Gas-Phase Peptide Fragmentation Induced by Hydrogen Attachment, from Principle to Sequencing of Amide Nitrogen-Methylated Peptides.

Tandem mass spectrometry (MS/MS) with radical-based fragmentation was developed recently, which involves the reaction of hydrogen atoms and peptides in a process called hydrogen attachment/abstraction dissociation (HAD). HAD mainly produces [cn + 2H]+ and [zm + 2H]+ via hydrogen attachment to the carbonyl oxygen on the peptide backbone. In addition, HAD often generates [an + 2H]+ and [xm + 2H]+. To explain the formation of [an + 2H]+ and [xm + 2H]+, hydrogen attachment to the carbonyl carbon atom on the peptide backbone is proposed to initiate Cα-C bond cleavage. The resultant hydrogen-abundant oxygen-centered radical intermediate undergoes radical-induced dissociation to give [an + H]+• and [xm + 2H]+. Subsequently, [an + 2H]+ was produced by the reaction of [an + H]+• and a hydrogen atom. The fragment ions formed by the cleavage of N-Cα and Cα-C bonds are observed in the HAD-MS/MS spectra, and the mass differences of these fragment ions correspond to the mass of peptide bonds. Consequently, HAD-MS/MS allows the identification of post-translational modifications on the peptide backbone. In addition, HAD-MS/MS provides a consecutive series of [cn + 2H]+ and [an + 2H]+ as the N-terminal fragments, as well as [zm + 2H]+ and [xm + 2H]+, which enables the sequencing of peptides with post-translational modification, including the discrimination of modifications on the side chain and backbone.

Hydrogen attachment dissociation of peptides containing disulfide bonds.

A combination of tandem mass spectrometry (MS/MS) and hydrogen attachment dissociation (HAD) is a useful method for peptide sequence analysis. In this study, gas-phase fragmentation induced by the attachment of hydrogen to peptides containing disulfide bonds was investigated. Hydrogen attachment induced the cleavage of either the disulfide or N-Cα bond, which competitively occurred during HAD. The disulfide bond cleavage proceeded through an intermediate, which contains a thiyl radical (-S˙) and a thiol group (-SH). In contrast, N-Cα bond cleavage produced an intermediate containing an enol-imine group and α-carbon radical. The intermediate α-carbon radical then attacked the disulfide bond, resulting in a cyclic [z]+ fragment. The counterpart, [c + H]+˙ with a thiyl radical underwent further hydrogen attachment, producing [c + 2H]+. Because both disulfide and N-Cα bonds were cleaved by a single hydrogen attachment event, HAD-MS/MS can provide sequence information for the backbone region in the disulfide loop.

Sequencing of Sulfopeptides Using Negative-Ion Tandem Mass Spectrometry with Hydrogen Attachment/Abstraction Dissociation.

Tandem mass spectrometry (MS/MS) with radical-based fragmentation involving the attachment or abstraction of hydrogen to peptides, in a process called hydrogen attachment/abstraction dissociation (HAD), has been recently developed. HAD-MS/MS is considered a useful method for the analysis of proteins with post-translational modification (PTM) because of its ability to determine the PTM site on proteins. In the present investigation, we analyzed highly acidic sulfopeptides and sulfoprotein digests using negative-ion HAD-MS/MS combined with matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI). In general, MALDI and ESI produced singly and multiply charged peptides, respectively. HAD of singly deprotonated sulfopeptides preferentially produced fragment ions with sulfonation, whereas both sulfonated and nonsulfonated fragment ions were observed in the HAD-MS/MS spectrum of multiply deprotonated sulfopeptides. A comparison of the MALDI and ESI HAD-MS/MS spectra allows the discrimination of sulfonated and nonsulfonated fragments, which would be helpful in performing de novo sequencing of sulfopeptides. In addition, the combination of ESI-based HAD-MS/MS and liquid chromatography (LC) allows the analysis of sulfopeptides present in protein digests. LC-ESI-MS/MS with HAD is a potentially useful method for sulfoproteomic application.

Hydrogen atom attachment to histidine and tryptophan containing peptides in the gas phase.

In this study, we use a combination of tandem mass spectrometry and hydrogen radical-mediated fragmentation techniques to analyze the sequence of peptides. We focus on fragmentation induced by the attachment of hydrogen atoms to the histidine and tryptophan residue side-chains in the peptide that occurs in the gas-phase. The hydrogen atom attached to the imidazole and indole rings in the histidine and tryptophan residues, respectively, and the resulting intermediate experienced Cα-Cß bond cleavage. The detailed fragmentation mechanism is investigated by computational analysis using density functional theory. According to the results, hydrogen attachment occurs at the C-5 position in histidine and at the C-2 position in the tryptophan, which has a lower activation energy compared with the other positions and the resulting intermediate radicals yielded fragments due to Cα-Cß bond cleavage. For the peptides that contain the histidine and tryptophan residues, cleavages in the Cα-Cß and N-Cα bonds occurred independently. Therefore, the method presented in this study is applicable when analyzing peptides that contain histidine and tryptophan residues.

Fundamental study of hydrogen-attachment-induced peptide fragmentation occurring in the gas phase and during the matrix-assisted laser desorption/ionization process.

Mass spectrometry with hydrogen-radical-mediated fragmentation techniques has been used for the sequencing of proteins/peptides. The two methods, matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) and hydrogen attachment/abstraction dissociation (HAD) are known as hydrogen-radical-mediated fragmentation techniques. MALDI-ISD occurs during laser induced desorption processes, whereas HAD utilizes the association of hydrogen with peptide ions in the gas phase. In this study, the general mechanisms of MALDI-ISD and HAD of peptides were investigated. We demonstrated the fragmentation of four model peptides and investigated the fragment formation pathways using density functional theory (DFT) calculations. The current experimental and computational joint study indicated that MALDI-ISD and HAD produce aminoketyl radical intermediates, which immediately undergo radical-induced cleavage at the N-Cα bond located on the C-terminal side of the radical site, leading to the c'/z˙ fragment pair. In the case of MALDI-ISD, the z˙ fragments undergo a subsequent reaction with the matrix to give z' and matrix adducts of the z fragments. In contrast, the c' and z˙ fragments react with hydrogen atoms during the HAD processes, and various fragment species, such as c˙, c', z˙ and z', were observed in the HAD-MS/MS mass spectra.

Tandem Mass Spectrometry of Peptide Ions by Microwave Excited Hydrogen and Water Plasmas.

A thermal cracking cell that served as the atomic hydrogen source for hydrogen attachment/abstraction dissociation (HAD) analysis has an intrinsic problem to produce a beam of atoms reactive against heated tungsten capillary. A plasma excited by 2.45 GHz microwave discharge can deliver reactive species to a quadrupole ion trap confining analyte ions without excessive heating of the radical source components. The radical (H•) production performance of the developed source was evaluated by optical emission spectroscopy and H• attachment reaction to fullerene ions. The source exhibited the H• attachment rate as high as a thermal cracking source forming H• in the high temperature tungsten capillary to induce fragmentation processes preserving post-translational modifications. Water vapor was introduced to the source to confirm the stability to generate oxygen containing radicals, which were found present in the water vapor plasma together with atomic hydrogen. Injection of radicals from a water vapor plasma successfully dissociated peptide ions to c-/z- and a-/x-type ions as the case of HAD induced by a thermal cracking cell.

Hydrogen Attachment/Abstraction Dissociation (HAD) of Gas-Phase Peptide Ions for Tandem Mass Spectrometry.

Dissociation of gas-phase peptide ions through interaction with low-energy hydrogen (H) radical (∼0.15 eV) was observed with a quadrupole ion trap mass spectrometry. The H radical generated by thermal dissociation of H2 molecules passing through a heated tungsten capillary (∼2000 °C) was injected into the ion trap containing target peptide ions. The fragmentation spectrum showed abundant c-/z- and a-/x-type ions, attributable to H attachment/abstraction to/from peptide ion. Because the low-energy neutral H radical initiated the fragmentation, the charge state of the precursor ion was maintained during the dissociation. As a result, precursor ions of any charge state, including singly charged positive and negative ions, could be analyzed for amino acid sequence. The sequence coverage exceeding 90% was obtained for both singly protonated and singly deprotonated substance P peptide. This mass spectrometry also preserved labile post-translational modification bonds. The modification sites of triply phosphorylated peptide (kinase domain of insulin receptor) were identified with the sequence coverage exceeding 80%.

Serum immunoglobulin G Fc region N-glycosylation profiling by matrix-assisted laser desorption/ionization mass spectrometry can distinguish breast cancer patients from cancer-free controls.

Herein, we report that breast cancer (BC) patients can be distinguished from cancer-free (NC) controls by serum immunoglobulin G (IgG) crystallizable fragment (Fc) region N-glycosylation profiling using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Recently, there has been much progress in the field of tumor immunology. However, to date, the role and biomarker potential of IgG Fc region N-glycosylation, which affects the function of antibodies, have not been examined in BC. In the present study, we profiled serum IgG Fc region N-glycans in BC patients (N = 90) and NC controls (N = 54) using MALDI-MS. An IgG Fc region N-glycan-based multiple logistic regression model was produced which could distinguish BC patients from NC controls (area under the receiver operative characteristic curve = 0.874). Furthermore, stage 0 patients could also be distinguished using this model. These results suggest that an unknown humoral factor or soluble mediator affects IgGs from the earliest stage of breast cancer, and also suggests that IgG Fc region N-glycosylation may play a role in tumor biology. Although further investigation is required, our findings are the evidence that IgG N-glycan profiling has the potential to be used as a breast cancer biomarker and may provide the insights into tumor immunology.

Association of EPAS1 gene rs4953354 polymorphism with susceptibility to lung adenocarcinoma in female Japanese non-smokers.

INTRODUCTION: Hypoxia-inducible factor-2α (also called endothelial periodic acid-Schiff domain protein 1 [EPAS1]) seems to play an important role in some carcinogenesis, though there is no information on the relationship between single nucleotide polymorphism of EPAS1 and lung cancer development. The aim of this study was to explore a possible association of the EPAS1 gene rs4953354 polymorphism with susceptibility to lung cancer. METHODS: A case-control study of 346 patients with non-small-cell lung carcinoma (adenocarcinoma = 249, squamous cell carcinoma = 97) and 247 healthy control subjects was carried out. A/G polymorphism within an intron 2 of the EPAS1 (rs4953354) was determined by direct sequencing. RESULTS: A frequency of lung adenocarcinoma patients with a minor allele G (A/G or G/G genotype) at the rs4953354 was much higher than that of controls (odds ratio, 1.800; 95% confidence interval, 1.161-2.791; p = 0.008). This association was more evident when analyzed using female never-smokers (odds ratio, 3.31; 95% confidence interval, 1.21-9.01; p = 0.017). Mutations in epidermal growth factor receptor tended to be frequent in patients with G allele at the rs4953354, compared with those with other genotypes. CONCLUSION: The EPAS1 rs4953354 may be a potentially susceptible marker for development of lung adenocarcinoma, especially in female never-smokers.

The C-terminal fragment of prostate-specific antigen, a 2331 Da peptide, as a new urinary pathognomonic biomarker candidate for diagnosing prostate cancer.

BACKGROUND AND OBJECTIVES: Prostate cancer (PCa) is one of the most common cancers and leading cause of cancer-related deaths in men. Mass screening has been carried out since the 1990s using prostate-specific antigen (PSA) levels in the serum as a PCa biomarker. However, although PSA is an excellent organ-specific marker, it is not a cancer-specific marker. Therefore, the aim of this study was to discover new biomarkers for the diagnosis of PCa. MATERIALS AND METHODS: We focused on urine samples voided following prostate massage (digital rectal examination [DRE]) and conducted a peptidomic analysis of these samples using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS(n)). Urinary biomaterials were concentrated and desalted using CM-Sepharose prior to the following analyses being performed by MALDI-TOF/MS(n): 1) differential analyses of mass spectra; 2) determination of amino acid sequences; and 3) quantitative analyses using a stable isotope-labeled internal standard. RESULTS: Multivariate analysis of the MALDI-TOF/MS mass spectra of urinary extracts revealed a 2331 Da peptide in urine samples following DRE. This peptide was identified as a C-terminal PSA fragment composed of 19 amino acid residues. Moreover, quantitative analysis of the relationship between isotope-labeled synthetic and intact peptides using MALDI-TOF/MS revealed that this peptide may be a new pathognomonic biomarker candidate that can differentiate PCa patients from non-cancer subjects. CONCLUSION: The results of the present study indicate that the 2331 Da peptide fragment of PSA may become a new pathognomonic biomarker for the diagnosis of PCa. A further large-scale investigation is currently underway to assess the possibility of using this peptide in the early detection of PCa.

Reversible hydrazide chemistry-based enrichment for O-GlcNAc-modified peptides and glycopeptides having non-reducing GlcNAc residues.

O-Linked N-acetylglucosamine (O-GlcNAc) is an emerging post-translational modification (PTM) of proteins. Analysis of O-GlcNAc modification using mass spectrometry (MS) is often problematic because of the low stoichiometry of the modification. In this study, we developed a new method for enriching O-GlcNAc-modified peptides using reversible hydrazide chemistry. O-GlcNAc-modified peptides were first labeled with N-azidoacetylgalactosamine (GalNAz) using gatactosyltransferase-T1 (Y289L) enzyme. The azide group on the GalNAz residue was then reacted with 3-ethynylbenzaldehyde via copper-catalyzed Huisgen 1,3-cycloaddition "click reaction" to form an aromatic aldehyde group of glycopeptides. Aromatic aldehyde-derivatized glycopeptides were enriched by reversible hydrazone formation with hydrazide resin. Reaction conditions for each step, especially for the click reaction, were optimized to achieve complete reaction without significant side reactions. This method was validated using a tryptic digest of bovine α-crystallin, which is an O-GlcNAc-modified glycoprotein. The developed method was also applied to structure-specific enrichment of N-linked glycopeptides having non-reducing terminal GlcNAc residues. All materials and chemicals required for this method are commercially available and there is no need to prepare any special reagents, facilitating the introduction of this method in any laboratory.

Phase I clinical and pharmacokinetic study of bi-weekly carboplatin/paclitaxel chemotherapy in elderly patients with advanced non-small cell lung cancer.

AIM: We evaluated the pharmacokinetics and quality of life of elderly patients with advanced non-small-cell lung cancer (NSCLC) treated with bi-weekly carboplatin and paclitaxel chemotherapy, and determined the maximum tolerated dose (MTD) of this treatment. PATIENTS AND METHODS: Eligible patients had histologically- or cytologically-proven inoperable NSCLC, age of 70 years or older, no prior treatment, and Eastern Cooperative Oncology Group performance status 0-2. Paclitaxel was administered in combination with carboplatin under a bi-weekly schedule. We determined the plasma concentrations of both drugs during therapy. RESULTS: The median patient age was 80 years. Using carboplatin at AUC 3, the MTD of paclitaxel was 100 mg/m(2). Both hematological and non-hematological toxicities were mostly mild and manageable. Although paclitaxel is predominantly metabolized in the liver, clearance was decreased in patients with lower estimated glomerular filtration rate. CONCLUSION: Bi-weekly treatment, as described here, is feasible for elderly patients as a conventional regimen, particularly in the outpatient setting, due to its lower toxicity.

Detection of the heterogeneous O-glycosylation profile of MT1-MMP expressed in cancer cells by a simple MALDI-MS method.

BACKGROUND: Glycosylation is an important and universal post-translational modification for many proteins, and regulates protein functions. However, simple and rapid methods to analyze glycans on individual proteins have not been available until recently. METHODS/PRINCIPAL FINDINGS: A new technique to analyze glycopeptides in a highly sensitive manner by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) using the liquid matrix 3AQ/CHCA was developed recently and we optimized this technique to analyze a small amount of transmembrane protein separated by SDS-PAGE. We used the MALDI-MS method to evaluate glycosylation status of membrane-type 1 matrix metalloproteinase (MT1-MMP). O-glycosylation of MT1-MMP is reported to modulate its protease activity and thereby to affect cancer cell invasion. MT1-MMP expressed in human fibrosarcoma HT1080 cells was immunoprecipitated and resolved by SDS-PAGE. After in-gel tryptic digestion of the protein, a single droplet of the digest was applied directly to the liquid matrix on a MALDI target plate. Concentration of hydrophilic glycopeptides within the central area occurred due to gradual evaporation of the sample solution, whereas nonglycosylated hydrophobic peptides remained at the periphery. This specific separation and concentration of the glycopeptides enabled comprehensive analysis of the MT1-MMP O-glycosylation. CONCLUSIONS/SIGNIFICANCE: We demonstrate, for the first time, heterogeneous O-glycosylation profile of a protein by a whole protein analysis using MALDI-MS. Since cancer cells are reported to have altered glycosylation of proteins, this easy-to-use method for glycopeptide analysis opens up the possibility to identify specific glycosylation patterns of proteins that can be used as new biomarkers for malignant tumors.

Rapid quantitative profiling of N-glycan by the glycan-labeling method using 3-aminoquinoline/α-cyano-4-hydroxycinnamic acid.

Protein glycosylation is a crucial phenomenon for understanding protein functions, since its patterns and degree are associated with many biological processes, such as intercellular signaling and immune response. We previously reported a novel glycan-labeling method using a 3-ainoquinoline/α-cyano-4-hydroxycinnamic acid (3-AQ/CHCA) liquid matrix for highly sensitive detection by matrix-assisted laser desorption/ionization (MALDI)-mass spectrometry (MS). In the present study, we examined the practicality of this method for qualitative and quantitative glycan profile analysis. We first investigated the reproducibility of the data for 16 N-glycans prepared from human epidermal growth factor receptor type 2 (HER2). All of the data obtained in intra-assays and interassays were highly correlated with statistical significance (R(2) > 0.9, p < 0.05). In addition, the HER2 glycosylation pattern differed significantly between different breast cancer cell lines SK-BR-3 and BT474 in a comparative analysis of profile data. Finally, the quantitative capability of this method was examined by using PA-labeled monosialylated N-glycan as an internal standard (IS). Using IS for AQ-labeled neutral and sialylated standard glycans, the ion peak intensity was highly linear (R(2) > 0.9) from 0.5 to 5000 fmol. Furthermore, using IS for HER2 N-glycans, all of the N-glycans were highly linear with their dilution factors (R(2) > 0.9). These results suggest that our developed AQ labeling method enabled rapid qualitative and quantitative analyses of glycans. This glycan analysis method should contribute to the field of biomarker discovery and biomedicine in applications such as quality control of biotechnology-based drugs.

Alkylated dihydroxybenzoic acid as a MALDI matrix additive for hydrophobic peptide analysis.

Hydrophobic peptides are generally difficult to detect using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) because the majority of MALDI matrixes are hydrophilic and therefore have a low affinity for hydrophobic peptides. Here, we report on a novel matrix additive, o-alkylated dihydroxybenzoic acid (ADHB), which is a 2,5-dihydroxybenzoic acid (DHB) derivative incorporating a hydrophobic alkyl chain on a hydroxyl group to improve its affinity for hydrophobic peptides, thereby improving MALDI-MS sensitivity. The addition of ADHB to the conventional matrix α-cyano-4-hydroxycinnamic acid (CHCA) improved the sensitivity of hydrophobic peptides 10- to 100-fold. The sequence coverage of phosphorylase b digest was increased using ADHB. MS imaging indicated that hydrophobic peptides were enriched in the rim of a matrix/analyte dried spot when ADHB was used. In conclusion, the addition of ADHB to the standard matrix led to improved sensitivity of hydrophobic peptides by MALDI-MS.

A retrospective analysis comparing the safety and efficacy of chemotherapy in elderly and non-elderly non-small-cell lung cancer patients.

AIM: The number of elderly patients with non-small-cell lung cancer (NSCLC) is increasing in Japan. We retrospectively analyzed and compared the safety and efficacy of chemotherapy in elderly and non-elderly NSCLC patients who received chemotherapy at Shimane University Hospital. METHODS: We carried out a retrospective analysis of survival in a series of 112 NSCLC patients treated from 2004 through 2009. We compared the data from the elderly group (≥ 70 years-of-age, 56 patients) with the non-elderly group (< 70 years-of-age, 56 patients) who had similar characteristics, such as sex and Eastern Cooperative Oncology Group performance status. We analyzed the patient characteristics, therapeutic regimen, dose intensity, toxicity and survival time in both groups. RESULTS: The patient characteristics were comparable between the two groups; however, there was a significant difference between the choice of first-line therapeutic regimen. A platinum-doublet regimen was more frequently used in the non-elderly population (39.3% vs 64.3% for the elderly patients vs the non-elderly patients, respectively; P < 0.01), whereas single agents and epidermal growth factor receptor-tyrosine kinase inhibitors were more frequent in the elderly population (26.8% vs 10.7%, 19.6% vs 7.1%; P < 0.05, respectively). The relative dose intensity was approximately 80% or higher for all regimens, and toxicity was acceptable. The median survival time was 24.4 months and 18.6 months in the elderly and non-elderly groups, respectively. CONCLUSION: This retrospective study suggests that elderly patients can safely receive effective chemotherapy similar to non-elderly patients under careful observation and management.

Rapid sequencing and disulfide mapping of peptides containing disulfide bonds by using 1,5-diaminonaphthalene as a reductive matrix.

MS/MS is indispensable for the amino acid sequencing of peptides. However, its use is limited for peptides containing disulfide bonds. We have applied the reducing properties of 1,5-diaminonaphthalene (1,5-DAN) as a MALDI matrix to amino acid sequencing and disulfide bond mapping of human urotensin II possessing one disulfide bond, and human guanylin possessing two disulfide bonds. 1,5-DAN was used in the same manner as the usual MALDI matrices without any pre-treatment of the peptide, and MS/MS was performed using a matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometer (MALDI QIT TOFMS). The results demonstrated that MS/MS of the molecular ions reduced by 1,5-DAN provided a series of significant b-/y-product ions. All 11 amino acid residues of urotensin II were identified using 1,5-DAN, while only 5 out of 11 residues were identified using 2,5-dihydroxybenzoic acid (DHB); similarly 11 out of 15 amino acid residues of guanylin were identified using 1,5-DAN, while only three were identified using DHB. In addition, comparison of the theoretical and measured values of the mass differences between corresponding MS/MS product ions using 1,5-DAN and DHB narrowed down the possible disulfide bond arrangement candidates. Consequently, 1,5-DAN as a reductive matrix facilitates rapid amino acid sequencing and disulfide mapping for peptides containing disulfide bonds.

Treatment of varicose veins: an assessment of intraoperative and postoperative compression sclerotherapy.

Since thrombotic complications, such as superficial thrombophlebitis and subsequent skin pigmentation, are common after sclerotherapy, we conducted a study to evaluate whether combining sclerotherapy with ligation of varicose veins minimizes complications and what timing for sclerotherapy would be most beneficial-accompanying surgery or several weeks postsurgery. Surgical intervention and compression sclerotherapy were performed consecutively on 111 limbs (group A), and sclerotherapy was performed 28 days after surgical intervention on 87 limbs (group B). The volume of sclerosant used and the frequency of complications (thrombus formation and pigmentation) were analyzed. Plasma levels of thrombin-antithrombin III complex (TAT) and D-dimer (DD), as markers for activation of coagulation, were compared. In group A, the total volume of sclerosant used in patients with complications was significantly higher than that in patients without complications. The frequency of thrombus formation and of pigmentation was significantly lower (p <0.01) in group B (10% and 18%, respectively) than in group A (21% and 37%, respectively). The plasma levels of TAT 7 days after treatment were significantly lower in group B (3.4 +/- 1.2 mg/L) than in group A (4.9 +/- 1.1 mg/L). Performing compression sclerotherapy 28 days after surgical intervention is effective for reducing complications and a good alternative for patients with an underlying hypercoagulable state.