Detection and characterization of variant and modified structures of proteins in blood and tissues by mass spectrometry

MALDI-TOF mass spectrometry profiling of bovine skim milk for subclinical mastitis detection

Introduction

Mastitis is one of most impacting health issues in bovine dairy farming that reduces milk yield and quality, leading to important economic losses. Subclinical forms of the disease are routinely monitored through the measurement of somatic cell count (SCC) and microbiological tests. However, their identification can be tricky, reducing the possibilities of early treatments. In this study, a MALDI-TOF mass spectrometry approach was applied to milk samples collected from cows classified according to the SCC, to identify differences in polypeptide/protein profiles.

Materials and methods

Twenty-nine raw milk samples with SCC >200,000 cell/ml (group H) and 91 samples with SCC lower than 200,000 (group L) were randomly collected from 12 dairy farms. Spectral profiles from skim milk were acquired in the positive linear mode within the 4,000–20,000 m/z mass acquisition range.

Results and discussion

Based on signal intensity, a total of 24 peaks emerged as significant different between the two groups. The most discriminant signals (4,218.2 and 4,342.98 m/z) presented a ROC curve with AUC values higher than 0.8. Classification algorithms (i.e., quick classifier, genetic algorithm, and supervised neural network) were applied for generating models able to classify new spectra (i.e., samples) into the two classes. Our results support the MALDI-TOF mass spectrometry profiling as a tool to detect mastitic milk samples and to potentially discover biomarkers of the disease. Thanks to its rapidity and low-cost, such method could be associated with the SCC measurement for the early diagnosis of subclinical mastitis.

Transthyretin proteoforms of intraocular origin in human subretinal fluid

Understanding the molecular composition of ocular tissues and fluids could inform new approaches to prevalent causes of blindness. Subretinal fluid accumulating between the photoreceptor outer segments and retinal pigment epithelium (RPE) is potentially a rich source of proteins and lipids normally cycling among outer retinal cells and choroid. Herein, intact post-translationally modified proteins (proteoforms) were extracted from subretinal fluids of five patients with rhegmatogenous retinal detachment (RRD), analyzed by tandem mass spectrometry, and compared to published data on these same proteins as synthesized by other organs. Single-nuclei transcriptomic data from non-diseased human retina/RPE were used to identify whether proteins in subretinal fluid were of potential ocular origin. Two human donor eyes with normal maculas were immunoprobed for transthyretin (TTR) with appropriate controls. The three most abundant proteins detected in subretinal fluid were albumin, TTR, and apolipoprotein A-I. Remarkably, TTR relative to the other proteins was more abundant than its serum counterpart, suggestive of TTR being synthesized predominantly locally. Six post-translationally modified protein forms (proteoforms) of TTR were detected, with the relative amount of glutathionylated TTR being much higher in the subretinal fluid (12-43%) than values reported for serum (<5%) and cerebrospinal fluid (0.4-13%). Moreover, a putative glycosylated TTR dimer of 32,428 Da was detected as the fourth most abundant protein. The high abundance of TTR and putative TTR dimer in subretinal fluid was supported by analysis of available single-nuclei transcriptomic data, which showed strong and specific signal for TTR in RPE. Immunohistochemistry further showed strong diffuse TTR immunoreactivity in choroidal stroma that contrasted with vertically aligned signal in the outer segment zone of the subretinal space and negligible signal in RPE cell bodies. These results suggest that TTR in the retina is synthesized intraocularly, and glutathionylation is crucial for its normal function. Further studies on the composition, function, and quantities of TTR and other proteoforms in subretinal fluid could inform mechanisms, diagnostic methods, and treatment strategies for age-related macular degeneration, familial amyloidosis, and other retinal diseases involving dysregulation of physiologic lipid transfer and oxidative stress.

First Report of a Coincidental Discovery of Hb Antibes-Juan-Les-Pins (HBB: c.349_350insGTGTGCTGGCCC) in a Greek Woman

The rare Hb Antibes-Juan-Les-Pins (HBB: c.349_350insGTGTGCTGGCCC) was first reported in France. Hb Antibes-Juan-Les-Pins seems to be an innocuous variant and few published data are available. Heterozygous carriers have mild clinical or hematological findings. The abnormal hemoglobin (Hb) is detected by high performance liquid chromatography (HPLC) or capillary zone electrophoresis (CZE), but confirmation of the variant requires molecular analysis. This is the first description of Hb Antibes-Juan-Les-Pins heterozygosity in a woman of Greek origin.

Exploring the expression bar code of SAA variants for gastric cancer detection

We reported an integrated platform to explore serum protein variant pattern in cancer and its utility as a new class of biomarker panel for diagnosis. On the model study of serum amyloid A (SAA), we employed nanoprobe-based affinity mass spectrometry for enrichment, identification and quantitation of SAA variants from serum of 105 gastric cancer patients in comparison with 54 gastritis patients, 54 controls, and 120 patients from other cancer. The result revealed surprisingly heterogeneous and most comprehensive SAA bar code to date, which comprises 24 SAA variants including SAA1- and SAA2-encoded products, polymorphic isoforms, N-terminal-truncated forms, and three novel SAA oxidized isotypes, in which the variant-specific peptide sequence were also confirmed by LC-MS/MS. A diagnostic model was developed for dimension reduction and computational classification of the 24 SAA-variant bar code, providing good discrimination (AUC = 0.85 ± 3.2E-3) for differentiating gastric cancer group from gastritis and normal groups (sensitivity, 0.76; specificity, 0.81) and was validated with external validation cohort (sensitivity, 0.71; specificity, 0.74). Our platform not only shed light on the occurrence and modification extent of under-represented serum protein variants in cancer, but also suggested a new concept of diagnostic platform by serum protein variant profile.

The epidemiologic transition of thalassemia and associated hemoglobinopathies in southern Taiwan

Since 1993, following the National Thalassemia Major Prevention Program and an increase in immigration and interracial marriages, especially in southern Taiwan, the distribution of hemoglobinopathies may have changed. This study investigates the epidemiologic transition of hemoglobinopathies. We analyzed 1870 specimens collected between 2003 and 2012 in southern Taiwan, used gap-polymerase chain reaction and PCR-restriction fragment length polymorphism-based methods, and confirmed genotypes of hemoglobinopathies by DNA sequencing. We found a 91% reduction in the incidence of thalassemia major compared with samples from between 1986 and 1995. The most common genotypes of α-thalassemia and α Hb variants were the SEA type (69.4%) and Hb Quong Sze (1.54%). The most common genotypes of β-thalassemia and β Hb variants were IVS-II-654 (46.2%) and Hb E (2.2%), respectively. Compared with studies performed in different areas of and time intervals in Taiwan, a higher prevalence of -α^3.7, Hb Quong Sze, and Hb E and a lower prevalence of the SEA type were found in this study. However, the SEA type remained the most common genotype observed. In addition, an increasing number of cases with an -α^3.7 type carrier, Hb Quong Sze carrier, and G^γ(A^γδβ)° were identified following a peak of interracial marriages between 2003 and 2005, reflecting a regional difference and the impact of interracial marriage. In conclusion, global migration and international marriage have changed the distribution of hemoglobinopathies in Taiwan. A more comprehensive prenatal screening for new immigrants with a longer follow-up is warranted.

Comparison of capillary electrophoresis and capillary liquid chromatography coupled to mass spectrometry for the analysis of transthyretin in human serum

Capillary electrophoresis and capillary liquid chromatography coupled to mass spectrometry (CE-MS and CapLC-MS, respectively) are nowadays very suitable techniques for the separation and characterization of intact proteins in biological fluids. In this paper, we compare the performance of both techniques for the analysis of transthyretin (TTR), which is a homotetrameric protein (relative molecular mass (Mr) ∼56,000) involved in different types of amyloidosis. Furthermore, it is also presented a novel sample pretreatment based on immunoprecipitation (IP) using Protein A Ultrarapid Agarose™ (UAPA) magnetic beads (MBs) to purify TTR from serum samples. This novel IP based on MBs allowed the detection of TTR monomeric proteoforms that were not possible to analyze by conventional IP in solution. In addition, UAPA MBs provided many other desirable advantages including higher selectivity and minimal unspecific binding of other proteins. CE-MS and CapLC-MS were applied to analyze serum samples from healthy controls and familial amyloidotic polyneuropathy type I (FAP-I) patients, who suffered from the most common hereditary systemic amyloidosis. Both techniques allowed detecting the same TTR proteoforms, including the mutant TTR (Met 30) variant (variation in relative molecular mass (ΔMr) was +32.07, from wild-type TTR). Migration/retention times and relative quantitation of the different proteoforms were similar and reproducible in both cases, but the limits of detection (LODs) achieved by CE-MS were slightly lower (2-2.5-fold). Some other differences were also found on separation selectivity (migration orders and separation of antibody), peak efficiency, total analysis time, calibration ranges and experimental Mr accuracy.

Artifacts to avoid while taking advantage of top-down mass spectrometry based detection of protein S-thiolation

Bottom-up MS studies typically employ a reduction and alkylation step that eliminates a class of PTM, S-thiolation. Given that molecular oxygen can mediate S-thiolation from reduced thiols, which are abundant in the reducing intracellular milieu, we investigated the possibility that some S-thiolation modifications are artifacts of protein preparation. Cu/Zn-superoxide dismutase (SOD1) was chosen for this case study as it has a reactive surface cysteine residue, which is readily cysteinylated in vitro. The ability of oxygen to generate S-thiolation artifacts was tested by comparing purification of SOD1 from postmortem human cerebral cortex under aerobic and anaerobic conditions. S-thiolation was ∼50% higher in aerobically processed preparations, consistent with oxygen-dependent artifactual S-thiolation. The ability of endogenous small molecule disulfides (e.g. cystine) to participate in artifactual S-thiolation was tested by blocking reactive protein cysteine residues during anaerobic homogenization. A 50-fold reduction in S-thiolation occurred indicating that the majority of S-thiolation observed aerobically was artifact. Tissue-specific artifacts were explored by comparing brain- and blood-derived protein, with remarkably more artifacts observed in brain-derived SOD1. Given the potential for such artifacts, rules of thumb for sample preparation are provided. This study demonstrates that without taking extraordinary precaution, artifactual S-thiolation of highly reactive, surface-exposed, cysteine residues can result.

Post-translational modification by cysteine protects Cu/Zn-superoxide dismutase from oxidative damage

Reactive oxygen species (ROS) are cytotoxic. To remove ROS, cells have developed ROS-specific defense mechanisms, including the enzyme Cu/Zn superoxide dismutase (SOD1), which catalyzes the disproportionation of superoxide anions into molecular oxygen and hydrogen peroxide. Although hydrogen peroxide is less reactive than superoxide, it is still capable of oxidizing, unfolding, and inactivating SOD1, at least in vitro. To explore the relevance of post-translational modification (PTM) of SOD1, including peroxide-related modifications, SOD1 was purified from postmortem human nervous tissue. As much as half of all purified SOD1 protein contained non-native post-translational modifications (PTMs), the most prevalent modifications being cysteinylation and peroxide-related oxidations. Many PTMs targeted a single reactive SOD1 cysteine, Cys111. An intriguing observation was that unlike native SOD1, cysteinylated SOD1 was not oxidized. To further characterize how cysteinylation may protect SOD1 from oxidation, cysteine-modified SOD1 was prepared in vitro and exposed to peroxide. Cysteinylation conferred nearly complete protection from peroxide-induced oxidation of SOD1. Moreover, SOD1 that has been cysteinylated and peroxide oxidized in vitro comprised a set of PTMs that bear a striking resemblance to the myriad of PTMs observed in SOD1 purified from human tissue.

Characterization of superoxide dismutase 1 (SOD-1) by electrospray ionization-ion mobility mass spectrometry

In this paper, we report nano-electrospray ionization-ion mobility mass spectrometry (nano-ESI-IM-MS) characterization of bovine superoxide dismutase (SOD-1) and human SOD-1 purified from erythrocytes. SOD-1 aggregates are characteristic of amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease in humans that could be triggered by dissociation of the native dimeric enzyme (Cu(2),Zn(2)-dimer SOD-1). In contrast to ESI-MS, nano-ESI-IM-MS allowed an extra dimension for ion separation, yielding three-way mass spectra (drift time, mass-to-charge ratio and intensity). Drift time provided valuable structural information related to ion size, which proved useful to differentiate between the dimeric and monomeric forms of SOD-1 under non denaturing conditions. In order to obtain detailed structural information, including the most relevant post-translational modifications, we evaluated several parameters of the IM method, such as sample composition (10 mM ammonium acetate, pH 7) and activation voltages (trap collision energy and cone voltage). Neutral pH and a careful selection of the most appropriate activation voltages were necessary to minimize dimer dissociation, although human enzyme resulted less prone to dissociation. Under optimum conditions, a comparison between monomer-to-dimer abundance ratios of two small sets of blood samples from healthy control and ALS patients demonstrated the presence of a higher relative abundance of Cu,Zn-monomer SOD-1 in patient samples.

Separation and characterization of superoxide dismutase 1 (SOD-1) from human erythrocytes by capillary electrophoresis time-of-flight mass spectrometry

Cu, Zn-superoxide dismutase (SOD-1) is a homodimeric metalloenzyme that has been related to ALS (amyotrophic lateral sclerosis). The majority of ALS cases are sporadic while approximately 10% are inherited (familial ALS, FALS). Mutations in the amino acid sequence of human SOD-1 cause only 25% of the FALS cases, while the explanation for the rest is not clear yet. In this way, several authors have suggested the importance of posttranslational modifications or dimer dissociation on formation of the characteristic fatal intraneuronal SOD-1 aggregates. In this paper, we used capillary electrophoresis-electrospray mass spectrometry with an accurate mass and high-resolution time-of-flight mass spectrometer (CE-TOF-MS) for separation and characterization of standard bovine SOD-1 and human SOD-1 purified from erythrocytes. Two background electrolytes (BGEs) were used for CE-TOF-MS experiments in positive ion mode. An acidic BGE allowed detection of apo-monomer SOD-1, because the metal ions were completely released during the electrophoretic separation. The better sensitivity at acidic pH was especially interesting to detect different isoforms of human SOD-1. In contrast, a neutral BGE provided enhanced conditions for detection of the fully metalated dimeric and monomeric enzyme, but selecting an appropriate fragmentor voltage value in the TOF analyzer was critical to obtain reliable quantitative information. Anyway, only the metalated forms involving the main isoform of human SOD-1 were detected due to the lower sensitivity. Hence, the combination of both methodologies resulted necessary to obtain detailed structural information from the enzyme.

Classification of variant forms of haemoglobin according to the ratio of glycated haemoglobin to glycated albumin

Background

Asymptomatic variant haemoglobin is increasingly being found in the measurement of glycated haemoglobin (HbA1c) for the management of diabetes mellitus. We compared the HbA1c concentrations measured by high-performance liquid chromatography (HPLC) and immunoassay and glycated albumin (GA) concentrations and calculated the respective ratios in order to classify the variant haemoglobin.

Methods

Twenty different haemoglobin variants from 43 subjects were identified by mass spectrometry and DNA analysis. Since GA accurately reflects glycaemic control in patients with variant haemoglobin, we calculated respective ratios of HbA1c and GA. Haemoglobin variants causing a low ratio of HbA1c measured by HPLC (HPLC-HbA1c) to GA with a normal ratio of HbA1c measured by immunoassay (IA-HbA1c) to GA were classified as C1. A further classification of α and β was used with abnormalities of the α chain or β chain in the haemoglobin gene. Other haemoglobin variants were classified as non-C1. Eight diabetic patients with stable glycaemic control were used as controls.

Results

Twenty forms of variant haemoglobins were classified as C1 α (2 variants; I-Interlaken and Hb J-Meerut), C1 β (15 variants) and non-C1 (3 variants; Hb Himeji, Hb Woolwich, Hb Peterborough). Positive correlations between GA and HPLC-HbA1c or IA-HbA1c were seen in the C1 β patients with diabetes mellitus. The regression line between GA and HPLC-HbA1c, but not that between GA and IA-HbA1c, showed a downward shift in comparison with the data obtained from the diabetic controls.

Conclusions

Variant haemoglobin could be classified by calculating the ratios of HPLC-HbA1c, IA-HbA1c and GA.

Advances in hemoglobinopathy detection and identification

Hemoglobin disorders consist of two different groups, the structural hemoglobin variants and the thalassemias. The structural hemoglobin variants typically are based on the point mutations in the alpha- or beta-globin chain that results in a single-amino acid substitution in the corresponding globin chain, whereas thalassemias are caused by quantitative reduction in globin chain synthesis. Various techniques are applied for the laboratory investigation of these diseases, among them mass spectrometry (MS) for the detection and identification of structural hemoglobin variants and array techniques for the thalassemias. In this review, we present in the first part the most important mass spectrometric techniques applied in hemoglobin variant detection and identification and discuss several important aspects of this analysis technique in hematology. In the second part, the DNA analysis techniques used in hemoglobin analysis, such as reverse hybridization or microarray-based comparative genomic hybridization (CGH) techniques, are briefly discussed.

Top-Down Analysis of Small Plasma Proteins Using an LTQ-Orbitrap. Potential for Mass Spectrometry-Based Clinical Assays for Transthyretin and Hemoglobin

Transthyretin (TTR) amyloidosis and hemoglobinopathies are the archetypes of molecular diseases where point mutation characterization is diagnostically critical. We have developed a Top-down analytical platform for variant and/or modified protein sequencing and are examining the feasibility of using this platform for the analysis of hemoglobin/TTR patient samples and evaluating the potential clinical applications. The platform is based on a commercial high resolution hybrid orbitrap mass spectrometer (LTQ-Orbitrap(™)) with automated sample introduction; automated data analysis is performed by our own software algorithm (BUPID topdown).The analytical strategy consists of iterative data capture, first recording a mass profile of the protein(s). The presence of a variant is revealed by a mass shift consistent with the amino acid substitution. Nozzle-skimmer dissociation (NSD) of the protein(s) yields a wide variety of sequence-defining fragment ions. The fragment ion containing the amino acid substitution or modification can be identified by searching for a peak exhibiting the mass shift observed in the protein mass profile. This fragment ion can then be selected for MS/MS analysis in the ion trap to yield sequence information permitting the identification of the variant. Substantial sequence coverage has been obtained in this manner. This strategy allows for a stepwise MS/MS analysis of the protein structure. The sequence information obtained can be supplemented with whole protein NSD fragmentation and MS/MS analysis of specific protein charge states. The analyses of variant forms of TTR and hemoglobin are presented to illustrate the potential of the method.

Multifactorial analysis of affinity-mass spectrometry data from serum protein samples: a strategy to distinguish patients with preeclampsia from matching control individuals

A multifactorial differential analysis of serum proteins using mass spectrometry distinguished samples from pregnant women with severe early-onset preeclampsia (n = 11) from those of control individuals with uneventful pregnancies (n = 13). Serum proteins were fractionated by either their affinities to reversed-phase material coated magnetic beads or by fractionated precipitation. The on-average most abundant ion signals were observed at m/z 9390, 9103, and 8886. The best differentiating ion signals between the two sample groups were found at m/z 13,715, 13,834, and 13,891. The normalized intensities of these ion signals were on-average lower in the preeclampsia group than in the control group. The six ion signal intensities enabled sorting of the individual spectra with high accuracy. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis showed that a protein band migrating just above the 14 kDa marker band contained transthyretin (P02766; M(r) (avg.): 13,761). Densitometric analysis of the transthyretin bands showed lower intensities in the preeclampsia samples with respect to those of the controls. Nephelometric analysis of the serum samples determined the mean concentration of transthyretin in the preeclampsia group were lower (0.16 mg/mL; range: 0.13 to 0.20; SD: 0.03) than that in the control group (0.19 mg/mL; range: 0.14 to 0.22; SD: 0.02), substantiating the role of transthyretin concentration differences in the comparison of the two groups. Altogether, our findings support the theory of preeclampsia being a heterogeneous disorder that might be sub-classified by a defined proteome signature in maternal blood using multifactorial analysis of affinity-fractionated serum samples.

Capillary electrophoresis/mass spectrometry for the separation and characterization of bovine Cu,Zn-superoxide dismutase

The native form of Cu,Zn-superoxide dismutase (SOD-1) is a homodimer that coordinates one Cu(2+) and one Zn(2+) per monomer. Cu(2+) and Zn(2+) ions play crucial roles in enzyme activity and structural stability, respectively. In addition, dimer formation is essential for SOD-1 functionality, and in humans several SOD-1 mutant isoforms have been associated with certain types of amyotrophic lateral sclerosis (ALS), a progressive neurodegenerative disorder. In this paper we used capillary electrophoresis and mass spectrometry to study the different structures of bovine SOD-1. The metal ions of the native enzyme (Cu(2),Zn(2)-dimer SOD-1) were released in acidic medium in order to obtain apo-SOD-1, which is a monomer. Both substances were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and capillary electrophoresis with ultraviolet and electrospray ionization mass spectrometry detection (CE/UV and CE/ESI-MS, respectively). With MALDI-TOF-MS, using matrices of sinapinic acid (SA) or 2,5-dihydroxybenzoic acid (DHB) with or without trifluoroacetic acid (TFA), similar mass spectra were obtained for the metalated and non-metalated samples. In both cases, an average molecular mass corresponding to the apo-monomer SOD-1 was calculated. This finding indicated that the metals were released from the Cu(2),Zn(2)-dimer SOD-1 during sample preparation or ionization. For CE/UV and CE/ESI-MS, two background electrolytes (BGEs) potentially compatible with ESI-MS detection were used, namely 1 M of acetic acid (pH 2.3) and 10 mM of ammonium acetate (pH 7.3). Using a sheath liquid of 2-propanol/water (60:40 v/v), with or without 0.1% v/v of formic acid, CE/ESI-MS sensitivity was enhanced when the acidic BGE and the acidic sheath liquid were used. However, the electrophoretic profiles and the mass spectra obtained suggested that the metals of Cu(2),Zn(2)-dimer SOD-1 were released, which generated the apo-monomer during the electrophoretic separation. The neutral BGE provided enhanced conditions for the detection of the native enzyme. The differences between the mass spectra obtained for the Cu(2),Zn(2)-dimer and the apo-monomer forms were significant and the presence of formic acid in the sheath liquid affected only sensitivity. Our results highlight the importance of selecting appropriate non-denaturing separation and detection conditions to obtain reliable structural information about non-covalent protein complexes by CE/ESI-MS.

Toward an "omic" physiopathology of reactive chemicals: thirty years of mass spectrometric study of the protein adducts with endogenous and xenobiotic compounds

Cancer and degenerative diseases are major causes of morbidity and death, derived from the permanent modification of key biopolymers such as DNA and regulatory proteins by usually smaller, reactive molecules, present in the environment or generated from endogenous and xenobiotic components by the body's own biochemical mechanisms (molecular adducts). In particular, protein adducts with organic electrophiles have been studied for more than 30 [see, e.g., Calleman et al., 1978] years essentially for three purposes: (a) as passive monitors of the mean level of individual exposure to specific chemicals, either endogenously present in the human body or to which the subject is exposed through food or environmental contamination; (b) as quantitative indicators of the mean extent of the individual metabolic processing which converts a non-reactive chemical substance into its toxic products able to damage DNA (en route to cancer induction through genotoxic mechanisms) or key proteins (as in the case of several drugs, pesticides or otherwise biologically active substances); (c) to relate the extent of protein modification to that of biological function impairment (such as enzyme inhibition) finally causing the specific health damage. This review describes the role that contemporary mass spectrometry-based approaches employed in the qualitative and quantitative study of protein-electrophile adducts play in the discovery of the (bio)chemical mechanisms of toxic substances and highlights the future directions of research in this field. A particular emphasis is given to the measurement of often high levels of the protein adducts of several industrial and environmental pollutants in unexposed human populations, a phenomenon which highlights the possibility that a number of small organic molecules are generated in the human organism through minor metabolic processes, the imbalance of which may be the cause of "spontaneous" cases of cancer and of other degenerative diseases of still uncharacterized etiology. With all this in mind, it is foreseen that a holistic description of cellular functions will take advantage of new analytical methods based on time-integrated metabolomic measurements of a new biological compartment, the "adductome," aimed at better understanding integrated organism response to environmental and endogenous stressors.

Plasma protein kinase C (PKC)alpha as a biomarker for the diagnosis of cancers

Protein kinase C (PKC)alpha plays a key role in the differentiation, proliferation and apoptosis of cancer cells, and its activity is higher in cancer cells than in normal cells. In the present study, we investigated the existence of activated PKCalpha in plasma and its possibility for cancer diagnosis. Plasma samples were prepared from xenograft mouse models of cancer and from normal mice. Phosphorylation ratios for a PKCalpha-specific peptide substrate (Alphatomega) were analyzed by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry and activated PKCalpha was identified by western blot analysis. Increased levels of activated PKCalpha were found in the plasma of cancer-bearing mice (U87, A549, A431, HuH-7 and B16 melanoma) compared with the levels found in control mice. Phosphorylation ratios for peptide substrate increased with an increase in tumor size. Moreover, the addition of Ro-31-7549, a highly specific inhibitor of PKCalpha, produced a concentration-dependent reduction of phosphorylation ratios, whereas the non-PKCalpha inhibitors, rottlerin and H-89, did not significantly effect phosphorylation ratios. In addition, the level of activated PKCalpha decreased after cancer resection but increased if the cancer recurred. From these results, we suggest that (i) activated PKCalpha in plasma can be a useful biomarker for the diagnosis of cancers and (ii) the level of activated PKCalpha can be monitored to assess the recurrence of cancer after surgical removal. To our knowledge, this is the first report demonstrating the existence of activated PKCalpha in plasma and its possibility for cancer diagnosis.

SELDI-TOF Mass Spectrometry Evaluation of Variant Transthyretins for Diagnosis and Pathogenesis of Familial Amyloidotic Polyneuropathy

Background: Mass spectrometric analyses are valuable for detection of transthyretin (TTR) variants, which cause familial amyloidotic polyneuropathy (FAP). However, those methods require an immunoprecipitation step with an anti-TTR antibody and are not suitable for quantitative detection. We investigated the usefulness of SELDI-TOF mass spectrometry (MS) without an immunoprecipitation step.

Methods: We used ProteinChips with chromatographic capture formats to detect TTRs. We attempted to correlate the intensity of mixed samples of amyloidogenic TTR (ATTR) V30M to wild-type (WT) TTR. We analyzed the proportion of ATTR V30M in amyloid-laden cardiac tissues from FAP patients, and also evaluated samples from FAP patients with 16 other TTR mutations.

Results: Detection of ATTR required only 3 h of SELDI-TOF MS analysis. We determined that SELDI-TOF MS was suitable for quantitative detection of ATTR V30M and demonstrated that the proportion of ATTR V30M to WT TTR was 46.6% in amyloid-laden cardiac tissue from an FAP patient who died 10 years after liver transplantation. With this method, we identified 12 of 17 TTR variants. Small mass shifts and low concentrations of variants prevented ATTR detection. By changing the analytical conditions, we achieved detection of low concentrations of ATTR Y114C in serum.

Conclusions: SELDI-TOF MS is a reliable tool for quantitative evaluation of TTR variants, in both tissue amyloid deposits and body fluids. This method is useful for the diagnosis and investigation of the pathogenesis of FAP.

Mass spectrometry in the characterization of human genetic N-glycosylation defects

Human genetic diseases that affect N-glycosylation result from the defective synthesis of the N-linked sugar moiety (glycan) of glycoproteins. The role of glycans for proper protein folding and biological functions is illustrated in the variety and severity of clinical manifestations shared by congenital disorders of glycosylation (CDG). This family of inherited metabolic disorders includes defects in the assembly of the oligosaccharide precursor that lead to an under-occupancy of N-glycosylation sites (CDG-I), and defects of glycan remodeling (CDG-II). Mass spectrometry constitutes a key tool for characterization of CDG-I defects by mass resolution of native protein glycoforms that differ for glycosylation-site occupancy. Glycan MS analyses in CDG-II is mandatory to detect whenever possible a repertoire of structures to pinpoint candidate enzymes and genes responsible for the abnormal N-glycan synthesis. In this manuscript, we review the MS applications in the area of CDG and related disorders with a special emphasis on those techniques that have been already applied or might become functional for diagnosis, characterization, and treatment monitoring in some specific conditions.

Probing hemoglobin structure by means of traveling-wave ion mobility mass spectrometry

Hemoglobin (Hb) is a tetrameric noncovalent complex consisting of two alpha- and two beta-globin chains each associated with a heme group. Its exact assembly pathway is a matter of debate. Disorders of hemoglobin are the most common inherited disorders and subsequently the molecule has been extensively studied. This work attempts to further elucidate the structural properties of the hemoglobin tetramer and its components. Gas-phase conformations of hemoglobin tetramers and their constituents were investigated by means of traveling-wave ion mobility mass spectrometry. Sickle (HbS) and normal (HbA) hemoglobin molecules were analyzed to determine whether conformational differences in their quaternary structure could be observed. Rotationally averaged collision cross sections were estimated for tetramer, dimer, apo-, and holo-monomers with reference to a protein standard with known cross sections. Estimates of cross section obtained for the tetramers were compared to values calculated from X-ray crystallographic structures. HbS was consistently estimated to have a larger cross section than that of HbA, comparable with values obtained from X-ray crystallographic structures. Nontetrameric species observed included apo- and holo- forms of alpha- and beta-monomers and heterodimers; alpha- and beta-monomers in both apo- and holo- forms were found to have similar cross sections, suggesting they maintain a similar fold in the gas phase in both the presence and the absence of heme. Heme-deficient dimer, observed in the spectrum when analyzing commercially prepared Hb, was not observed when analyzing fresh blood. This implies that holo-alpha-apo-beta is not an essential intermediate within the Hb assembly pathway, as previously proposed.

Characterization of recombinant protein mutants by top-down sequencing using quadrupole time-of-flight mass spectrometry

Top-down sequencing using quadrupole time-of-flight mass spectrometry is used as a direct way of locating the mutated sites of recombinant proteins and posttranslational modification in a protein. Several mutants of barstar, expressed in E.coli, were confirmed by analyzing the fragmentation pattern of mutants. A contaminant protein, that appeared while purifying mutants of barstar, was identified as acyl carrier protein from E.coli with a posttranslational modification on serine residue, indicating that the protein was biologically active. A mutant of ribosomal protein S6 has been characterized with neutral loss of ammonia at the N-terminal region of the protein. The power of the "top-down" approach in characterizing the mutants of recombinant proteins has been demonstrated.

Rapid and sensitive method for detection of Y402, H402, I62, and V62 variants of complement factor H in human plasma samples using mass spectrometry

PURPOSE

Variations in the complement factor H (CFH) gene are tightly associated with age-related macular degeneration (AMD) across diverse populations. Of the many nonsynonymous coding variants in CFH, two are most strongly associated with increased risk of AMD: isoleucine 62 to valine (I62V) and tyrosine 402 to histidine (Y402H). Detection of these variations in a patient's blood is important for a risk assessment of AMD and disease prognosis. However, traditional methods of genetic analysis cannot be used for measuring CFH allotypes in some sources of human plasma and other biological fluids not containing DNA. The purpose was to develop a protein-based method of detecting CFH allotypes.

METHODS

A combination of a single-step affinity enrichment of CFH, gel separation, and mass spectrometry identification of the CFH peptides spanning amino acids at positions 62 and 402 was used to identify individual CFH allotypes.

RESULTS

The CFH isoforms V62, I62, H402, and Y402 were reliably detected based on identification of tryptic peptides with masses of 1148.59 Da, 1162.60 Da, 2031.88 Da, and 2057.88 Da, respectively, using MALDI-TOF-TOF. The presence or absence pattern of these peptides in mass spectra of different CFH samples robustly correlated with all nine genotypes of CFH, as a result of variations at positions 62 and 402.

CONCLUSIONS

A rapid and sensitive method has been developed for detection of V62, I62, H402, and Y402 variants of CFH in human plasma samples using mass spectrometry. This method can be used in clinical laboratories equipped with a basic inexpensive mass spectrometer capable of performing peptide fingerprinting.

Detection of citrullinated proteins in synovial fluids derived from patients with rheumatoid arthritis by proteomics-based analysis

BACKGROUND

Rheumatoid arthritis (RA) is the most common inflammatory joint disease. The aetiology of RA remains unknown, but autoimmune responses are considered to play an important role in the disease pathophysiology. Currently available data suggests that the process of diagnosing RA may benefit from testing for anticyclic citrullinated peptides. Identification of the presence of citrullinated proteins in rheumatoid synovial fluids is important for the elucidation of the aetiology of RA as well as in the differential diagnosis of rheumatic-related diseases.

METHODS

A proteomics-based approach using electrophoresis/mass spectrometry was applied to identify the citrullinated proteins in synovial fluids from patients with RA. Synovial fluids from patients with RA were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot analysis to detect the citrullinated proteins. Identification bands were then subjected to mass spectrometry.

RESULTS

Three proteins - citrullinated fibrinogen, citrullinated fibronectin and citrullinated vimentin - in synovial fluids from RA patients were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

CONCLUSIONS

Proteomics-based analysis can be used to detect citrullinated proteins in synovial fluids from RA patients.

Mass Spectrometry: A Tool for Enhanced Detection of Hemoglobin Variants

Background: More than 900 hemoglobin (Hb) variants are currently known. Common techniques used in Hb analysis are electrophoretic and chromatographic assays. In our laboratory, we routinely apply chromatographic methods. To ascertain whether Hb variants are missed with our procedures, we additionally analyzed all samples with mass spectrometry (MS).

Methods: Database evaluation was performed using all entries made in the Hb variant database HbVar, and possible Hb variants were calculated based on DNA variations. During a 5-year period, we analyzed 2105 lysates with cation-exchange HPLC (PolyCAT A column) and reversed-phase HPLC and additionally with electrospray ionization or MALDI-TOF MS. Globin chains were identified by their molecular masses.

Results: Database evaluation revealed that 43.2% of all possible Hbα- and β-chain variants were found to date (considering only single-point mutations). Currently, 68.2% of the possible charge difference variants and only 28.7% of the neutral variants are found. Among 2105 Hb samples we identified 4 samples with Hb variants that were detected only with the MS method; 2 were new Hb variants (Hb Zurich-Hottingen and Hb Zurich-Langstrasse). With cation-exchange HPLC, 1 sample was found to be a β-thalassemia and was identified by MS to be a β-variant (Hb Malay). More common variants, such as Hb C, Hb D, and Hb E, and thalassemias could not be detected with the MS method.

Conclusions: Application of MS improves the sensitivity of Hb analysis. The combination of MS with electrophoretic and chromatographic methods is optimal for the detection of Hb variants.

Self-assembled monolayers for MALDI-TOF mass spectrometry for immunoassays of human protein antigens

This paper reports a method that combines self-assembled monolayers with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to perform immunoassays on clinical samples. The immunosensors are prepared by immobilizing His-tagged protein G (or A) to a monolayer presenting the Ni2+ chelates, followed by immobilization of IgG antibodies with specificity for the intended analyte. The SAMDI mass spectrometry technique confirms the presence of the two proteins on the immunosensor and additionally provides a label-free analysis of antigens that bind to the sensor. This paper reports examples of detecting several proteins from human serum, including multianalyte assays that resolve each analyte according to their mass-to-charge ratio in the SAMDI spectra. An example is described wherein SAMDI is used to identify a proteolytic fragment of cystatin C in cerebral spinal fluids from patients diagnosed with multiple sclerosis. The SAMDI-TOF immunoassay, which combines well-defined surface chemistries for the selective and reproducible localization of analytes with mass spectrometry for label-free detection of analytes, may offer an alternative methodology to address many of the issues associated with standardized clinical diagnostics.