Comparison of laser-induced dissociation and high-energy collision-induced dissociation using matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI-TOF/TOF) for peptide and protein identification

Algorithms for de-novo sequencing of peptides by tandem mass spectrometry: A review

Peptide sequencing is of great significance to fundamental and applied research in the fields such as chemical, biological, medicinal and pharmaceutical sciences. With the rapid development of mass spectrometry and sequencing algorithms, de-novo peptide sequencing using tandem mass spectrometry (MS/MS) has become the main method for determining amino acid sequences of novel and unknown peptides. Advanced algorithms allow the amino acid sequence information to be accurately obtained from MS/MS spectra in short time. In this review, algorithms from exhaustive search to the state-of-art machine learning and neural network for high-throughput and automated de-novo sequencing are introduced and compared. Impacts of datasets on algorithm performance are highlighted. The current limitations and promising direction of de-novo peptide sequencing are also discussed in this review.

Structural Characterization of Daunomycin-Peptide Conjugates by Various Tandem Mass Spectrometric Techniques

The use of peptide-drug conjugates has generated wide interest as targeted antitumor therapeutics. The anthracycline antibiotic, daunomycin, is a widely used anticancer agent and it is often conjugated to different tumor homing peptides. However, comprehensive analytical characterization of these conjugates via tandem mass spectrometry (MS/MS) is challenging due to the lability of the O-glycosidic bond and the appearance of MS/MS fragment ions with little structural information. Therefore, we aimed to investigate the optimal fragmentation conditions that suppress the prevalent dissociation of the anthracycline drug and provide good sequence coverage. In this study, we comprehensively compared the performance of common fragmentation techniques, such as higher energy collisional dissociation (HCD), electron transfer dissociation (ETD), electron-transfer higher energy collisional dissociation (EThcD) and matrix-assisted laser desorption/ionization–tandem time-of-flight (MALDI-TOF/TOF) activation methods for the structural identification of synthetic daunomycin-peptide conjugates by high-resolution tandem mass spectrometry. Our results showed that peptide backbone fragmentation was inhibited by applying electron-based dissociation methods to conjugates, most possibly due to the “electron predator” effect of the daunomycin. We found that efficient HCD fragmentation was largely influenced by several factors, such as amino acid sequences, charge states and HCD energy. High energy HCD and MALDI-TOF/TOF combined with collision induced dissociation (CID) mode are the methods of choice to unambiguously assign the sequence, localize different conjugation sites and differentiate conjugate isomers.

An antibody-free sample pretreatment method for osteopontin combined with MALDI-TOF MS/MS analysis

Osteopontin is an osteoblast-secreted protein with an aspartic acid-rich, highly phosphorylated, and glycosylated structure. Osteopontin can easily bind to integrins, tumor cells, extracellular matrix and calcium, and is related to bone diseases, various cancers, inflammation etc. Here, DEAE-Cibacron blue 3GA was used to extract recombinant osteopontin from human plasma, and to deplete abundant plasma proteins with an antibody-free method. Using selected buffer systems, osteopontin and human serum albumin could be bound to DEAE-Cibacron blue 3GA, while immunoglobulin G was excluded. The bound osteopontin could then be separated from albumin by using different sequential elution buffers. By this method, 1 μg/mL recombinant osteopontin could be separated from the major part of the most abundant proteins in human plasma. After trypsin digestion, the extracted osteopontin could be successfully detected and identified by MALDI-TOF MS/MS using the m/z 1854.898 peptide and its fragments.

Rapid, automated characterization of disulfide bond scrambling and IgG2 isoform determination

Human antibodies of the IgG2 subclass exhibit complex inter-chain disulfide bonding patterns that result in three structures, namely A, A/B, and B. In therapeutic applications, the distribution of disulfide isoforms is a critical product quality attribute because each configuration affects higher order structure, stability, isoelectric point, and antigen binding. The current standard for quantification of IgG2 disulfide isoform distribution is based on chromatographic or electrophoretic techniques that require additional characterization using mass spectrometry (MS)-based methods to confirm disulfide linkages. Detailed characterization of the IgG2 disulfide linkages often involve MS/MS approaches that include electrospray ionization or electron-transfer dissociation, and method optimization is often cumbersome due to the large size and heterogeneity of the disulfide-bonded peptides. As reported here, we developed a rapid LC-MALDI-TOF/TOF workflow that can both identify the IgG2 disulfide linkages and provide a semi-quantitative assessment of the distribution of the disulfide isoforms. We established signature disulfide-bonded IgG2 hinge peptides that correspond to the A, A/B, and B disulfide isoforms and can be applied to the fast classification of IgG2 isoforms in heterogeneous mixtures.

Structural Architectural Features of Cyclodextrin Oligoesters Revealed by Fragmentation Mass Spectrometry Analysis

Cyclodextrins (CDs) were used in the present study for the ring-opening oligomerization (ROO) of l-lactide (LA) in order to synthesize biodegradable products with possible applications in pharmaceutical and medical fields. The practical importance of ROO reactions may reside in the possibility of synthesizing novel CD derivatives with high purity due to the dual role played by CDs, the role of the initiator through the hydroxylic groups, and the role of the catalyst by monomer inclusion in the CD cavity. The analyzed compounds were CDs modified with oligolactides obtained through ROO reactions of l-lactide in dimethylformamide. The resulting CD isomeric mixtures were investigated using classical characterization techniques such as gel permeation chromatography and nuclear magnetic resonance. Moreover, advanced mass spectrometry (MS) techniques were employed for the determination of the average number of monomer units attached to the cyclodextrin and the architecture of the derivatives (if the monomer units were attached as a single chain or as multiple chains). Thus, fragmentation studies effectuated on two different instruments (ESI Q-TOF and MALDI TOF) allowed us to correlate the size of the oligolactide chains attached to the CD with the observed fragmentation patterns.

Full validation of therapeutic antibody sequences by middle-up mass measurements and middle-down protein sequencing

The regulatory bodies request full sequence data assessment both for innovator and biosimilar monoclonal antibodies (mAbs). Full sequence coverage is typically used to verify the integrity of the analytical data obtained following the combination of multiple LC-MS/MS datasets from orthogonal protease digests (so called “bottom-up” approaches). Top-down or middle-down mass spectrometric approaches have the potential to minimize artifacts, reduce overall analysis time and provide orthogonality to this traditional approach. In this work we report a new combined approach involving middle-up LC-QTOF and middle-down LC-MALDI in-source decay (ISD) mass spectrometry. This was applied to cetuximab, panitumumab and natalizumab, selected as representative US Food and Drug Administration- and European Medicines Agency-approved mAbs. The goal was to unambiguously confirm their reference sequences and examine the general applicability of this approach. Furthermore, a new measure for assessing the integrity and validity of results from middle-down approaches is introduced – the “Sequence Validation Percentage.” Full sequence data assessment of the 3 antibodies was achieved enabling all 3 sequences to be fully validated by a combination of middle-up molecular weight determination and middle-down protein sequencing. Three errors in the reference amino acid sequence of natalizumab, causing a cumulative mass shift of only −2 Da in the natalizumab Fd domain, were corrected as a result of this work.

Differentiation of isomeric amino acid residues in proteins and peptides using mass spectrometry

Characterization and differentiation of isomers in biological macromolecules using mass spectrometry is one of the most significant challenges facing scientists in the field. The capability of high-resolution MS instruments along with the development of new fragmentation methods now provides the ability to indirectly differentiate between some isomers. This ability has enabled mass spectrometry to evolve into a multidisciplinary technique incorporating areas such as pharmaceutical research, proteomics, polymer science, medicine, environmental chemistry, and recently archeology. This article aims to review recent developments in mass spectrometry methodologies in the identification of structural and spatial isomers in biological macromolecules, such as aspartic acid and isoaspartic acid (Asp/IsoAsp), leucine and isoleucine (Leu/Ile), glutamic acid and γ-glutamic acid, and D/L enantiomers.

Occurrence of C-terminal residue exclusion in peptide fragmentation by ESI and MALDI tandem mass spectrometry

By screening a data set of 392 synthetic peptides MS/MS spectra, we found that a known C-terminal rearrangement was unexpectedly frequently occurring from monoprotonated molecular ions in both ESI and MALDI tandem mass spectrometry upon low and high energy collision activated dissociations with QqTOF and TOF/TOF mass analyzer configuration, respectively. Any residue localized at the C-terminal carboxylic acid end, even a basic one, was lost, provided that a basic amino acid such arginine and to a lesser extent histidine and lysine was present in the sequence leading to a fragment ion, usually depicted as (b(n-1) + H(2)O) ion, corresponding to a shortened non-scrambled peptide chain. Far from being an epiphenomenon, such a residue exclusion from the peptide chain C-terminal extremity gave a fragment ion that was the base peak of the MS/MS spectrum in certain cases. Within the frame of the mobile proton model, the ionizing proton being sequestered onto the basic amino acid side chain, it is known that the charge directed fragmentation mechanism involved the C-terminal carboxylic acid function forming an anhydride intermediate structure. The same mechanism was also demonstrated from cationized peptides. To confirm such assessment, we have prepared some of the peptides that displayed such C-terminal residue exclusion as a C-terminal backbone amide. As expected in this peptide amide series, the production of truncated chains was completely suppressed. Besides, multiply charged molecular ions of all peptides recorded in ESI mass spectrometry did not undergo such fragmentation validating that any mobile ionizing proton will prevent such a competitive C-terminal backbone rearrangement. Among all well-known nondirect sequence fragment ions issued from non specific loss of neutral molecules (mainly H(2)O and NH(3)) and multiple backbone amide ruptures (b-type internal ions), the described C-terminal residue exclusion is highly identifiable giving raise to a single fragment ion in the high mass range of the MS/MS spectra. The mass difference between this signal and the protonated molecular ion corresponds to the mass of the C-terminal residue. It allowed a straightforward identification of the amino acid positioned at this extremity. It must be emphasized that a neutral residue loss can be misattributed to the formation of a y(m-1) ion, i.e., to the loss of the N-terminal residue following the a(1)-y(m-1) fragmentation channel. Extreme caution must be adopted when reading the direct sequence ion on the positive ion MS/MS spectra of singly charged peptides not to mix up the attribution of the N- and C-terminal amino acids. Although such peculiar fragmentation behavior is of obvious interest for de novo peptide sequencing, it can also be exploited in proteomics, especially for studies involving digestion protocols carried out with proteolytic enzymes other than trypsin (Lys-N, Glu-C, and Asp-N) that produce arginine-containing peptides.

On the high-resolution mass analysis of the product ions in tandem time-of-flight (TOF/TOF) mass spectrometers using a time-dependent re-acceleration technique

The time-dependent reacceleration of product ions produced as a result of dissociation of a single precursor ion in a tandem time-of-flight mass spectrometer is considered for the first time. Analytical expressions for the shapes of electric pulses bringing all the kinetic energies of the product ions to the same value are derived for two cases: forward acceleration mode and deceleration, followed by re-acceleration in the reversed direction (reversed mode). Secondary time-of-flight focusing resulting from the re-acceleration in the reversed mode is shown to be mass-dependent and, when averaged over a wide mass range, the focusing is tight enough to provide mass resolution exceeding 10,000. After time-dependent re-acceleration, additional compression of the ion packet width leading to better mass resolution can be obtained by decelerating the ions in a constant field.

Comparison of LID versus CID activation modes in tandem mass spectrometry of peptides

We report our contribution to the systematic investigation of peptide fragmentations performed on high-performance Tof equipment, operating in MS and MS/MS modes, such as ESI-QqTof and MALDI-Tof/Tof instruments that are commonly available today in proteomic laboratories. Whereas the former analyzer's configuration provides low-energy collision-induced dissociations (CID), the latter allows tunable activation methods of the selected parent ion to induce either metastable laser-induced dissociations (LID) or high-energy CID ('gas on spectra LID'). Fragmentation of the monoprotonated ion of 53 peptides (FW 807-2853 g/mol) was undertaken upon low-energy CID on an ESI-QTof mass spectrometer (Waters) as well as high-energy CID and LID conditions on a MALDI Ultraflex mass spectrometer (Bruker). Systematic comparison of MS/MS spectra provided useful information on the performance of each piece of equipment for efficient peptide sequencing and also insights into the observed fragmentation behaviors.

Toward top-down determination of PEGylation site using MALDI in-source decay MS analysis

A novel matrix assisted laser desorption/ionization (MALDI)-based mass spectrometric approach has been evaluated to rapidly analyze a custom designed PEGylated peptide that is 31 residues long and conjugated with 20 kDa linear polyethylene glycol (PEG) at the side chain of Lys. MALDI-TOF MS provided sufficiently high resolution to allow observation of each of the oligomers of the heterogeneous PEGylated peptide (m/Deltam of ca. 500), while a typical ESI-MS spectrum of this molecule was extremely complex and unresolved. Reflector in-source decay (reISD) analysis using MALDI-TOF MS was attempted to identify the PEGylation site at intact molecular level without any sample treatment. An reISD spectrum of the free peptide was observed with abundant c-, y-, and [z + 2]-fragment ion series, whereas, in the fragmented PEGylated peptide, the fragment ion series were truncated at the residue where PEG was attached. Therefore, a direct comparison of these top-down reISD spectra suggested the location of the PEGylation site. Results from this study demonstrate a clear analytical utility of the ISD technique to characterize structural aspects of heterogeneous biomolecules.

On-target sample preparation of 4-sulfophenyl isothiocyanate-derivatized peptides using AnchorChip Targets

De novo sequencing of tryptic peptides by post source decay (PSD) or collision induced dissociation (CID) analysis using MALDI TOF-TOF instruments is due to the easy interpretation facilitated by the introduction of N-terminal sulfonated derivatives. Recently, a stable and cheap reagent, 4-sulfophenyl isothiocyanate (SPITC), has been successfully used for N-terminal derivatization. Previously described methods have always used desalting and concentration by reverse-phase chromatography prior to mass spectrometric analysis. Here we present an on-target sample preparation method based on AnchorChip target technology. The method was optimized for reduction of by-products and sensitivity with SPITC-derivatized tryptic BSA peptides, and successfully applied to protein identification from silver-stained two-dimensional electrophoretic gels of fish liver extracts. The method is simple and sensitive and allowed protein identification based on de novo sequencing and BLAST search from species with limited sequence information.

A novel approach using MALDI-TOF/TOF mass spectrometry and prestructured sample supports (AnchorChip Technology) for proteomic profiling and protein identification

Mass spectrometry (MS)-based proteomic profiling and protein identification has become a powerful tool for the discovery of new disease biomarkers. Among the MS platforms, matrix-assisted laser desorption/ionization time-of-flight/time-of-flight (MALDI-TOF/TOF) MS offers high sample throughput and the flexibility to couple with different off-line sample fractionation techniques. Here, we present a strategy using MALDI-TOF/TOF MS to analyze fractionated human serum samples for proteomic profiling and then identify serum peptides from these proteomic profiles. We achieve the profiling analyses by using different functionalized magnetic beads to enrich specific subsets of serum proteins/peptides based on their absorption to these beads. This step is followed by elution, transfer onto prestructured sample supports (AnchorChip targets), and analysis in a MALDI-TOF/TOF mass spectrometer. Selected serum peptides are then analyzed in the tandem MS (TOF/TOF) mode to generate fragment ions for determination of their amino acid sequences. We have demonstrated that using this approach, proteomic profiling and protein identification can be done in a single MS instrument.

From the genome sequence to the proteome and back: evaluation of E. coli genome annotation with a 2-D gel-based proteomics approach

The ambition of systems biology to understand complex biological systems at the molecular level implies that we need to have a concrete and correct understanding of each molecular entity and its function. However, even for the best-studied organism, Escherichia coli, a large number of proteins have never been identified and characterised from wild-type cells, and/or await unravelling of their biological role. Instead, the ORF models for these proteins have been predicted by suitable algorithms and/or through comparison with known, homologous proteins from other organisms, approaches which may be prone to error. In the present study, we used a combination of 2-DE, MALDI-TOF-MS and PMF to identify 1151 different proteins in E. coli K12 JM109. Comparison of the experimental with the theoretical Mr and pI values (4000 experimental values each) allowed the identification of numerous proteins with incorrect or incomplete ORF annotations in the current E. coli genome databases. Several inconsistencies in genome annotation were verified experimentally, and up to 55 candidates await further investigation. Our findings demonstrate how an up-to-date 2-D gel-based proteomics approach can be used for improving the annotation of prokaryotic genomes. They also highlight the need for harmonization among the different E. coli genome databases.

Comparison of vacuum matrix-assisted laser desorption/ionization (MALDI) and atmospheric pressure MALDI (AP-MALDI) tandem mass spectrometry of 2-dimensional separated and trypsin-digested glomerular proteins for database search derived identification

Mass spectrometric based sequencing of enzymatic generated peptides is widely used to obtain specific sequence tags allowing the unambiguous identification of proteins. In the present study, two types of desorption/ionization techniques combined with different modes of ion dissociation, namely vacuum matrix-assisted laser desorption/ionization (vMALDI) high energy collision induced dissociation (CID) and post-source decay (PSD) as well as atmospheric pressure (AP)-MALDI low energy CID, were applied for the fragmentation of singly protonated peptide ions, which were derived from two-dimensional separated, silver-stained and trypsin-digested hydrophilic as well as hydrophobic glomerular proteins. Thereby, defined properties of the individual fragmentation pattern generated by the specified modes could be observed. Furthermore, the compatibility of the varying PSD and CID (MS/MS) data with database search derived identification using two public accessible search algorithms has been evaluated. The peptide sequence tag information obtained by PSD and high energy CID enabled in the majority of cases an unambiguous identification. In contrast, part of the data obtained by low energy CID were not assignable using similar search parameters and therefore no clear results were obtainable. The knowledge of the properties of available MALDI-based fragmentation techniques presents an important factor for data interpretation using public accessible search algorithms and moreover for the identification of two-dimensional gel separated proteins.

The N-terminal lobes of both regulatory light chains interact with the tail domain in the 10 S-inhibited conformation of smooth muscle myosin

In the presence of ATP, unphosphorylated smooth muscle myosin can form a catalytically inactive monomer that sediments at 10 Svedbergs (10 S). The tail of 10 S bends into thirds and interacts with the regulatory domain. ADP-P(i) is "trapped" at the active site, and consequently the ATPase activity is extremely low. We are interested in the structural basis for maintenance of this off state. Our prior photocross-linking work with 10 S showed that tail residues 1554-1583 are proximal to position 108 in the C-terminal lobe of one of the two regulatory light chains ( Olney, J. J., Sellers, J. R., and Cremo, C. R. (1996) J. Biol. Chem. 271, 20375-20384 ). These data suggested that the tail interacts with only one of the two regulatory light chains. Here we present data, using a photocross-linker on position 59 on the N-terminal lobe of the regulatory light chain (RLC), demonstrating that both regulatory light chains of a single molecule can cross-link to the light meromyosin portion of the tail. Mass spectrometric data show four specific cross-linked regions spanning residues 1428-1571 in the light meromyosin portion of the tail, consistent with cross-linking two RLC to one light meromyosin. In addition, we find that position 59 can cross-link internally to residues 42-45 within the same RLC subunit. The internal cross-link only forms in 10 S and not in unphosphorylated heavy meromyosin (lacking the light meromyosin), suggesting a structural rearrangement within the RLC attributed to the interaction of the tail with the head.

Proteome Profiling in the Rat Harderian Gland

The Harderian gland is an orbital gland located behind the ocular bulb in most terrestrial vertebrates probably functioning for production of lipid secretion to protect the eye. We herein present a protein reference database of the rat Harderian gland that may serve as analytical tool for future proteomic work, report lipid and porphyrin handling cascades, address sequence conflicts and report structures that have not been so far described by proteomics methods.

Mass spectrometrical verification of stomatin-like protein 2 (SLP-2) primary structure

Stomatin-like protein 2 (SLP-2) (syn.: EPB72-like 2 [NP_038470], HSPC108 [AAF29073]), a protein of unknown function, has been described in several tissues and cells but its primary structure is still not completely elucidated. Moreover, sequence conflicts appear in several databases. It was the aim of the study to further describe SLP-2 primary sequence and to solve existing sequence conflicts. For this purpose a protein extract was run on two-dimensional gel electrophoresis and SLP-2 was identified by MALDI-TOF/TOF. SLP-2 was digested with trypsin, chymotrypsin, Lys-C, and de novo sequencing studies as well as Nano-HPLC-ESI-MS/MS analysis were carried out. By the use of several proteases sequence coverage of 90% was obtained but the N-terminal 34 amino acids harbouring database conflict 1 were not covered. The presence of Leucine 129 (sequence conflict 2) and Alanine 202 (sequence conflict 3) was verified by three independent approaches. High sequence coverage resulting from multiple proteolytic cleavage, MALDI-TOF/TOF, Nano-HPLC-ESI-MS/MS and de novo sequencing completed unambiguous analysis of SLP-2 primary structure of approximately = 90% of sequence coverage. In addition, methodology used was able to solve so far pending sequence conflicts in databases and literature. SLP-2 is a high abundance protein in several tissues and cells and may play an important biological role and therefore characterization of its primary structure is of importance.

Comparative studies of 193-nm photodissociation and TOF-TOFMS analysis of bradykinin analogues: the effects of charge site(s) and fragmentation timescales

The dissociation reactions of [M + H]+, [M + Na]+, and [M + Cu]+ ions of bradykinin (amino acid sequence RPPGFSPFR) and three bradykinin analogues (RPPGF, RPPGFSPF, PPGFSPFR) are examined by using 193-nm photodissociation and post-source decay (PSD) TOF-TOF-MS techniques. The photodissociation apparatus is equipped with a biased activation cell, which allows us to detect fragment ions that are formed by dissociation of short-lived (<1 mus) photo-excited ions. In our previously reported photodissociation studies, the fragment ions were formed from ions dissociating with lifetimes that exceeded 10 mus; thus these earlier photofragment ion spectra and post-source decay (PSD) spectra [composite of both metastable ion (MI) and collision-induced dissociation (CID)] were quite similar. On the other hand, short-lived photo-excited ions dissociate by simple bond cleavage reactions and other high-energy dissociation channels. We also show that product ion types and abundances vary with the location of the charge on the peptide ion. For example, H+ and Na+ cations can bind to multiple polar functional groups (basic amino acid side chains) of the peptide, whereas Cu+ ions preferentially bind to the guanidino group of the arginine side-chain and the N-terminal amine group. Furthermore, when Cu+ is the charge carrier, the abundances of non-sequence informative ions, especially loss of small neutral molecules (H2O and NH3) is decreased for both photofragment ion and PSD spectra relative to that observed for [M + H]+ and [M + Na]+ peptide ions.

Identification of PVK/CAP2b neuropeptides from single neurohemal organs of the stable fly and horn fly via MALDI-TOF/TOF tandem mass spectrometry

MALDI-TOF/TOF tandem mass spectrometry has been applied to determine the complete sequences of the PVK/CAP2b neuropeptides in the stable fly Stomoxys calcitrans and horn fly Haematobia irritans, insect pests of livestock. This peptidomic analysis of single neurohemal organ preparations allows the unambiguous assignment of internal Leu/Ile positions not distinguishable by previous mass spectrometric techniques. The sequences are as follows: Stoca-PVK/CAP2b-1, AGGASGLYAFPRVa; Stoca-PVK/CAP2b-2, NAKLYPVPRVa; and Haeir-PVK/CAP2b-1, AGGASGLYAFPRVa; Haeir-PVK/CAP2b-1, NAKLYPMPRVa. Both Stoca-PVK/CAP2b-1 and -2 stimulate Malpighian tubule fluid secretion in the stable fly, with EC50 values between 3 and 11 nM. The identification of these novel neuropeptides adds to our knowledge of the peptidomes of flies, and can aid in the development of neuropeptide-based control strategies of these insect pests.

MALDI MS imaging of amyloid

Label-free molecular imaging by mass spectrometry allows simultaneous mapping of multiple analytes in biological tissue sections. In this chapter, the application of this new technology to the detection Abeta peptides in mouse brain sections is discussed.

Top-Down Proteomics for Rapid Identification of Intact Microorganisms

We apply MALDI-TOF/TOF mass spectrometry for the rapid and high-confidence identification of intact Bacillus spore species. In this method, fragment ion spectra of whole (undigested) protein biomarkers are obtained without the need for biomarker prefractionation, digestion, separation, and cleanup. Laser-induced dissociation (unimolecular decay) of higher mass (>5 kDa) precursor ions in the first TOF analyzer is followed by reacceleration and subsequent high-resolution mass analysis of the resulting sequence-specific fragments in a reflectron TOF analyzer. In-house-developed software compares an experimental MS/MS spectrum with in silico-generated tandem mass spectra from all protein sequences, contained in a proteome database, with masses within a preset range around the precursor ion mass. A p-value, the probability that the observed matches between experimental and in silico-generated fragments occur by chance, is computed and used to rank the database proteins to identify the most plausible precursor protein. By inference, the source microorganism is then identified on the basis of the identification of individual, unique protein biomarker(s). As an example, intact Bacillus atrophaeus and Bacillus cereus spores, either pure or in mixtures, were unambiguously identified by this method after fragmenting and identifying individual small, acid-soluble spore proteins that are specific for each species. Factors such as experimental mass accuracy and number of detected fragment ions, precursor ion charge state, and sequence-specific fragmentation have been evaluated with the objective of extending the approach to other microorganisms. MALDI-TOF/TOF-MS in a lab setting is an efficient tool for in situ confirmation/verification of initial microorganism identification.

Mass spectrometric assignment of Leu/Ile in neuropeptides from single neurohemal organ preparations of insects

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF-TOF) tandem mass spectrometry has been applied for the first time on an insect/arthropod target, focusing on PVK/CAP2b neuropeptides in the housefly Musca domestica and flesh fly Neobellieria bullata. The peptidomic analysis of single neurohemal organ preparations allows the unambiguous assignment of internal Leu/Ile positions not distinguishable by previous mass spectrometric techniques. The confirmation of side-chain fragments which allows assignment of Leu/Ile even from samples as small as neurohemal organs will greatly accelerate the identification of novel neuropeptides that are implicated in the regulation of critical physiological processes in insects. The unnatural Ile analog is 4.5 times more active than the native Leu sequence in a housefly Malpighian tubule fluid secretion assay, which reinforces the caveat that potency values in a biological assay cannot be relied upon to predict the native sequence.

Collisional activation by MALDI tandem time-of-flight mass spectrometry induces intramolecular migration of amide hydrogens in protonated peptides

Considerable controversy exists in the literature as to the occurrence of intramolecular migration of amide hydrogens upon collisional activation of protonated peptides and proteins. This phenomenon has important implications for the application of CID as an experimental tool to obtain site-specific information about the incorporation of deuterium into peptides and proteins in solution. Using a unique set of peptides with their carboxyl-terminal half labeled with deuterium we have shown unambiguously that hydrogen (1H/2H) scrambling is such a dominating factor during low energy collisional activation of doubly protonated peptides that the original regioselective deuterium pattern of these peptides is completely erased (Jørgensen, T. J. D., Gårdsvoll, H., Ploug, M., and Roepstorff, P. (2005) Intramolecular migration of amide hydrogens in protonated peptides upon collisional activation. J. Am. Chem. Soc.127, 2785-2793). Taking further advantage of this unique test system we have now investigated the influence of the charge state and collision energy on the occurrence of scrambling in protonated peptides. Our MALDI tandem time-of-flight experiments clearly demonstrate that complete positional randomization among all exchangeable sites (i.e. all N- and O-linked hydrogens) also occurs upon high energy collisional activation of singly protonated peptides. This intense proton/deuteron traffic precludes the use of MALDI tandem time-of-flight mass spectrometry to obtain reliable information on the specific incorporation pattern of deuterons obtained during exchange experiments in solution.

Current literature in mass spectrometry

In order to keep subscribers up‐to‐date with the latest developments in their field, John Wiley & Sons are providing a current awareness service in each issue of the journal. The bibliography contains newly published material in the field of mass spectrometry. Each bibliography is divided into 11 sections: 1 Books, Reviews & Symposia; 2 Instrumental Techniques & Methods; 3 Gas Phase Ion Chemistry; 4 Biology/Biochemistry: Amino Acids, Peptides & Proteins; Carbohydrates; Lipids; Nucleic Acids; 5 Pharmacology/Toxicology; 6 Natural Products; 7 Analysis of Organic Compounds; 8 Analysis of Inorganics/Organometallics; 9 Surface Analysis; 10 Environmental Analysis; 11 Elemental Analysis. Within each section, articles are listed in alphabetical order with respect to author (5 Weeks journals ‐ Search completed at 8th. Sept. 2004)