Biomarker Characterization by MALDI-TOF/MS

Technical considerations regarding saliva sample collection to achieve comparable protein identification and detection via one- and two-dimensional gel electrophoresis among humans

Background and aims

Recently, demands towards identifying various molecules in support of stress detection and potential clinical utilization are dramatically increasing. Moreover, the accuracy with which researchers quantify these informative molecules is now far more improved when compared to the past. As RNA or protein markers are conventionally detected via repeated invasive procedures from blood, it is critical to develop secure technologies to obtain the desired information via less stressful methodologies, such as saliva collection. Moreover, for superb interpretation, it became equally significant to obtain the information from the same exact specimen. RNA is easily degradable, thus it is paramount to supplement the samples with protective agents, such as RNAlater, to achieve accurate quantitative results.

Methods

In our research we investigated whether and how this commonly applied RNA protection procedure influences protein and peptide separation of the human saliva via quantitative two-dimensional protein electrophoresis.

Results

Our results revealed, in contrary to previously published data regarding plasma, the addition of RNAlater to saliva samples negatively influences isoelectric focusing and protein detection. We equally found the application oftentimes employed referred to as selective precipitation and reduction-alkylation, partially rescued separation, however, with a significant loss in protein yield and quality when compared to untreated samples.

Conclusion

Our results suggest collection of human saliva for biomarker identification must be performed with extreme diligence. We propose application of RNAlater should be avoided and snap freezing of the collected saliva is recommended when joint protein and RNA quantification is the ultimate goal.

Discriminating fingerprints of chronic neuropathic pain following spinal cord injury using artificial neural networks and mass spectrometry analysis of female mice serum

Spinal cord injury (SCI) often leads to central neuropathic pain, a condition associated with significant morbidity and is challenging in terms of the clinical management. Despite extensive efforts, identifying effective biomarkers for neuropathic pain remains elusive. Here we propose a novel approach combining matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with artificial neural networks (ANNs) to discriminate between mass spectral profiles associated with chronic neuropathic pain induced by SCI in female mice. Functional evaluations revealed persistent chronic neuropathic pain following mild SCI as well as minor locomotor disruptions, confirming the value of collecting serum samples. Mass spectra analysis revealed distinct profiles between chronic SCI and sham controls. On applying ANNs, 100% success was achieved in distinguishing between the two groups through the intensities of m/z peaks. Additionally, the ANNs also successfully discriminated between chronic and acute SCI phases. When reflexive pain response data was integrated with mass spectra, there was no improvement in the classification. These findings offer insights into neuropathic pain pathophysiology and underscore the potential of MALDI-TOF MS coupled with ANNs as a diagnostic tool for chronic neuropathic pain, potentially guiding attempts to discover biomarkers and develop treatments.

A Graphene-Coated Silicon Wafer Plate Improves the Sensitivity and Reproducibility of MALDI-TOF MS Analysis of Proteins

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is widely used to analyze small and large molecules. However, proteins are difficult to analyze with MALDI-TOF MS in clinical applications because of their low ionization efficiency and heterogeneous crystallization with the matrix on the sample spots. Here, we investigate the potential of a customized graphene-coated silicon wafer (G/SiO2) plate for MALDI-TOF MS analysis of a clinically important protein, KPC-2, in comparison with a conventional stainless steel (SUS) plate. Our results demonstrate that the G/SiO2 plate outperforms the SUS plate in terms of sensitivity, reproducibility, and mass accuracy/precision across a wide range of molecular weights, even with highly complex samples. Furthermore, a five-day robustness test confirms the practical applicability of the G/SiO2 plate for the reliable identification of target protein(s) in MALDI-TOF MS analysis. Overall, our findings suggest that the use of the G/SiO2 plate holds great potential for improving the sensitivity and reproducibility of MALDI-TOF MS analysis for the identification of proteins, making it a promising tool for clinical applications.

Target-allele-specific probe single-base extension (TASP-SBE): a novel MALDI-TOF-MS strategy for multi-variants analysis and its application in simultaneous detection of α-/β-thalassemia mutations

Single-nucleotide variants (SNVs) and copy number variations (CNVs) are the most common genomic variations that cause phenotypic diversity and genetic disorders. MALDI-TOF-MS is a rapid and cost-effective technique for multi-variant genotyping, but it is challenging to efficiently detect CNVs and clustered SNVs, especially to simultaneously detect CNVs and SNVs in one reaction. Herein, a novel strategy termed Target-Allele-Specific Probe Single-Base Extension (TASP-SBE) was devised to efficiently detect CNVs and clustered SNVs with MALDI-TOF-MS. By comprehensive use of traditional SBE and TASP-SBE strategies, a MALDI-TOF-MS assay was also developed to simultaneously detect 28 α-/β-thalassemia mutations in a single reaction system, including 4 α-thalassemia deletions, 3 HBA and 21 HBB SNVs. The results showed that all 28 mutations were sensitively identified, and the CNVs of HBA/HBB genes were also accurately analyzed based on the ratio of peak height (RPH) between the target allele and reference gene. The double-blind evaluation results of 989 thalassemia carrier samples showed a 100% concordance of this assay with other methods. In conclusion, a one-tube MALDI-TOF-MS assay was developed to simultaneously genotype 28 thalassemia mutations. This novel TASP-SBE was also verified a practicable strategy for the detection of CNVs and clustered SNVs, providing a feasible approach for multi-variants analysis with MALDI-TOF-MS technique.

Artificial Neural Networks Coupled with MALDI-TOF MS Serum Fingerprinting To Classify and Diagnose Pathological Pain Subtypes in Preclinical Models

Pathological pain subtypes can be classified as either neuropathic pain, caused by a somatosensory nervous system lesion or disease, or nociplastic pain, which develops without evidence of somatosensory system damage. Since there is no gold standard for the diagnosis of pathological pain subtypes, the proper classification of individual patients is currently an unmet challenge for clinicians. While the determination of specific biomarkers for each condition by current biochemical techniques is a complex task, the use of multimolecular techniques, such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), combined with artificial intelligence allows specific fingerprints for pathological pain-subtypes to be obtained, which may be useful for diagnosis. We analyzed whether the information provided by the mass spectra of serum samples of four experimental models of neuropathic and nociplastic pain combined with their functional pain outcomes could enable pathological pain subtype classification by artificial neural networks. As a result, a simple and innovative clinical decision support method has been developed that combines MALDI-TOF MS serum spectra and pain evaluation with its subsequent data analysis by artificial neural networks and allows the identification and classification of pathological pain subtypes in experimental models with a high level of specificity.

Portable Colorimetric Device with Commercial Microplates for Quantitative Detection of Urine Biomarkers: Design, Development, and Clinical Evaluation

Urine biomarkers are important in monitoring diseases related to human kidney function. The current processes for measuring biomarker levels in urine samples require patients to regularly visit clinical facilities, which is inconvenient and sometimes impossible for patients in rural areas. Therefore, portable analysis devices for the measurement of urine biomarkers are urgently requested. In this study, a portable platform using colorimetry, a common and simple-to-operate chemical analysis technique, was developed to measure urine biomarkers. The device, using commercial test kits as recognising reagents and a 96-well microplate as a solution container, provides quantitative measures of biomarker concentration. Moreover, the proposed device introduces a calibration method to minimise the dependence of regular maintenance. The device's performance was evaluated with urine from 73 renal patients and its results matched with clinical results well. The device has the potential for measuring urine creatinine, in addition to performing a variety of commercial assays for biomarker detection in human body fluids in general.

Evaluation of the diagnostic value of serum-based proteomics for colorectal cancer

BACKGROUND

Colorectal cancer (CRC) is a highly malignant cancer with a high incidence and mortality in China. It is urgent to find a diagnostic marker with higher sensitivity and specificity than the traditional approaches for CRC diagnosis.

AIM

To provide new ideas for the diagnosis of CRC based on serum proteomics.

METHODS

Specimens from 83 healthy people, 62 colon polyp (CRP) patients, and 101 CRC patients were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The diagnostic value of the profiles of differentially expressed proteins was then analyzed.

RESULTS

Compared with the healthy control group, CRC patients had elevated expression of 5 proteins and reduced expression of 14 proteins. The area under the curve (AUC) for a differentially expressed protein with a mass-to-charge ratio of 2022.34 was the largest; the AUC was 0.843, which was higher than the AUC of 0.717 observed with carcinoembryonic antigen (CEA), and the sensitivity and specificity of this identified marker were 75.3% and 79.5%, respectively. After cross-validation, the accuracy of diagnosis using levels of this differentially expressed protein was 82.37%. Compared with the CRP group, the expression of 3 proteins in the serum of CRC patients was elevated and 11 proteins were expressed at reduced levels. Proteins possessing mass-to-charge ratio values of 2899.38 and 877.3 were selected to establish a classification tree model. The results showed that the accuracy of CRC diagnosis was 89.5%, the accuracy of CRP diagnosis was 81.6%, and the overall accuracy of this approach was 86.3%. The overall sensitivity and specificity of diagnosis using the proteomics approach were 81.8% and 66.75%, respectively. The sensitivities and specificities of diagnoses based on CEA and carbohydrate antigen 19-9 expression were 55.6% and 91.3% and 65.4% and 65.2%, respectively.

CONCLUSION

We demonstrated that serum proteomics may be helpful for the detection of CRC, and it may assist clinical practice for CRC diagnosis.

MALDI-TOF MS: application in diagnosis, dereplication, biomolecule profiling and microbial ecology

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized scientific research over the past few decades and has provided a unique platform in ongoing technological developments. Undoubtedly, there has been a bloom chiefly in the field of biological sciences with this emerging technology, and has enabled researchers to generate critical data in the field of disease diagnoses, drug development, dereplication. It has received well acceptance in the field of microbial identification even at strain level, as well as diversified field like biomolecule profiling (proteomics and lipidomics) has evolved tremendously. Additionally, this approach has received a lot more attention over conventional technologies due to its high throughput, speed, and cost effectiveness. This review aims to provide a detailed insight regarding the application of MALDI-TOF MS in the context of medicine, biomolecule profiling, dereplication, and microbial ecology. In general, the expansion in the application of this technology and new advancements it has made in the field of science and technology has been highlighted.

Rapid Detection of Viral Envelope Lipids Using Lithium Adducts and AP-MALDI High-Resolution Mass Spectrometry

There is an unmet need to develop analytical strategies that not only characterize the lipid composition of the viral envelope but also do so on a time scale that would allow for high-throughput analysis. With that in mind, we report the use of atmospheric pressure (AP) matrix-assisted laser desorption/ionization (MALDI) high-resolution mass spectrometry (HRMS) combined with lithium adduct consolidation to profile total lipid extracts rapidly and confidently from enveloped viruses. The use of AP-MALDI reduced the dependency of using a dedicated MALDI mass spectrometer and allowed for interfacing the MALDI source to a mass spectrometer with the desired features, which included high mass resolving power (>100000) and tandem mass spectrometry. AP-MALDI combined with an optimized MALDI matrix system, featuring 2',4',6'-trihydroxyacetophenone spiked with lithium salt, resulted in a robust and high-throughput lipid detection platform, specifically geared to sphingolipid detection. Application of the developed workflow included the structural characterization of prominent sphingolipids and detection of over 130 lipid structures from Influenza A virions. Overall, we demonstrate a high-throughput workflow for the detection and structural characterization of total lipid extracts from enveloped viruses using AP-MALDI HRMS and lithium adduct consolidation.

Serum profiling of anorexia nervosa: A 1H NMR-based metabolomics study

Our understanding of pathophysiological mechanisms underlying anorexia nervosa (AN) is incomplete. The aim was to conduct a metabolomics profiling of serum samples from women with AN (n = 65), women who have recovered from AN (AN-REC, n = 65), and age-matched healthy female controls (HC, n = 65). Serum concentrations of 21 metabolites were measured using proton nuclear magnetic resonance (¹H NMR). We used orthogonal partial least-squares discriminant analysis (OPLS-DA) modeling to assign group classification based on the metabolites. Analysis of variance (ANOVA) was used to test for metabolite concentration differences across groups. The OPLS-DA model could distinguish between the AN and HC groups (p = 9.05 × 10-11 R2Y = 0.36, Q2 = 0.37) and between the AN-REC and HC groups (p = 8.47 × 10-6, R2Y = 0.36, Q2 = 0.24,), but not between the AN and AN-REC groups (p = 0.63). Lower methanol concentration in the AN and AN-REC group explained most of the variance. Likewise, the strongest finding in the univariate analyses was lower serum methanol concentration in both AN and AN-REC compared with HC, which withstood adjustment for body mass index (BMI). We report for the first time lower serum concentrations of methanol in AN. The fact that low methanol was also found in recovered AN suggests that low serum concentration of methanol could either be trait marker or a scar effect of AN.

Optical-Based Biosensors and Their Portable Healthcare Devices for Detecting and Monitoring Biomarkers in Body Fluids

The detection and monitoring of biomarkers in body fluids has been used to improve human healthcare activities for decades. In recent years, researchers have focused their attention on applying the point-of-care (POC) strategies into biomarker detection. The evolution of mobile technologies has allowed researchers to develop numerous portable medical devices that aim to deliver comparable results to clinical measurements. Among these, optical-based detection methods have been considered as one of the common and efficient ways to detect and monitor the presence of biomarkers in bodily fluids, and emerging aggregation-induced emission luminogens (AIEgens) with their distinct features are merging with portable medical devices. In this review, the detection methodologies that use optical measurements in the POC systems for the detection and monitoring of biomarkers in bodily fluids are compared, including colorimetry, fluorescence and chemiluminescence measurements. The current portable technologies, with or without the use of smartphones in device development, that are combined with optical biosensors for the detection and monitoring of biomarkers in body fluids, are also investigated. The review also discusses novel AIEgens used in the portable systems for the detection and monitoring of biomarkers in body fluid. Finally, the potential of future developments and the use of optical detection-based portable devices in healthcare activities are explored.

Peptidomic changes of saliva after nonsurgical treatment of stage I / II generalized periodontitis

OBJECTIVE

To explore the changes of peptidome profiles of saliva, serum and gingival crevicular fluid (GCF) before and after nonsurgical periodontal treatment in patients with generalized periodontitis (stage I / II).

SUBJECTS AND METHODS

Saliva, serum and GCF samples were collected from 17 patients at baseline (T₀ ), one week after ultrasonic supragingival scaling (T₁ ) and eight weeks after subgingival scaling and root planning (T₂ ). Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) was carried out to detect changes in peptidomic profiles. Then nano-liquid chromatography-electrospray ionization-tandem mass spectrometry (nano-LC/ESI-MS/MS) was performed to identify potential peptide biomarkers.

RESULTS

Most of the peptides from the patients exhibited a decreasing trend from the time point of pre-treatment to that of post-treatment. Cluster analysis and scatter plots using these peptides indicated that salivary peptidome has an acceptable capability of reflecting the status of stage I / II generalized periodontitis. Seven of these peptides were successfully identified as α-1-antitrypsin, immunoglobulin κ variable 4-1, haptoglobin and immunoglobulin heavy constant γ2.

CONCLUSIONS

Certain peptides in saliva, serum and GCF were down-regulated after nonsurgical periodontal treatment, demonstrating the application prospects of saliva in monitoring and surveillance of periodontal diseases in both clinical settings and communities.

Mass Spectrometry: A Powerful Method for Monitoring Various Type of Leukemia, Especially MALDI-TOF in Leukemia's Proteomics Studies Review

Recent success in studying the proteome, as a source of biomarkers, has completely changed our understanding of leukemia (blood cancer). The identification of differentially expressed proteins, such as relapse and drug resistance proteins involved in leukemia by using various ionization sources and mass analyzers of mass spectrometry techniques, has helped scientists find better diagnosis, prognosis, and treatment strategies. With the aid of this powerful analytical technique, we can investigate the qualification/quantification of proteins, protein-protein interactions, post-translational modifications, and find the correlation between proteins and their genes with the hope of finding the missing parts of the successful therapy puzzle. In this review, we followed different MS sources and analyzers which used for monitoring various type of leukemia, then focused on MALDI-TOF MS as a quick and reliable method for studying proteins. Due to several review published for other techniques, the present review is the first work in this field. Also, by classifying more than 400 proteins, we have found 42 proteins are involved in two or three different stages of leukemia. Finally, we have suggested six specific biomarkers for AML, one for ALL, three biomarkers with a role in the etiology of leukemia and 13 markers with the potential for further studies.

A Meta-Analysis of Proteomic Blood Markers of Colorectal Cancer

BACKGROUND

Early diagnosis will significantly improve the survival rate of colorectal cancer (CRC); however, the existing methods for CRC screening were either invasive or inefficient. There is an emergency need for novel markers in CRC's early diagnosis. Serum proteomics has gained great potential in discovering novel markers, providing markers that reflect the early stage of cancer and prognosis prediction of CRC. In this paper, the results of proteomics of CRC studies were summarized through a meta-analysis in order to obtain the diagnostic efficiency of novel markers.

METHODS

A systematic search on bibliographic databases was performed to collect the studies that explore blood-based markers for CRC applying proteomics. The detection and validation methods, as well as the specificity and sensitivity of the biomarkers in these studies, were evaluated. Newcastle- Ottawa Scale (NOS) case-control studies version was used for quality assessment of included studies.

RESULTS

Thirty-four studies were selected from 751 studies, in which markers detected by proteomics were summarized. In total, fifty-nine proteins were classified according to their biological function. The sensitivity, specificity, or AUC varied among these markers. Among them, Mammalian STE20-like protein kinase 1/ Serine threonine kinase 4 (MST1/STK4), S100 calcium-binding protein A9 (S100A9), and Tissue inhibitor of metalloproteinases 1 (TIMP1) were suitable for effect sizes merging, and their diagnostic efficiencies were recalculated after merging. MST1/STK4 obtained a sensitivity of 68% and a specificity of 78%. S100A9 achieved a sensitivity of 72%, a specificity of 83%, and an AUC of 0.88. TIMP1 obtained a sensitivity of 42%, a specificity of 88%, and an AUC of 0.71.

CONCLUSION

MST1/STK4, S100A9, and TIMP1 showed excellent performance for CRC detection. Several other markers also presented optimized diagnostic efficacy for CRC early detection, but further verification is still needed before they are suitable for clinical use. The discovering of more efficient markers will benefit CRC treatment.

Proteomic profiling of biomarkers by MALDI-TOF mass spectrometry for the diagnosis of tracheobronchial stenosis after tracheobronchial tuberculosis

Tracheobronchial tuberculosis (TB) leads to airway stenosis, irreversible airway damage and even death. The present study aimed to identify biomarkers for the diagnosis of tracheobronchial stenosis (TBS) secondary to tracheobronchial TB. A cohort was recruited, including patients with TBS after tracheobronchial TB, TBS after tracheal intubation or tracheotomy (TIT) and no stenosis of early-stage lung cancer,. Proteomic profiling was performed to gain insight into the mechanisms of the pathological processes. Differentially expressed proteins in the serum and bronchial alveolar lavage fluid (BALF) from patients were detected by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Subsequently, ELISA was performed to validate the changes of protein levels in an additional cohort. MALDI-TOF MS revealed that 8 peptides in the serum, including myeloid-associated differentiation marker, keratin type I cytoskeletal 18, fibrinogen α-chain, angiotensinogen (AGT), apolipoprotein A-I (APOAI), clusterin and two uncharacterized peptides, and nine peptides in BALF, including argininosuccinate lyase, APOAI, AGT and five uncharacterized peptides, were differentially expressed (molecular-weight range, 1,000-10,000 Da) in the TB group compared with the TIT group. The ELISA results indicated that the changes in the protein levels had a similar trend as those identified by proteomic profiling. In conclusion, the present study identified proteins that may serve as potential biomarkers and provide novel insight into the molecular mechanisms underlying TBS after tracheobronchial TB.

The stability of children's salivary peptidome profiles in response to short-term beverage consumption

BACKGROUND

Salivary peptidome profiling analysis has advantages of simplicity and non-invasiveness and great potentiality for screening, monitoring or primary diagnosis of diseases, but may be subjected to change against interferences like diet.

METHODS

We conducted a 5-day study to investigate the influence of 3 kinds of beverages (orange juice, sugar-free tea, and sugar-free liquid yoghurt; water as control) on children's salivary peptidome using mass spectrometry techniques.

RESULTS

All the groups shared a relatively stable pattern in heatmaps during the experimental days. Principal component analysis plot presented slight shifts in all the intervention groups between the baseline and intervention period while samples were not distinctly separated by date. The numbers of significantly changed peptides after short-term orange juice and tea intervention were four and three, respectively, while no changes occurred in the yoghurt group and control. Four of these peptides were identified as histatin-3, collagen alpha-1(IV) chain, zinc finger protein 805, and quinolinate synthase A.

CONCLUSIONS

Salivary peptidome has its own stability against beverage intervention, confirming the feasibility and validity of using it as a potential reference for the healthy state of the body, with diet habits recorded and considered as a confounder if necessary.

Rapid Proteomic Profiling by MALDI-TOF Mass Spectrometry for Better Brain Tumor Classification

PURPOSE

Glioblastoma is one of the most aggressive primary brain cancers. The precise grading of tumors is important to adopt the best follow-up treatment but complementary methods to histopathological diagnosis still lack in achieving an unbiased and reliable classification.

EXPERIMENTAL DESIGN

To progress in the field, a rapid Matrix Assisted Laser Desorption Ionization - Time of Flight Mass spectrometry (MALDI-TOF MS) protocole, devised for the identification and taxonomic classification of microorganisms and based on the analysis of whole cell extracts, was applied to glioma cell lines.

RESULTS

The analysis of different human glioblastoma cell lines permitted to identify distinct proteomic profiles thus demonstrating the ability of MALDI-TOF to distinguish different malignant cell types.

CONCLUSIONS AND CLINICAL RELEVANCE

In the study, the authors showed the ability of MALDI-TOF profiling to discriminate glioblastoma cell lines, demonstrating that this technique could be used in complement to histological tumor classification. The proposed procedure is rapid and inexpensive and could be used to improve brain tumors classification and help propose a personalized and more efficient treatment.

Screening and identification of serum biomarkers of osteoarticular tuberculosis based on mass spectrometry

BACKGROUND

In view of the current difficulty of clinically diagnosing osteoarticular tuberculosis, our aim was to use mass spectrometry to establish diagnostic models and to screen and identify serum proteins which could serve as potential diagnostic biomarkers for early detection of osteoarticular tuberculosis.

METHODS

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to select an osteoarticular tuberculosis-specific serum peptide profile and establish diagnostic models. Further, liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to identify potential serum biomarkers that could be used for auxiliary diagnosis of osteoarticular tuberculosis, and then clinical serum samples were used to verify these biomarkers by enzyme-linked immunosorbent assay (ELISA).

RESULTS

We established four diagnostic models that can distinguish osteoarticular tuberculosis from rheumatoid arthritis, ankylosing spondylitis, osteoarticular infections, and healthy adults. The models were osteoarticular tuberculosis-rheumatoid arthritis, osteoarticular tuberculosis-ankylosing spondylitis, osteoarticular tuberculosis-osteoarticular infections, and osteoarticular tuberculosis-healthy adult, and their accuracy was 76.78%, 79.02%, 83.77%, and 88.16%, respectively. Next, we selected and identified 18 proteins, including complement factor H-related protein 1 (CFHR1) and complement factor H-related protein 2 (CFHR2), which were upregulated in the tuberculosis group only.

CONCLUSIONS

We successfully established four diagnostic models involving osteoarticular tuberculosis, rheumatoid arthritis, ankylosing spondylitis, osteoarticular infections, and healthy adults. Furthermore, we found that CFHR1 and CFHR2 may be two valuable auxiliary diagnostic indicators for osteoarticular tuberculosis. These results provide reference values for rapid and accurate diagnosis of osteoarticular tuberculosis.

Molecular diagnostics in oral cancer and oral potentially malignant disorders-A clinician's guide

Current risk stratification of individuals for the development of oral squamous cell carcinoma (OSCC), including those with oral potentially malignant disorders (OPMD), remains based on clinical detection of visibly abnormal mucosa and tissue biopsy with histological assessment for the presence of OSCC or oral epithelial dysplasia (OED). In OPMD, the presence of OED remains the only prognostic tool used in standard care for the development of future OSCC, despite its ample limitations. There is assured potential that the analysis of the genome, transcripts and proteome can provide insight into what is occurring at a cellular level preceding the appearance of clinically observable change. The landscape of the role of the genome and its transcriptome on the development of OSCC and relationships with OPMDs are immense with exploration occurring on several fronts. For clinicians involved in the diagnosis and care of patients with OSCC and OPMD, understanding of commonly used molecular diagnostic techniques is imperative to gain useful insight from the expanding literature investigating the development of OSCC and the relationship with the clinical presentations which encompass OPMDs. Here we present an introduction to molecular diagnostic methods used in the study of OSCC and OPMD.

Kininogen-1 as a protein biomarker for schizophrenia through mass spectrometry and genetic association analyses

BACKGROUND

Schizophrenia (SCZ) is a complex and severe mental illness. There is a lack of effective biomarkers for SCZ diagnosis. The aim of this study was to explore the possibility of using serum peptides for the diagnosis of SCZ as well as analyze the association of variants in genes coding for these peptides and SCZ.

METHODS

After bead-based fractionation, the matrix-assisted laser desorption ionization/time-of-flight mass spectrometry technique was used to identify peptides that showed different expressions between 166 SCZ patients and 201 healthy controls. Differentially expressed peptides were verified in a second set of samples (81 SCZ patients and 103 healthy controls). The association of SCZ and three tagSNPs selected in genes coding for differentially expressed peptides was performed in 1,126 SCZ patients and 1,168 controls.

RESULTS

The expression level of peptides with m/z 1,945.07 was significant lower in SCZ patients than in healthy controls (P < 0.000001). The peptide with m/z 1,945.07 was confirmed to be a fragment of Kininogen-1. In the verification tests, Kininogen-1 had a sensitivity of 95.1% and a specificity of 97.1% in SCZ prediction. Among the three tagSNPs (rs13037490, rs2983639, rs2983640) selected in the Cystatin 9 gene (CST9) which encodes peptides including Kininogen-1, tagSNP rs2983640 had its genotype distributions significantly different between SCZ patients and controls under different genetic models (P < 0.05). Haplotypes CG (rs2983639-rs2983640) and TCG (rs13037490-rs2983639-rs2983640) were significantly associated with SCZ (CG: OR = 1.21, 95% CI [1.02-1.44], P = 0.032; TCG: OR = 24.85, 95% CI [5.98-103.17], P < 0.0001).

CONCLUSIONS

The present study demonstrated that SCZ patients had decreased expression of Kininogen-1 and genetic variants in Kininogen-1 coding gene CST9 were significantly associated with SCZ. The findings from both protein and genetic association studies suggest that Kininogen-1 could be a biomarker of SCZ.

Nanoporous silica coupled MALDI-TOF MS detection of Bence-Jones proteins in human urine for diagnosis of multiple myeloma

Bence-Jones protein is a biomarker in urine for multiple myeloma. Traditional methods for urine Bence-Jones protein detection are either less-sensitive or laborious. Herein, we describe a new method for the detection of urine Bence-Jones protein using nanoporous materials and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Macroporous ordered silica foams (MOSF) were used to enrich proteins in urine, and then the materials-proteins composites were analyzed by MALDI-TOF MS. Based on the presence of specific mass spectrometric signals, Bence-Jones protein can be detected for the diagnosis of multiple myeloma. Twenty-one clinical positive and twenty-seven clinical negative urine samples were analyzed by the method. High sensitivity (95.24%, 20/21) and specificity (100%, 27/27) for the diagnosis of multiple myeloma were achieved. Compared to other methods for multiple myeloma diagnosis, e.g. immunofixation electrophoresis and immunonephelometry, our approach is more rapid, economical and convenient, which can be a new choice for the clinical diagnosis of Bence-Jones protein related diseases.

Assessment of Proteolytic Activities in the Bone Marrow Microenvironment

During cytokine- or chemotherapy-induced hematopoietic stem cell (HSC) mobilization, a highly proteolytic microenvironment can be observed in the bone marrow that has a strong influence on adhesive and chemotactic interactions of HSC with their niches. The increase of proteases during mobilization goes along with a decrease of endogenous protease inhibitors. Prominent members of the proteases involved in HSC mobilization belong to the families of matrix metalloproteinases and cathepsins, which are able to degrade chemokines/cytokines, extracellular matrix components, and membrane-bound adhesion receptors. To determine the functional activity of different proteolytic enzymes, zymographic analyses with different substrates and pH conditions can be employed. An involvement of cysteine cathepsins can be determined by the "active site labeling" technique using a modified inhibitor irreversibly binding to the active center of the enzymes. Intact or degraded chemokines and cytokines, which fall into the range between 1000 and 20,000 Da, can readily be detected by MALDI-TOF analysis. These three methods can help to detect proteolytic activities directly involved in the mobilization process.

Venomous Arachnid Diagnostic Assays, Lessons from Past Attempts

Diagnostic tests for arachnid accidents remain unavailable for patients and clinicians. Together with snakes, these accidents are still a global medical concern, and are recognized as neglected tropical issues. Due to arachnid toxins’ fast mechanism of action, quick detection and quantification of venom is required to accelerate treatment decisions, rationalize therapy, and reduce costs and patient risks. This review aims to understand the current limitations for arachnid venom identification and quantification in biological samples. We benchmarked the already existing initiatives regarding test requirements (sample or biomarkers of choice), performances (time, detection limit, sensitivity and specificity) and their validation (on animal models or on samples from envenomed humans). Our analysis outlines unmet needs for improving diagnosis and consequently treatment of arachnid accidents. Hence, based on lessons from past attempts, we propose a road map for raising best practice guidelines, leading to recommendations for future progress in the development of arachnid diagnostic assays.

Applications of MALDI-TOF mass spectrometry in clinical proteomics

INTRODUCTION

The development of precision medicine requires advanced technologies to address the multifactorial disease stratification and to support personalized treatments. Among omics techniques, proteomics based on Mass Spectrometry (MS) is becoming increasingly relevant in clinical practice allowing a phenotypic characterization of the dynamic functional status of the organism. From this perspective, Matrix Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) MS is a suitable platform for providing a high-throughput support to clinics. Areas covered: This review aims to provide an updated overview of MALDI-TOF MS applications in clinical proteomics. The most relevant features of this analysis have been discussed, highlighting both pre-analytical and analytical factors that are crucial in proteomics studies. Particular emphasis is placed on biofluids proteomics for biomarkers discovery and on recent progresses in clinical microbiology, drug monitoring, and minimal residual disease (MRD). Expert commentary: Despite some analytical limitations, the latest technological advances together with the easiness of use, the low time and low cost consuming and the high throughput are making MALDI-TOF MS instruments very attractive for the clinical practice. These features offer a significant potential for the routine of the clinical laboratory and ultimately for personalized medicine.

Identification of MST1 as a potential early detection biomarker for colorectal cancer through a proteomic approach

Colorectal cancer (CRC) is a common malignant neoplasm worldwide. It is important to identify new biomarkers for the early detection of CRC. In this study, magnetic beads and the Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) platform were used to analyse CRC and healthy control (HC) serum samples. The CRC diagnosis pattern was established to have a specificity of 94.7% and sensitivity of 92.3% in a blind test. The candidate biomarker serine/threonine kinase 4 (STK4, also known as MST1) was identified by Tandem mass spectrometry (MS/MS) and verified with western blotting and enzyme-linked immunosorbent assay (ELISA). The results indicated that there was a higher concentration of MST1 in HC subjects than stage I CRC patients for the early detection of CRC and a lower concentration in stage IV patients than in other CRC patients. The sensitivity and specificity of MST1 combined with carcinoembryonic antigen (CEA) and faecal occult blood test (FOBT) in diagnosis of colorectal cancer were 92.3% and 100%, respectively. Additionally, low MST1 expression was associated with the poor prognosis. These results illustrate that MST1 is a potential biomarker for early detection, prognosis and prediction of distant metastasis of CRC.

Chemical Proteomic Approaches Targeting Cancer Stem Cells: A Review of Current Literature

Cancer stem cells (CSCs) have been proposed as central drivers of tumor initiation, progression, recurrence, and therapeutic resistance. Therefore, identifying stem-like cells within cancers and understanding their properties is crucial for the development of effective anticancer therapies. Recently, chemical proteomics has become a powerful tool to efficiently determine protein networks responsible for CSC pathophysiology and comprehensively elucidate molecular mechanisms of drug action against CSCs. This review provides an overview of major methodologies utilized in chemical proteomic approaches. In addition, recent successful chemical proteomic applications targeting CSCs are highlighted. Future direction of potential CSC research by integrating chemical genomic and proteomic data obtained from a single biological sample of CSCs are also suggested in this review.

Rapid and simple analysis of disease-associated biomarkers of Taiwanese patients with schizophrenia using matrix-assisted laser desorption ionization mass spectrometry

BACKGROUND

Matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF MS) is an extremely sensitive analytical tool for characterizing biological compounds in bio samples. In this study, we applied MALDI-TOF MS to assess potential protein biomarkers in the peripheral blood mononuclear cells (PBMCs) of patients with schizophrenia in the acute phase, recovery phase and healthy controls in Taiwan.

METHODS

We recruited 40 participants, including 20 pairs of patients diagnosed with schizophrenia in the acute phase, after four-week treatment with drug in the recovery phase, and 20 healthy controls. The schizophrenic patients were diagnosed using Structured Clinical Interview for DSM-IV Axis I Disorders (SCID), and severity was assessed by a positive and negative symptom scale at baseline and at endpoint following four-week treatment with drug. The patients' PBMCs biomarkers were rapidly measured using a technique that combines MALDI-TOF MS and principle component analysis. A receiver operating characteristic curve was created for the evaluated biomarker.

RESULTS

Significant differences in α-defensins 1-3 were found between the patients in acute phase with schizophrenia and the healthy controls, but not between the schizophrenic patients in recovery phase and healthy controls or between the schizophrenic patients in acute phase and in recovery phase.

CONCLUSIONS

α-Defensins can be biomarkers of Taiwanese patients with schizophrenia, thus supporting the hypothesis that the inflammatory response and immunity system is correlated with the pathophysiology of schizophrenia. Moreover, the result also implies that α-defensins may be related in schizophrenia-associated disease not in efficacy of drug-treatment.

Applications of Mass Spectrometry Imaging to Cancer

Pathologists play an essential role in the diagnosis and prognosis of benign and cancerous tumors. Clinicians provide tissue samples, for example, from a biopsy, which are then processed and thin sections are placed onto glass slides, followed by staining of the tissue with visible dyes. Upon processing and microscopic examination, a pathology report is provided, which relies on the pathologist's interpretation of the phenotypical presentation of the tissue. Targeted analysis of single proteins provide further insight and together with clinical data these results influence clinical decision making. Recent developments in mass spectrometry facilitate the collection of molecular information about such tissue specimens. These relatively new techniques generate label-free mass spectra across tissue sections providing nonbiased, nontargeted molecular information. At each pixel with spatial coordinates (x/y) a mass spectrum is acquired. The acquired mass spectrums can be visualized as intensity maps displaying the distribution of single m/z values of interest. Based on the sample preparation, proteins, peptides, lipids, small molecules, or glycans can be analyzed. The generated intensity maps/images allow new insights into tumor tissues. The technique has the ability to detect and characterize tumor cells and their environment in a spatial context and combined with histological staining, can be used to aid pathologists and clinicians in the diagnosis and management of cancer. Moreover, such data may help classify patients to aid therapy decisions and predict outcomes. The novel complementary mass spectrometry-based methods described in this chapter will contribute to the transformation of pathology services around the world.

Clinical proteomics-driven precision medicine for targeted cancer therapy: current overview and future perspectives

Cancer is a common disease that is a leading cause of death worldwide. Currently, early detection and novel therapeutic strategies are urgently needed for more effective management of cancer. Importantly, protein profiling using clinical proteomic strategies, with spectacular sensitivity and precision, offer excellent promise for the identification of potential biomarkers that would direct the development of targeted therapeutic anticancer drugs for precision medicine. In particular, clinical sample sources, including tumor tissues and body fluids (blood, feces, urine and saliva), have been widely investigated using modern high-throughput mass spectrometry-based proteomic approaches combined with bioinformatic analysis, to pursue the possibilities of precision medicine for targeted cancer therapy. Discussed in this review are the current advantages and limitations of clinical proteomics, the available strategies of clinical proteomics for the management of precision medicine, as well as the challenges and future perspectives of clinical proteomics-driven precision medicine for targeted cancer therapy.