O-145 Green Tea catechins EGCG and pro-drug of EGCG (Pro-EGCG) inhibit endometriosis through targeting molecules regulating macrophages and B cells

Study question

What are the therapeutic targets and mechanisms of green tea EGCG and Pro-EGCG in treating endometriosis?

Summary answer

EGCG and Pro-EGCG have unique molecular targets to regulate interactions of B cells, macrophages and endometriotic cells and limit the growth and development of endometriosis.

What is known already

Current treatments of endometriosis are mainly hormonal suppression and surgical ablation or removal. Our previous studies showed EGCG significantly inhibits development of experimental endometriosis in mice. Pro-EGCG is more effective than EGCG in term of anti-endometriosis, anti-angiogenesis and anti-oxidation (Wang, et. al., 2013; Xu, et al., 2011). Dysfunctional immunological activities of macrophages and B cells were found in women with endometriosis. The molecular targets, underlying mechanism and differential therapeutic efficacy of EGCG and Pro-EGCG, as well as their anti-inflammatory activities are still not known.

Study design, size, duration

Multiplexed Proteome Integral Stability Alteration (PISA) assay (Gaetani et al.,2019), followed by MS/MS was applied to identify the molecular targets of EGCG and Pro-EGCG in endometriotic cells. Pharmacological studies of EGCG and Pro-EGCG on endometriotic cell line and endometriosis models in mice were performed to characterise their anti-endometriosis and anti-inflammatory effects. Gene silencing and over-expression experiments were conducted to confirm the immunoregulatory mechanisms.

Participants/materials, setting, methods

Endometriotic (Hs832(C)T) cell lines in culture and lysate were treated for chemical proteomics analysis. SiRNA and overexpression vectors were transfected to the cells in vitro and lesions in vivo. Hs832(C).T, monocytic cells (THP-1) and control B cell (Raji null) lines were used for co-culture assays to study the interaction between endometriotic and immune cells in vitro. Endometriosis mice model was established for immunostaining and microarray analysis of lesions to characterise the molecular pathways in vivo.

Main results and the role of chance

MTDH and PXK were the strongest and most differential targets of EGCG and Pro-EGCG in both cells lysate and cell culture of Hs832(C).T, respectively. Gene silencing and overexpression of the protein targets in vitro and in vivo significantly altered expressions of downstream proteins, including BLK and EGF after PXK, and MYC and AKT after MTDH, as well as endometriosis-related genes such as VEGFC and MMP9. Co-culture assays of Hs832(C).T with Raji null or THP-1 induced macrophages showed that expressions of PXK, MTDH, downstream targets, and immune-related genes were significantly increased after incubation of recombinant proteins, but were significantly decreased after EGCG and Pro-EGCG treatment. M1 and M2 macrophages, as well as B cells were significantly reduced after the treatments in vitro and in vivo. Double immunofluorescent staining of lesions showed that CD68, CD163 or CD20 co-expressed with MTDH, PXK and downstream targets, and numbers of the co-expressed cells were significantly reduced after treatments in vivo. Microarray experiment further identified the upstream and downstream genes of MTDH or PXK contributing to the growth and development of endometriosis.

Limitations, reasons for caution

Results of this pharmacological and mechanistic study require clinical samples to validate the anti-endometriosis effects of EGCG and Pro-EGCG. Effects of other potential pharmaceuticals targeting the macrophages and B cells on endometriosis are needed.

Wider implications of the findings

The findings provide pharmacological and mechanistic data for future development of EGCG and Pro-EGCG as new treatment for endometriosis. This study shows that macrophage and B cell could be potential therapeutic targets for treatment of endometriosis, which opens up new horizon for the novel immunotherapy for endometriosis.

Trial registration number

NA

Differentiation of Central Slovenian and Moscow populations of Rana temporaria frogs using peptide biomarkers of temporins family

Skin secretion represents the only means of defense for the majority of frog species. That phenomenon is based on the fact that the main components of the secretion are peptides demonstrating greatly varying types of bioactivity. They fulfill regulatory functions, fight microorganisms and may be even helpful against predators. These peptides are considered to be rather promising pharmaceuticals of future generation as according to the present knowledge microorganisms are unlikely to develop resistance to them. Mass spectrometry sequencing of these peptides is the most efficient first step of their study providing reliably their primary structures, i.e., amino acids sequence and S-S bond motif. Besides discovering new bioactive peptides, mass spectrometry appears to be an efficient tool of taxonomy studies, allowing for distinguishing not only between closely related species, but also between populations of the same species. Application of several tandem mass spectrometry tools (CID, HCD, ETD, EThcD) available with Orbitrap mass analyzer allowed us to obtain full sequence of about 60 peptides in the secretion of Slovenian population of brown ranid frog Rana temporaria. The problem of sequence inside C-terminal cycle formed by two Cys and differentiation of isomeric Leu and Ile residues was done in top-down mode without any derivatization steps. Besides general biomarkers of Rana temporaria species, Central Slovenian population of Rana temporaria demonstrates six novel temporins and one brevinin 1, which may be treated as biomarkers of that population.

Brain Proteome of Drosophila melanogaster Is Enriched with Nuclear Proteins

The brain proteome of Drosophila melanogaster was characterized by liquid chromatography/high-resolution mass spectrometry and compared to the earlier characterized Drosophila whole-body and head proteomes. Raw data for all the proteomes were processed in a similar manner. Approximately 4000 proteins were identified in the brain proteome that represented, as expected, the subsets of the head and body proteomes. However, after thorough data curation, we reliably identified 24 proteins unique for the brain proteome; 13 of them have never been detected before at the protein level. Fourteen of 24 identified proteins have been annotated as nuclear proteins. Comparison of three used datasets by label-free quantitation showed statistically significant enrichment of the brain proteome with nuclear proteins. Therefore, we recommend the use of isolated brain preparations in the studies of Drosophila nuclear proteins.

Validation and development of MTH1 inhibitors for treatment of cancer

BACKGROUND

Previously, we showed cancer cells rely on the MTH1 protein to prevent incorporation of otherwise deadly oxidised nucleotides into DNA and we developed MTH1 inhibitors which selectively kill cancer cells. Recently, several new and potent inhibitors of MTH1 were demonstrated to be non-toxic to cancer cells, challenging the utility of MTH1 inhibition as a target for cancer treatment.

MATERIAL AND METHODS

Human cancer cell lines were exposed in vitro to MTH1 inhibitors or depleted of MTH1 by siRNA or shRNA. 8-oxodG was measured by immunostaining and modified comet assay. Thermal Proteome profiling, proteomics, cellular thermal shift assays, kinase and CEREP panel were used for target engagement, mode of action and selectivity investigations of MTH1 inhibitors. Effect of MTH1 inhibition on tumour growth was explored in BRAF V600E-mutated malignant melanoma patient derived xenograft and human colon cancer SW480 and HCT116 xenograft models.

RESULTS

Here, we demonstrate that recently described MTH1 inhibitors, which fail to kill cancer cells, also fail to introduce the toxic oxidized nucleotides into DNA. We also describe a new MTH1 inhibitor TH1579, (Karonudib), an analogue of TH588, which is a potent, selective MTH1 inhibitor with good oral availability and demonstrates excellent pharmacokinetic and anti-cancer properties in vivo.

CONCLUSION

We demonstrate that in order to kill cancer cells MTH1 inhibitors must also introduce oxidized nucleotides into DNA. Furthermore, we describe TH1579 as a best-in-class MTH1 inhibitor, which we expect to be useful in order to further validate the MTH1 inhibitor concept.

Protein biomarkers in vernix with potential to predict the development of atopic eczema in early childhood

Background

Atopic eczema (AE) is a chronic inflammatory skin disease, which has increased in prevalence. Evidence points toward lifestyle as a major risk factor. AE is often the first symptom early in life later followed by food allergy, asthma, and allergic rhinitis. Thus, there is a great need to find early, preferentially noninvasive, biomarkers to identify individuals that are predisposed to AE with the goal to prevent disease development.

Objective

To investigate whether the protein abundances in vernix can predict later development of AE.

Methods

Vernix collected at birth from 34 newborns within the Assessment of Lifestyle and Allergic Disease During INfancy (ALADDIN) birth cohort was included in the study. At 2 years of age, 18 children had developed AE. Vernix proteins were identified and quantified with liquid chromatography coupled to tandem mass spectrometry.

Results

We identified and quantified 203 proteins in all vernix samples. An orthogonal projections to latent structures-discriminant analysis (OPLS-DA) model was found with R² = 0.85, Q² = 0.39, and discrimination power between the AE and healthy group of 73.5%. Polyubiquitin-C and calmodulin-like protein 5 showed strong negative correlation to the AE group, with a correlation coefficient of 0.73 and 0.68, respectively, and a P-value of 8.2 E-7 and 1.8 E-5, respectively. For these two proteins, the OPLS-DA model showed a prediction accuracy of 91.2%.

Conclusion

The protein abundances in vernix, and particularly that of polyubiquitin-C and calmodulin-like protein 5, are promising candidates as biomarkers for the identification of newborns predisposed to develop AE.

Composition and antimicrobial activity of the skin peptidome of Russian brown frog Rana temporaria

A nano-HPLC-ESI-OrbiTrap study involving HCD and ETD spectra has been carried out to clarify the composition of the skin peptidome of brown Russian frogs Rana temporaria. This approach allowed determinantion of 76 individual peptides, increasing 3-fold the identified portion of the peptidome in comparison to that obtained earlier with FTICR MS. A search for the new bradykinin related peptides (BRPs) was carried out by reconstructing mass chromatograms based on the ion current of characteristic b- and y-ions. Several peptides were reported in the secretion of R. temporaria for the first time. The overall antibacterial activity of the skin secretion in general and of one individual peptide (Brevinin 1Tb) was determined using PMEU Spectrion (Portable Microbe Enrichment Unit) technology. The inhibitory effects of these peptides on Staphylococcus aureus and Salmonella enterica Serovar typhimutium were equal in scale to that reported for some antibiotics.

Increased throughput of proteomics analysis by multiplexing high-resolution tandem mass spectra

High-resolution and high-accuracy Fourier transform mass spectrometry (FTMS) is becoming increasingly attractive due to its specificity. However, the speed of tandem FTMS analysis severely limits the competitive advantage of this approach relative to faster low-resolution quadrupole ion trap MS/MS instruments. Here we demonstrate an entirely FTMS-based analysis method with a 2.5-3.0-fold greater throughput than a conventional FT MS/MS approach. The method consists of accumulating together the MS/MS fragments ions from multiple precursors, with subsequent high-resolution analysis of the mixture. Following acquisition, the multiplexed spectrum is deconvoluted into individual MS/MS spectra which are then combined into a single concatenated file and submitted for peptide identification to a search engine. The method is tested both in silico using a database of MS/MS spectra as well as in situ using a modified LTQ Orbitrap mass spectrometer. The performance of the method in the experiment was consistent with theoretical expectations.

Mass spectrometric study of bradykinin-related peptides (BRPs) from the skin secretion of Russian ranid frogs

Amphibian skin secretion is known to contain biologically active peptides. Bradykinins and related peptides (BRPs) can be found in these animals, while frogs from the genus Rana are considered to be leaders in the levels and variety of these peptides. A reasonable rationalization of this fact is that bradykinins are efficient defense compounds against predators. Forty-four various BRPs have been identified in the skin secretions of five ranid frog species (R. ridibunda, R. lessonae, R. esculenta, R. temporaria, R. arvalis) from the Zvenigorod region (Moscow district, Russia). Some of these peptides are already known, but the novel ones constitute a significant portion. An interesting group of novel peptides was isolated from R. lessonae. These are bradykinin analogues bearing a tyrosine residue in the 5th or 8th position. [Arg(0), Trp(5), Leu(8)]bradykinin and [Thr(6), Leu(8)]bradykinin that had been isolated from fish and avian species, respectively, were also detected in the frog secretion, supporting the predator defense hypothesis. Furthermore, a novel group of BRPs named 'lessonakinins' was discovered in R. lessonae and R. esculenta. All of them include the [Arg(0), Trp(5), Leu(8)]bradykinin sequence and have some structural resemblance to the precursor of this peptide cloned by Chen and coworkers recently. However, the C-terminal part of the lessonakinins does not match the sequence predicted by Chen, demonstrating possible incompleteness of information obtained by cDNA cloning.

High levels of the adhesion molecule CD44 on leukemic cells generate acute myeloid leukemia relapse after withdrawal of the initial transforming event

Multiple genetic hits are detected in patients with acute myeloid leukemia (AML). To investigate this further, we developed a tetracycline-inducible mouse model of AML, in which the initial transforming event, overexpression of HOXA10, can be eliminated. Continuous overexpression of HOXA10 is required to generate AML in primary recipient mice, but is not essential for maintenance of the leukemia. Transplantation of AML to secondary recipients showed that in established leukemias, ∼80% of the leukemia-initiating cells (LICs) in bone marrow stopped proliferating upon withdrawal of HOXA10 overexpression. However, the population of LICs in primary recipients is heterogeneous, as ∼20% of the LICs induce leukemia in secondary recipients despite elimination of HOXA10-induced overexpression. Intrinsic genetic activation of several proto-oncogenes was observed in leukemic cells resistant to inactivation of the initial transformation event. Interestingly, high levels of the adhesion molecule CD44 on leukemic cells are essential to generate leukemia after removal of the primary event. This suggests that extrinsic niche-dependent factors are also involved in the host-dependent outgrowth of leukemias after withdrawal of HOXA10 overexpression event that initiates the leukemia.

Fourier transform ion cyclotron resonance mass spectrometer with coaxial multi-electrode cell ('O-trap'): first experimental demonstration

The conceptual design of the O-trap Fourier transform ion cyclotron resonance (FT-ICR) cell addresses the speed of analysis issue in FT-ICR mass spectrometry. The concept of the O-trap includes separating the functions of ion excitation and detection between two different FT-ICR cell compartments. The detection compartment of the O-trap implements additional internal coaxial electrodes around which ions with excited cyclotron motion revolve. The expected benefits are higher resolving power and the lesser effect of the space charge. In this work we present the first experimental demonstration of the O-trap cell and its features, including the high ion transfer efficiency between two distinct compartments of an ICR cell after excitation of the coherent cyclotron motion. We demonstrate that utilization of the multiple-electrode detection in the O-trap provides mass resolving power enhancement (achieved over a certain time) equal to the order of the frequency multiplication. In an O-trap installed in a 5 T desk-top cryogen-free superconducting magnet, the resolving power of R = 80,000 was achieved for bradykinin [M + 2H](2+) (m/z 531; equivalent to 100,000 when recalculated for m/z 400) in 0.2 s analysis time (transient length), and R = 300,000 at m/z 531 for a 1 s transient. In both cases, detection on the third multiple of the cyclotron frequency was implemented. In terms of the acquisition speed at fixed resolving power, such performance is equivalent to conventional FT-ICR detection using a 15 T magnet.

Novel natural peptides from Hyla arborea schelkownikowi skin secretion

Hyla arborea schelkownikowi is one of the leaf frog species inhabiting the southern territories of Russia and the former USSR. This frog species is a member of the Hylidae Rafinesque, 1815 batrachians family. The present study deals with the previously uninvestigated peptidome of the Hyla arborea schelkownikowi skin secretion. Nano-electrospray ionization Fourier transform mass spectrometry (nanoESI-FTMS) of the skin secretion, in the intact form and after acetylation, was selected as the general method of analysis. Electron-capture dissociation (ECD) and collision-induced dissociation (CID) fragmentation were both employed, while de novo sequencing was performed by manual interpretation of the MS data. The suppression of the cyclization of b-ions in the mass spectrometer by the acetylation reaction proved to be very efficient for the de novo sequencing of short peptides. Ten skin peptides were found and all of them, except for bradykinin, had not previously been reported. Six of the peptides belong to the tryptophyllins and related peptides, while three peptides are similar to the aureins.

Mass spectrometric study of peptides secreted by the skin glands of the brown frog Rana arvalis from the Moscow region

A high-performance liquid chromatography nano-electrospray ionization Fourier transform mass spectrometry (HPLC/nanoESI-FTMS) approach involving recording of collision-activated dissociation (CAD) and electron-capture dissociation (ECD) spectra of an intact sample and two its modifications after performic oxidation and reduction followed by carboxamidomethylation helps to establish peptide profiles in the crude secretion of frog species at mid-throughput level, including de novo sequencing. The proposed derivatization procedures allow increasing of the general sequence coverage in the backbone, providing complementary information and, what is more important, reveal the amino acid sequence in the cystine ring ('rana box'). Thus purely mass spectrometric efficient sequencing becomes possible for longer than usual proteolytic peptides. Seventeen peptides belonging to four known families were identified in the secretion of the European brown frog Rana arvalis inhabiting the Moscow region in Russia. Ranatuerins, considered previously a unique feature of the North American species, as well as a new melittin-related peptide, are worth special mention. The developed approach was previously successfully used for the identification of peptides in the skin secretion of the Caucasian green frog Rana ridibunda.

Electrospray ionization tandem mass spectrometry sequencing of novel skin peptides from Ranid frogs containing disulfide bridges

Tandem mass spectrometry sequencing, as well as Edman sequencing of peptides belonging to the Rana genus, represents a difficult task due to the presence of a disulfide bridge at the C-terminus and their rather high molecular masses (over 2000 Da). The present study throws light upon the sequence of three rather long peptides (more than 20 amino acid residues each) isolated from the skin secretion of Russian frogs, Rana ridibunda and Rana arvalis. This novel aspect involves the fact that the sequences (including two sequences established de novo) were determined exclusively by means of mass spectrometry. A combination of electron capture dissociation (ECD) and collision-induced dissociaiton (CID) data accompanied by exact mass measurements (LTQ Fourier transform ion cyclotron resonance mass spectrometer) facilitated reaching the goal. To overcome the difficulty dealing with disulphide bridges ("Rana box"), reduction of the S-S bond with dithiotreitol followed by derivatization of Cys residues with iodoacetamide was used. The sequence was determined using combined spectral data on y and b series of fragment ions. A multiple mass spectrometry (MS(3)) experiment was also used to elucidate the sequence inside the "Rana box" after cysteine derivatization. Exact mass measurements were used to differentiate between Lys and Gln residues, while characteristic losses of 29 and 43 Da (d and w fragment ions) in CID and ECD experiments allowed us to distinguish between Ile and Leu isomeric acids.

Dissociative recombination cross section and branching ratios of protonated dimethyl disulfide and N-methylacetamide

Dimethyl disulfide (DMDS) and N-methylacetamide are two first choice model systems that represent the disulfide bridge bonding and the peptide bonding in proteins. These molecules are therefore suitable for investigation of the mechanisms involved when proteins fragment under electron capture dissociation (ECD). The dissociative recombination cross sections for both protonated DMDS and protonated N-methylacetamide were determined at electron energies ranging from 0.001 to 0.3 eV. Also, the branching ratios at 0 eV center-of-mass collision energy were determined. The present results give support for the indirect mechanism of ECD, where free hydrogen atoms produced in the initial fragmentation step induce further decomposition. We suggest that both indirect and direct dissociations play a role in ECD.

Applications of electron-ion dissociation reactions for analysis of polycationic chitooligosaccharides in Fourier transform mass spectrometry

Singly protonated, doubly protonated, and sodiated pentaglucosamide (GlcNAc)(5), oligoglucosamines (GlcN)(m)(), and (GlcN)(3)GlcN(3OH14:0) were analyzed in an FTICR mass spectrometer by electron-ion dissociation reactions and compared to collision activation. The general fragmentation mode was found as the asymmetrical sequence fragments (B(n)() and minor C(n)() ion series) with full sequence coverage. Molecular mass information of each glucosamide or glucosamine residue can be readily obtained from the ion series. Fragmentation by electron capture dissociation revealed additional fragmentation of the N-acetyl moiety compared to sustained off-resonance irradiation collision-activated dissociation (SORI-CAD) and electron-induced dissociation (EID). Sodiated GlcNAc(5) molecular adduct ions were analyzed by EID and compared to CAD. Both techniques provided full sequence coverage. EID was more effective, but CAD resulted in the cross-ring ion products (0,2)A(n)() and (2,4)A(n)() for all relevant glucosamide residues.

De novo sequencing of antimicrobial peptides isolated from the venom glands of the wolf spider Lycosa singoriensis

Antimicrobial peptides (AMPs), named lycocitin 1, 2 and 3, and a peptide with a monoisotopic molecular mass of 3038.70 Da were detected in the venom glands of the wolf spider Lycosa singoriensis. Two of the peptides, lycocitin 1 and 2, are new AMPs whereas lycocitin 3 is highly homologous to lycotoxin II isolated from the venom of spider Lycosa carolinensis. In addition, two other peptides with monoisotopic masses of 2034.20 and 2340.28 Da showing the motif typical for antimicrobial peptides were also identified. These peptides and lycocitin 1, 2 and 3 were de novo sequenced using electron capture dissociation and low-energy collisional tandem mass spectrometry. The amino acid sequence of lycocitin 1 was determined as GKLQAFLAKMKEIAAQTL-NH(2). Lycocitin 2 differs from lycocitin 1 by a replacement of a lysine residue for an arginine residue at the second position. Lycocitin 3 differs from the known lycotoxin II consisting of 27 amino acid residues by a deletion of Gly-26. Both lycocitin 1 and 2 inhibit growth of Gram-positive (Staphylococcus aureus, Bacillus subtilis) and Gram-negative (Escherichia coli) bacteria and fungi (Candida albicans, Pseudomonas aeruginosa) at micromolar concentrations.

Towards the standard-module approach to disulfide-linked polypeptide nanostructures. I. Methodological prerequisites and mass spectrometric characterization of the test two-loop structure

Potentially biologically-active nanostructures can be created from single chains of unmodified peptides by cross-linking different regions of the chain by disulfide bonds and cleaving the chain at specified sites to obtain the final configuration. The availability of techniques for assembly and characterization of such structures was tested on a two-loop structure created from a 21-residue linear peptide. Directed intra-molecular disulfide bond formation was performed by inserting partial sequences favoring intra-molecular SS bond formation ("loops") separated by partial sequences disfavoring such a process ("spacers") into the precursor sequence. Peptide bond cleavage by partial acid hydrolysis at specific sites (GG, NP/DP) inside the loops opened them; the same process in the spacer separated the loops. Synthesis, oxidation and bond cleavage were monitored by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI ToF MS). The hydrolysis fragments of the produced nanostructures were characterized by tandem electrospray ionization Fourier transform mass spectrometry (ESI FT-MS) with collisional and electron capture dissociations. The latter technique was especially useful as it cleaves SS bonds preferentially. The feasibility of the proposed synthesis approach and the adequacy of the analysis techniques for the test structure were demonstrated.

Advantages of external accumulation for electron capture dissociation in Fourier transform mass spectrometry

A combination of external accumulation (XA) with electron capture dissociation (ECD) improves the electron capture efficiency, shortens the analysis time, and allows for rapid integration of multiple scans in Fourier transform mass spectrometry. This improves the signal-to-noise ratio and increases the number of detected products, including structurally important MS3 fragments. With XA-ECD, the range of the labile species amenable to ECD is significantly extended. Examples include the first-time determination of the positions of six GalNAc groups in a 60-residue peptide, five sialic acid and six O-linked GalNAc groups in a 25-residue peptide, and the sulfate group position in a 11-residue peptide. Even weakly bound supramolecular aggregates, including nonspecific peptide complexes, can be analyzed with XA-ECD. Preliminary results are reported on high-rate XA-ECD that uses an indirectly heated dispenser cathode as an electron source. This shortens the irradiation time to > or = 1 ms and increases the acquisition rate to 3 scans/s, an improvement by a factor of 10-100.

Electron capture dissociation of gaseous multiply charged ions by Fourier-transform ion cyclotron resonance

Fourier-transform ion cyclotron resonance instrumentation is uniquely applicable to an unusual new ion chemistry, electron capture dissociation (ECD). This causes nonergodic dissociation of far larger molecules (42 kDa) than previously observed (<1 kDa), with the resulting unimolecular ion chemistry also unique because it involves radical site reactions for similarly larger ions. ECD is highly complementary to the well known energetic methods for multiply charged ion dissociation, providing much more extensive protein sequence information, including the direct identification of N- versus C-terminal fragment ions. Because ECD only excites the molecule near the cleavage site, accompanying rearrangements are minimized. Counterintuitively, cleavage of backbone covalent bonds of protein ions is favored over that of noncovalent bonds; larger (>10 kDa) ions give far more extensive ECD if they are first thermally activated. This high specificity for covalent bond cleavage also makes ECD promising for studying the secondary and tertiary structure of gaseous protein ions caused by noncovalent bonding.

Comparison of electron capture dissociation and collisionally activated dissociation of polycations of peptide nucleic acids

Electron capture dissociation (ECD) in Fourier transform ion cyclotron resonance mass spectrometry coupled with electrospray ionization enhances the sequence elucidation of peptide nucleic acids compared with conventional low-energy collisionally activated dissociation (CAD). Examples are shown where ECD produced complete or extensive sequence coverage in PNAs six to ten nucleobases long. However, facile base losses from the reduced species and low abundances of backbone ECD fragments presented a significant problem. This was rationalized through the lower degree of charge solvation on the backbone compared to polypeptides. Combination of both CAD and ECD data is advantageous, as these techniques produce cleavages at different sites.

Improved low-energy electron injection systems for high rate electron capture dissociation in Fourier transform ion cyclotron resonance mass spectrometry

New low-energy electron injection systems based on indirectly heated dispenser cathodes facilitate electron capture dissociation (ECD) in Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. In this joint report, details are presented of the design and performance of these systems on two commercial FTICR instruments, 9.4 T Bruker BioAPEX in Uppsala and 4.7 T IonSpec Ultima in Odense. New results include obtaining meaningful one-scan MS/MS data for isolated precursor ions with millisecond irradiation times. The ECD rate improvement is not only due to the larger total electron current, but the larger emitting area as well.

Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry

A de novo sequencing program for proteins is described that uses tandem MS data from electron capture dissociation and collisionally activated dissociation of electrosprayed protein ions. Computer automation is used to convert the fragment ion mass values derived from these spectra into the most probable protein sequence, without distinguishing Leu/Ile. Minimum human input is necessary for the data reduction and interpretation. No extra chemistry is necessary to distinguish N- and C-terminal fragments in the mass spectra, as this is determined from the electron capture dissociation data. With parts-per-million mass accuracy (now available by using higher field Fourier transform MS instruments), the complete sequences of ubiquitin (8.6 kDa) and melittin (2.8 kDa) were predicted correctly by the program. The data available also provided 91% of the cytochrome c (12.4 kDa) sequence (essentially complete except for the tandem MS-resistant region K(13)-V(20) that contains the cyclic heme). Uncorrected mass values from a 6-T instrument still gave 86% of the sequence for ubiquitin, except for distinguishing Gln/Lys. Extensive sequencing of larger proteins should be possible by applying the algorithm to pieces of approximately 10-kDa size, such as products of limited proteolysis.

Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules

Here a fully automated computer algorithm is applied to complex mass spectra of peptides and proteins. This method uses a subtractive peak finding routine to locate possible isotopic clusters in the spectrum, subjecting these to a combination of the previous Fourier transform/Patterson method for primary charge determination and the method for least-squares fitting to a theoretically derived isotopic abundance distribution for m/z determination of the most abundant isotopic peak, and the statistical reliability of this determination. If a predicted protein sequence is available, each such m/z value is checked for assignment as a sequence fragment. A new signal-to-noise calculation procedure has been devised for accurate determination of baseline and noise width for spectra with high peak density. In 2 h, the program identified 824 isotopic clusters representing 581 mass values in the spectrum of a GluC digest of a 191 kDa protein; this is >50% more than the number of mass values found by the extremely tedious operator-applied methodology used previously. The program should be generally applicable to classes of large molecules, including DNA and polymers. Thorough high resolution analysis of spectra by Horn (THRASH) is proposed as the program's verb.

Low-mass ions observed in plasma desorption mass spectrometry of high explosives

The low-mass ions observed in both positive and negative plasma desorption mass spectrometry (PDMS) of the high explosives HMX, RDX, CL-20, NC, PETN and TNT are reported. Possible identities of the most abundant ions are suggested and their presence or absence in the different spectra is related to the properties of the explosives as matrices in PDMS. The detection of abundant NO+ and NO2- ions for HMX, RDX and CL-20, which are efficient matrices, indicates that explosive decomposition takes place in PDMS of these three substances and that a contribution from the corresponding chemical energy release is possible. The observation of abundant C2H4N+ and CH2N+ ions, which have high protonation properties, might also explain the higher protein charge states observed with these matrices. Also, the observation of NO2-, possibly formed by electron scavenging which increases the survival probability of positively charged protein molecular ions, completes the pattern. TNT does not give any of these ions and it is thereby possible to explain why it does not work as a PDMS matrix. For NC and PETN, decomposition does not seem to be as pronounced as for HMX, RDX and CL-20, and also no particularly abundant ions with high protonation properties are observed. The fact that NC works well as a matrix might be related to other properties of this compound, such as its high adsorption ability.

Electron capture dissociation for structural characterization of multiply charged protein cations

For proteins of < 20 kDa, this new radical site dissociation method cleaves different and many more backbone bonds than the conventional MS/MS methods (e.g., collisionally activated dissociation, CAD) that add energy directly to the even-electron ions. A minimum kinetic energy difference between the electron and ion maximizes capture; a 1 eV difference reduces capture by 10(3). Thus, in an FTMS ion cell with added electron trapping electrodes, capture appears to be achieved best at the boundary between the potential wells that trap the electrons and ions, now providing 80 +/- 15% precursor ion conversion efficiency. Capture cross section is dependent on the ionic charge squared (z2), minimizing the secondary dissociation of lower charge fragment ions. Electron capture is postulated to occur initially at a protonated site to release an energetic (approximately 6 eV) H. atom that is captured at a high-affinity site such as -S-S- or backbone amide to cause nonergodic (before energy randomization) dissociation. Cleavages between every pair of amino acids in mellitin (2.8 kDa) and ubiquitin (8.6 kDa) are represented in their ECD and CAD spectra, providing complete data for their de novo sequencing. Because posttranslational modifications such as carboxylation, glycosylation, and sulfation are less easily lost in ECD than in CAD, ECD assignments of their sequence positions are far more specific.

Electron capture dissociation of b (2+) peptide fragments reveals the presence of the acylium ion structure

Electron capture dissociation (ECD) of peptides and their fragments has now been extended to b ( n) ( 2+) ions, where it also produced far more structural information than collisional activation. Interestingly, b ( n) ( 2+) ions revealed abundant loss of CO from radical monocations and the presence of c ((n - 1)) ( +.) fragments. The CO loss from peptide radical cations is unusual and was attributed to neutralization of the -C identical with O(+) group in the acylium ion structure, supported by the observation of c ( (n - 1)) ( +.) ions that can only be formed from an open-chain ion. These characteristic features were most prominent for b ( 12)( 2+) ions of renin substrate and least prominent for b ( n) ( 2+) ions of substance P (n = 9,10). Totally, out of seven b ( n) ( 2+) ions studied, CO loss above 3% level was present in all spectra as well as c ( (n - 1))( +.) fragments of three species, suggesting that the acylium ion structure plays a significant role for at least some b ( 2+) ions. This is an unexpected result in view of the literature data for small, singly charged b ions, for which the protonated oxazolone structure is favoured in ab initio calculations. Apparently, more studies are required before extrapolating the small molecule results to large species. The CO loss in ECD can be used for distinguishing between b and y ions in the MS/MS spectrum of larger molecules.

Benefits of 2.94 micron infrared matrix-assisted laser desorption/ionization for analysis of labile molecules by Fourier transform mass spectrometry

A 2.94 microm Er:YAG laser was used together with a commercial Fourier transform mass spectrometer to study labile biomolecules. The combination has shown superior performance over conventional 337 nm ultraviolet matrix-assisted laser desorption/ionization (UV-MALDI) Fourier transform mass spectrometry (FTMS), especially for the analysis of peptides with post-translational modifications. With succinic acid as a matrix, the sensitivity of the single-shot analysis was increased by an order of magnitude to the low femtomole level, with significantly less fragmentation observed. Intact molecular ions of a range of O-glycosylated and sulfated peptides were detected. Urea was found to induce even less fragmentation, although at the expense of the total ion yield. Molecular ions of a noncovalent complex (vancomycin + diacetyl-L-Lys-D-Ala-D-Ala) have been observed for the first time in MALDI-FTMS. 2.94 microm infrared (IR) MALDI also produced abundant molecular ions of a range of nonbiological samples, including C60 and C70 fullerenes as well as dimetal coordination complexes.

Electron capture dissociation of singly and multiply phosphorylated peptides

Analysis of phosphotyrosine and phosphoserine containing peptides by nano-electrospray Fourier transform ion cyclotron resonance (FTICR) mass spectrometry established electron capture dissociation (ECD) as a viable method for phosphopeptide sequencing. In general, ECD spectra of synthetic and native phosphopeptides appeared less complex than conventional collision activated dissociation (CAD) mass spectra of these species. ECD of multiply protonated phosphopeptide ions generated mainly c- and z(.)-type peptide fragment ion series. No loss of water, phosphate groups or phosphoric acid from intact phosphopeptide ions nor from the c and z(.) fragment ion products was observed in the ECD spectra. ECD enabled complete or near-complete amino acid sequencing of phosphopeptides for the assignment of up to four phosphorylation sites in peptides in the mass range 1400 to 3500 Da. Nano-scale Fe(III)-affinity chromatography combined with nano-electrospray FTMS/ECD facilitated phosphopeptide analysis and amino acid sequencing from crude proteolytic peptide mixtures.

Localization of O-glycosylation sites in peptides by electron capture dissociation in a Fourier transform mass spectrometer

The novel technique electron capture dissociation (ECD) of electrospray generated [M + nH]n+ polypeptide cations produces rapid cleavage of the backbone NH-Ca bond to form c and z ions (in the modified notation of Roepstorff and Fohlman). The potential of the Fourier transform mass spectrometry equipped with ECD in structure analysis of O-glycosylated peptides in the 3 kDa range has been investigated. Totally, 85% of the available interresidue bonds were cleaved in five glycopeptides; more stable c ions accounted for 62% of the observed fragmentation. The c series provided direct evidence on the glycosylation sites in every case studied, with no glycan (GalNAc and dimannose) losses observed from these species. Less stable z ions supported the glycan site assignment, with minor glycan detachments. These losses, as well as the observed formation of even-electron z ions, are attributed to radical-site-initiated reactions. In favorable cases, complete sequence and glycan position information is obtained from a single-scan spectrum. The "mild" character of ECD supports the previously proposed non-ergodic (cleavage prior to energy randomization) mechanism, and the low internal energy increment of fragments.

Localization of labile posttranslational modifications by electron capture dissociation: the case of gamma-carboxyglutamic acid

Tandem mass spectrometry (MS/MS) of 28 residue peptides harboring gamma-carboxylated glutamic acid residues, a posttranslational modification of several proenzymes of the blood coagulation cascade, using either collisions or infrared photons results in complete ejection of the gamma-CO2 moieties (-44 Da) before cleavage of peptide-backbone bonds. However, MS/MS using electron capture dissociation (ECD) in a Fourier transform mass spectrometer cleaves backbone bonds without ejecting CO2, allowing direct localization of this labile modification. Sulfated side chains are also retained in ECD backbone fragmentations of a 21-mer peptide, although CAD causes extensive SO3 loss. ECD thus is a unique complement to conventional methods for MS/MS, causing less undesirable loss of side-chain functionalities as well as more desirable backbone cleavages.

Interaction between explosive and analyte layers in explosive matrix-assisted plasma desorption mass spectrometry

An HMX/insulin two-layer system was chosen as a model for further investigation of the matrix properties of explosive materials for protein analytes in plasma desorption mass spectrometry. The dependencies of the molecular ion yield and average charge state as a function of the analyte thickness were studied. An increase in the charge state of multiply protonated molecular species was confirmed as the major matrix effect, with the average charge state z at the smallest thickness studied being higher than in matrix-assisted laser desorption/ionization and closer to the value obtained in electrospray ionization under standard acidic conditions. Observed charge state distributions are significantly narrower than the corresponding Poisson distributions, which suggests that the protonation of insulin is limited in plasma desorption by the number of basic sites in the molecule, similar to electrospray ionization. Both the curve displaying total molecular ion yield and the one showing the total charge (proton) yield as a function of the insulin thickness have maxima at a thickness different from an insulin monolayer. These observations diminish the significance of a matrix/analyte interface mechanism for the explosive matrix assistance. Instead, a mechanism related to the chemical energy release during conversion of the explosive after the ion impact is proposed. As additional mechanisms, enhanced protonation of the analyte through collisions with products of the explosive decay is considered, as well as electron scavenging by other products, which leads to a higher survival probability of positively charged protein molecular ions. Copyright 1999 John Wiley & Sons, Ltd.

Two-dimensional mass spectrometry of biomolecules at the subfemtomole level

Multiple dimensions of unique molecular structure information can now be obtained from proteins and DNA using mass spectrometry. Less than 10(-16) mol of the active major histocompatibility complex signaling peptide in a mixture of thousands can be identified. For large proteins (> 40 kDa), the high resolving power (> 10(5) and 10(-17) mol sensitivity of Fourier-transform mass spectrometry provide exact molecular weight values (+/- 1 or 2 Da) for mixture components, indicating error or modifications compared with the predicted DNA sequence. Selecting a specific molecular species, its two-dimensional spectrum indicates the part of the molecule that is modified; a three-dimensional spectrum of that fragment further isolates the modification site.

Enhancement of the molecular ion yield in plasma desorption mass spectrometry using explosive matrices

The working hypothesis of this study was that the chemical energy of matrix material may be released, although only on a microscale, under MeV ion bombardment and may assist ejection of large intact bioorganic molecules. To test the hypothesis, the performance of several common explosives, as matrices in plasma desorption mass spectrometry, was compared to the standard matrix, nitrocellulose (NC), which is also a high explosive. Two explosives, RDX and HMX, were found to be new, effective matrices for peptides and proteins. While the performance of RDX was comparable with that of nitrocellulose, HMX gave a superior molecular ion yield and a higher average charge state of desorbed molecular ions compared with NC. Noth RDX and HMX have a similar chemical composition and structure, although the latter is a more powerful explosive. The measured total ion yield allows the conclusion that the increase in the amount of ejected material, due to the chemical energy release in high explosives under MeV ion bombardment, is limited, perhaps to a factor of 2 to 3. The fact that not all tested explosives gave molecular ions from peptides and proteins suggests that other factors, such as gas-phase chemistry, may play a significant role in molecular ion formation.

[An improved method of preparing protein and peptide probes in mass spectrometry with ionization of division fragments by californium-252 (TOF-PDMS)]

The addition of organic acids (picric, oxalic, citric, or tartaric) to peptide and protein samples was found to significantly increase the yield of their quasi-molecular ions (QMI) in time-of-flight 252Cf plasma desorption mass spectrometry. The yield of the ions depended on the pKa of the acid added.

Peptide sequencing by partial acid hydrolysis and high resolution plasma desorption mass spectrometry

A method of deriving peptide sequence information using partial acid hydrolysis in combination with accurate mass measurements and immonium ion analysis provided by high-resolution plasma desorption mass spectrometry has been developed. The technique is very simple in terms of the chemistry and involves a short-time (3-30 min) incubation of the peptide in 1N-6N HCl at 100-110 degrees C with subsequent mass spectrometric analysis. Partial acid hydrolysis is found to produce sequence-specific segments, often ladder-like, although not always a complete set. Two application examples of the method are given: the linear peptide bradykinin and desmopressin, a peptide with an internal S-S bond and a non-amino-acid constituent. The technique has proved to be particularly useful in cases where some a priori information on the peptide structure was already known or where the automated Edman degradation technique might yield erratic results or not work at all.

[(252)Cf-plasma desorption mass spectra of bacterial oligosaccharides]

252Cf plasma desorption mass spectrometry on a "reflect" desorption instrument (MSBX) was used to study oligosaccharides from bacterial O-specific antigenic chains. The data obtained for galacturonic acid, neutral and aminouronic oligosaccharides are discussed. This method is suggested for determining the composition of oligosaccharides from the O-specific polysaccharides and for elucidating their structures after modifications.

Combination of HPLC and 252-Cf plasma desorption mass spectrometry for identifying composition of ginseng tinctures

The 252-Cf plasma desorption mass spectrometry (252-Cf PDMS) determination or confirmation of the ginsenoside saponins has been proposed to investigate the composition of high performance liquid chromatography (HPLC) peaks of ginseng tinctures and galenic preparations. That ionization technique is well suitable for the analysis of natural mixtures of these saponins. The 252-Cf PD mass spectra of standard ginsenosides Rb1, Rb2, Rc, Re, Rg1, Rd, NG-R2, Z-R1 contain the peaks of two types of ions, namely, molecular adduct ions (MAI) and aglycone ions. By mass the latter may be referred to either protopanaxadiol or protopanaxatriol. The masses of MAI and aglycone ions are determined by the carbohydrate chains. The collected HPLC fractions of P ginseng tincture can be tested for content of ginsenosides. After studying two MAI peaks from the 252-Cf PD mass spectra of the basic ginsenosides, an example of distinction between two galenic preparations from different Panax has been shown.

Design and optimization of a micropump-based electrospray device for preparation of nitrocellulose substrates for plasma desorption time-of-flight mass spectrometry

Details of a nitrocellulose (NC) substrate preparation technique in 252Cf plasma desorption time-of-flight mass spectrometry were investigated using an electrospray device, in which a micropump was employed for solution delivery. The molecular ion yields for three standard proteins (porcine insulin, chicken-egg lysozyme and chymotrypsinogen A) were studied as a function of the electrosprayed NC layer thickness, spray rate, NC solution concentration and some other parameters. Optimal parameters of the NC substrate preparation procedure were determined, which include deposition of a layer of 250-750 micrograms cm-2 at up to 15 microliters min-1 spray rate and up to 15 micrograms microliters-1 solution concentration.

[Study of the interaction of triethylenethiophosphamide with nucleotides by mass spectrometry with ionization by fission fragments of californium-252]

Study of interaction of the antitumor alkylating drug triethylenethiophosphoramide (thioTEPA) with nucleotides (dGMP and dCMP) suggests highly perspective employment of 252-Cf fission fragment induced desorption mass spectrometry (252-Cf PDMS) in biochemical pharmacology. Using the 252-Cf PDMS the molecular masses of the unstable, unvolatile, high-molecular substances of biological origin and the chemical adducts or complexes with drugs can be used to establish some structural-functional parameters of the above mentioned biomolecules and their derivatives in microvolumes of the incubation medium. The resulting data may be used for modelling chemotherapeutic processes of "drug-biomolecule-target" type. Using 252-Cf PDMS the complexes (dGMP (thioTEPA) n), n = 1, 2, 3 and (dCMP (thioTEPA) n), n = 1, were obtained. Some quantitative parameters and stability of these complexes were studied. Binding of dGMP with drug in the presence of dCMP was shown preferential. The data are compatible with the predictions concerning the mechanism of the antitumor property of the thioTEPA which can be manifested in the impairment structure of DNA of the malignant cells.