tree frog Hyla savignyi

Novel peptides were identified in the skin secretion of the tree frog Hyla savignyi. Skin secretions were collected by mild electrical stimulation. Peptides were separated by reversed-phase high-performance liquid chromatography. Mass spectra were acquired by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), and fragment ion spectra were obtained after collision-induced dissociation and electron capture dissociation. Peptides were analyzed by manual de novo sequencing and composition-based sequencing (CBS). Sequence analyses of three so far undescribed, structurally unrelated peptides are presented in this paper, having the sequences DDSEEEEVE-OH, P*EEVEEERJK-OH, and GJJDPJTGJVGGJJ-NH(2). The glutamate-rich sequences are assumed to be acidic spacer peptides of the prepropeptide. One of these peptides contains the modified amino acid hydroxyproline, as identified and localized by high-accuracy FTICR-MS. Combination of CBS and of experience-based manual sequence analysis as complementary and database-independent sequencing strategies resulted in peptide identification with high reliability.

Identification of collagen IV derived danger/alarm signals in insect immunity by nanoLC-FTICR MS

The immune system can be stimulated by microbial molecules as well as by endogenously derived danger/alarm signals of host origin. Using the lepidopteran model insectGalleria mellonella, we recently discovered that fragments of collagen IV, resulting from hydrolysis by microbial metalloproteinases, represent danger/alarm signals in insects. Here, we characterized immune-stimulatory peptides generated by thermolysin-mediated degradation of collagen IV using nanospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) after separation by nanoscale liquid chromatography (nanoLC). The combination of FTICR MS analysis andde novopeptide sequencing resulted in the identification of 38 specific collagen IV fragments of which several peptides included the integrin-binding motif RGD/E known from numerous mammalian immune-related proteins. Custom-synthesized peptides corresponding either to the presently identified collagen peptide GIRGEHyp or to a well-known integrin-binding RGD peptide (GRGDS) were injected intoG. mellonellato determine their immune-stimulatory activitiesin vivo. Both peptides stimulated immune cells and systemically the expression of lysozyme and a specific inhibitor of microbial metalloproteinases. Further examination using specific MAP kinase inhibitors indicated that MEK/ERK and p38 are involved in RGD/E-mediated immune-signaling pathways, whereas JNK seems to play only a minor role.

Simplified validation of borderline hits of database searches

Along with unequivocal hits produced by matching multiple MS/MS spectra to database sequences, LC-MS/MS analysis often yields a large number of hits of borderline statistical confidence. To simplify their validation, we propose to use rapid de novo interpretation of all acquired MS/MS spectra and, with the help of a simple software tool, display the candidate sequences together with each database search hit. We demonstrate that comparing hit database sequences and independent de novo interpretations of the same MS/MS spectra assists in rapid examination of ambiguous matches.

Mass-based classification (MBC) of peptides: highly accurate precursor ion mass values can be used to directly recognize peptide phosphorylation

Accurate mass values as obtainable by Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) were employed in a theoretical study to differentiate between nonmodified and phosphorylated peptides. It was found that for peptide masses up to 1,000 u more than 98% of all theoretical monophosphorylated peptides (all possible combinations of proteinogenic amino acids having one phosphorylation on S, T, or Y) can be distinguished from nonphosphorylated peptides directly by their mass, if mass values are determined with an accuracy of better than +/-0.1 ppm. At a peptide mass of 1,500 u still 70% of all possible monophosphorylated peptides are distinguishable from nonmodified peptides by their accurate mass alone. In contrast to established techniques of data-dependent multidimensional mass spectrometry, only the mass of the precursor ion is necessary to decide upon subsequent fragment ion analysis of a peptide for sequence analysis in an LC-MS/MS investigation of a complex sample, when using a precalculated mass distribution table of theoretical peptides. A mass distribution table of nonphosphorylated and monophosphorylated peptides with a bin width of 0.1 mu was made available via the open web site www.peptidecomposer.com.

A high-resolution scanning microprobe matrix-assisted laser desorption/ionization ion source for imaging analysis on an ion trap/Fourier transform ion cyclotron resonance mass spectrometer

A new scanning microprobe matrix-assisted laser desorption/ionization (SMALDI) ion source for high spatial resolution has been developed for linear ion trap and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). The source is fully compatible with commercial ion trap flanges (such as the LTQ series, Thermo Fisher Scientific). The source is designed for atmospheric pressure (AP) operation but is also suitable for mid-pressure operation. The AP mode is especially useful for investigating volatile compounds. The source can be interchanged with other ion sources within a minute when operated in the AP mode. Combining high-lateral resolution MALDI imaging with high mass resolution and high mass accuracy mass spectrometry, available in the FT-ICR mode, provides a new quality of analytical information, e.g. from biological samples. First results obtained with the new ion source demonstrate a maximum lateral resolution of 0.6 by 0.5 microm. Depending on the limit of detection of the chosen mass analyzer, however, the size of the focus had to be enlarged to a diameter of up to 8 microm in the FT-ICR mode, in order to create enough ions for detection. Mass spectra acquired for analytical imaging were obtained from single laser pulses per pixel in all the experiments. This mode allows us to investigate biological thin sections with desorption focus diameters in the micrometer range, known to cause complete evaporation of material under the laser focus with a very limited number of laser pulses. As a first example, peptide samples deposited in microstructures were investigated with the new setup. A high quality and validity of the acquired images were obtained in the ion trap mode due to the low limit of detection. High mass resolution and accuracy but poorer image quality were obtained in the ICR mode due to the lower detection sensitivity of the ICR detector.

Accurate mass as a bioinformatic parameter in data-to-knowledge conversion: Fourier transform ion cyclotron resonance mass spectrometry for peptide de novo sequencing

With the availability of ultra-precise mass spectrometric biomolecular data, the accurate mass is becoming a physical quantity of high interest for bioinformatics tools and strategies. Fourier transform ion cyclotron resonance mass spectrometry with electrospray ionization or matrix-assisted laser desorption/ionization sources now allows the easy determination of amino acid composition of medium size, unknown peptides when employing combinatorial calculation of hypothetical parent and fragment ion masses. This new method, which in a second step, allows the reliable de-novo sequencing of completely unknown peptides ["composition-based sequencing (CBS)"(1)] appears to open a wide new field of bioanalytical investigation. It has been shown that even unspecifically cleaved proteins can be identified easily and reliably when accurate mass evaluation is combined with protein database search tools.(2) It is quite clear that, while the nominal mass of a peptide has obviously no useful correlation to biomolecular structure, the accurate mass, instead, has a strong and direct correlation to structure that so far has not been exploited considerably by bioinformatic tools. It has already become obvious that accurate mass evaluation is going to become a central goal for bioinformatics strategies in the near future.(3-11) Strategies for extracting structural, and even functional, information out of accurate mass values of biomolecules still have to be developed. Examples and prospects of accurate mass evaluation in bioinformatics for the field of proteomics are outlined in the following.

Rapid Validation of Protein Identifications with the Borderline Statistical Confidence via De Novo Sequencing and MS BLAST Searches

Protein identifications with the borderline statistical confidence are typically produced by matching a few marginal quality MS/MS spectra to database peptide sequences and represent a significant bottleneck in the reliable and reproducible characterization of proteomes. Here, we present a method for rapid validation of borderline hits that circumvents the need in, often biased, manual inspection of raw MS/MS spectra. The approach takes advantage of the independent interpretation of corresponding MS/MS spectra by PepNovo de novo sequencing software followed by mass spectrometry-driven BLAST (MS BLAST) sequence-similarity database searches that utilize all partially inaccurate, degenerate and redundant candidate peptide sequences. In a case study involving the identification of more than 180 Caenorhabditis elegans proteins by nanoLC-MS/MS analysis on a linear ion trap LTQ mass spectrometer, the approach enabled rapid assignment (confirmation or rejection) of more than 70% of Mascot hits of borderline statistical confidence.