Reproducibility in Protein Profiling by MALDI-TOF Mass Spectrometry

Proteome allocation is linked to transcriptional regulation through a modularized transcriptome

It has proved challenging to quantitatively relate the proteome to the transcriptome on a per-gene basis. Recent advances in data analytics have enabled a biologically meaningful modularization of the bacterial transcriptome. We thus investigate whether matched datasets of transcriptomes and proteomes from bacteria under diverse conditions can be modularized in the same way to reveal novel relationships between their compositions. We find that; (1) the modules of the proteome and the transcriptome are comprised of a similar list of gene products, (2) the modules in the proteome often represent combinations of modules from the transcriptome, (3) known transcriptional and post-translational regulation is reflected in differences between two sets of modules, allowing for knowledge-mapping when interpreting module functions, and (4) through statistical modeling, absolute proteome allocation can be inferred from the transcriptome alone. Quantitative and knowledge-based relationships can thus be found at the genome-scale between the proteome and transcriptome in bacteria.

In Situ Array Microextraction and Metabolic Profiling of Small Extracellular Vesicles to Guide and Monitor Maternal Delivery

The advantages of small extracellular vesicles (sEV) in disease management have become increasingly prominent, with the main challenge lying in meeting the demands of large-scale extraction and high-throughput analysis, a crucial aspect in the realm of precision medicine. To overcome this challenge, an engineered on-plate aptamer array (16×24 spots) is developed for continuous scale-up microextraction of plasma sEV and their in situ metabolic analysis using mass spectrometry. With this integrated array strategy, metabolic profiles of sEV are acquired from the plasma of 274 antenatal or postpartum women, reducing analysis time by half (7.5 h) and sample volume by 95% (only 0.125 µL usage) compared to the traditional suspension method. Moreover, using machine learning algorithms on sEV metabolic profiles, a risk score system is constructed that accurately assesses the need for epidural analgesia during childbirth and the likelihood of post-administration fever. The system, based on admission samples, achieves an impressive 94% accuracy. Furthermore, post-administration fever can be identified from delivery samples, reaching an overall accuracy rate of 88%. This work offers real-time monitoring of the childbirth process that can provide timely guidance for maternal delivery, underscoring the significance of sEV detection in large-scale clinical samples for medicine innovation and advancement.

A statistical approach to system suitability testing for mass spectrometry imaging

RATIONALE

Mass spectrometry imaging (MSI) elevates the power of conventional mass spectrometry (MS) to multidimensional space, elucidating both chemical composition and localization. However, the field lacks any robust quality control (QC) and/or system suitability testing (SST) protocols to monitor inconsistencies during data acquisition, both of which are integral to ensure the validity of experimental results. To satisfy this demand in the community, we propose an adaptable QC/SST approach with five analyte options amendable to various ionization MSI platforms (e.g., desorption electrospray ionization, matrix-assisted laser desorption/ionization [MALDI], MALDI-2, and infrared matrix-assisted laser desorption electrospray ionization [IR-MALDESI]).

METHODS

A novel QC mix was sprayed across glass slides to collect QC/SST regions-of-interest (ROIs). Data were collected under optimal conditions and on a compromised instrument to construct and refine the principal component analysis (PCA) model in R. Metrics, including mass measurement accuracy and spectral accuracy, were evaluated, yielding an individual suitability score for each compound. The average of these scores is utilized to inform if troubleshooting is necessary.

RESULTS

The PCA-based SST model was applied to data collected when the instrument was compromised. The resultant SST scores were used to determine a statistically significant threshold, which was defined as 0.93 for IR-MALDESI-MSI analyses. This minimizes the type-I error rate, where the QC/SST would report the platform to be in working condition when cleaning is actually necessary. Further, data scored after a partial cleaning demonstrate the importance of QC and frequent full instrument cleaning.

CONCLUSIONS

This study is the starting point for addressing an important issue and will undergo future development to improve the efficiency of the protocol. Ultimately, this work is the first of its kind and proposes this approach as a proof of concept to develop and implement universal QC/SST protocols for a variety of MSI platforms.

New insight from MALDI-TOF MS and multivariate data analysis on the botanical origin of polysaccharide-based paint binders in ancient Egypt

Polysaccharide-based materials of plant origin are known to have been used as binding media in paint and ground layers of artifacts from ancient Egypt, including wall paintings, cartonnages and sarcophagi. The use of gums from Acacia, Astragalus and Prunus genera has been suggested in the literature on the basis of their qualitative or quantitative monosaccharide profile after complete chemical hydrolysis. The introduction of partial enzymatic digestion of the polysaccharide material, followed by analysis of the released oligosaccharides by matrix assisted laser desorption ionization-time-of-flight mass spectrometry, has proved effective in discriminating among gums from different genera, as well as among species within the Acacia genus. In this study, the previously built Acacia database was expanded, principal component analysis (PCA) was used to aid in grouping of the samples, and data interpretation was refined following a modified acacieae taxonomy. Application of the analytical strategy to investigate the paint binders in artworks from ancient Egypt allowed qualitative discrimination of gums at a species level, and provided new insights into the artists' material choices.

Origins, Technological Advancement, and Applications of Peptidomics

Peptidomics is the comprehensive characterization of peptides from biological sources instead of heading for a few single peptides in former peptide research. Mass spectrometry allows to detect a multitude of peptides in complex mixtures and thus enables new strategies leading to peptidomics. The term was established in the year 2001, and up to now, this new field has grown to over 3000 publications. Analytical techniques originally developed for fast and comprehensive analysis of peptides in proteomics were specifically adjusted for peptidomics. Although it is thus closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. Fundamental technological advancements of peptidomics since have occurred in mass spectrometry and data processing, including quantification, and more slightly in separation technology. Different strategies and diverse sources of peptidomes are mentioned by numerous applications, such as discovery of neuropeptides and other bioactive peptides, including the use of biochemical assays. Furthermore, food and plant peptidomics are introduced similarly. Additionally, applications with a clinical focus are included, comprising biomarker discovery as well as immunopeptidomics. This overview extensively reviews recent methods, strategies, and applications including links to all other chapters of this book.

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.

MALDI-TOF MS Is an Effective Technique To Classify Specific Microbiota

MALDI-TOF MS is well-recognized for single microbial identification and widely used in research and clinical fields due to its specificity, speed of analysis, and low cost of consumables. Multiple commercial platforms have been developed and approved by the U.S. Food and Drug Administration. Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has been used for microbial identification. However, microbes can present as a specific microbiota, and detection and classification remain a challenge. Here, we constructed several specific microbiotas and tried to classify them using MALDI-TOF MS. Different concentrations of nine bacterial strains (belonging to eight genera) constituted 20 specific microbiotas. Using MALDI-TOF MS, the overlap spectrum of each microbiota (MS spectra of nine bacterial strains with component percentages) could be classified by hierarchical clustering analysis (HCA). However, the real MS spectrum of a specific microbiota was different than that of the overlap spectrum of component bacteria. The MS spectra of specific microbiota showed excellent repeatability and were easier to classify by HCA, with an accuracy close to 90%. These results indicate that the widely used MALDI-TOF MS identification method for individual bacteria can be expanded to classification of microbiota. IMPORTANCE MALDI-TOF MS can be used to classify specific model microbiota. The actual MS spectrum of the model microbiota was not a simple superposition of every single bacterium in a certain proportion but had a specific spectral fingerprint. The specificity of this fingerprint can enhance the accuracy of microbiota classification.

Biomarker Reproducibility Challenge: A Review of Non-Nucleotide Biomarker Discovery Protocols from Body Fluids in Breast Cancer Diagnosis

Breast cancer has now become the most commonly diagnosed cancer, accounting for one in eight cancer diagnoses worldwide. Non-invasive diagnostic biomarkers and associated tests are superlative candidates to complement or improve current approaches for screening, early diagnosis, or prognosis of breast cancer. Biomarkers detected from body fluids such as blood (serum/plasma), urine, saliva, nipple aspiration fluid, and tears can detect breast cancer at its early stages in a minimally invasive way. The advancements in high-throughput molecular profiling (omics) technologies have opened an unprecedented opportunity for unbiased biomarker detection. However, the irreproducibility of biomarkers and discrepancies of reported markers have remained a major roadblock to clinical implementation, demanding the investigation of contributing factors and the development of standardised biomarker discovery pipelines. A typical biomarker discovery workflow includes pre-analytical, analytical, and post-analytical phases, from sample collection to model development. Variations introduced during these steps impact the data quality and the reproducibility of the findings. Here, we present a comprehensive review of methodological variations in biomarker discovery studies in breast cancer, with a focus on non-nucleotide biomarkers (i.e., proteins, lipids, and metabolites), highlighting the pre-analytical to post-analytical variables, which may affect the accurate identification of biomarkers from body fluids.

Rapid detection of serum free light chains by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Introduction: Serum free light chain (FLC) measurements are increasingly prominent for patients with plasma cell disorders (PCDs) in screening, prognostic stratification, and monitoring therapy responses. Objectives: We aimed to develop a sensitive, reliable, and accurate method for diagnosing PCDs that can notably decrease the time and cost of current methods. Methods: Here, we present a novel approach for FLC measurement using immunoenrichment on micro-affinity chromatography in combination with matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) detection. In this study, serum free kappa (κ) and free lambda (λ) light chain (LC) levels in the serum of 105 patients were compared between the nephelometric serum FLC quantification and MALDI-TOF MS detection. Results: Cohen's kappa coefficient between the MALDI-TOF MS-based method and the FLC assay revealed an almost perfect agreement in the case of normal (negative) results (κ = 0.92; 95% confidence interval (CI): 0.837 to 0.968) and a good agreement in the case of increased (positive) results (κ = 0.76; 95% CI: 0.608 to 0.870). In Spearman's correlation analysis, the best correlation was found between serum free κ/λ ratios (r = 0.628, 0.496 to 0.732; p <0.0001). Our method showed sensitivity (92.5%) and specificity (76.3%) for discrimination between the κ/λ FLC ratio compared to the serum FLC assay. Conclusion: The proposed method can significantly contribute to diagnosing and monitoring PCDs as it can significantly be time-saving, cost-effective in FLC measurement.

Proteome allocation is linked to transcriptional regulation through a modularized transcriptome

It has proved challenging to quantitatively relate the proteome to the transcriptome on a per-gene basis. Recent advances in data analytics have enabled a biologically meaningful modularization of the bacterial transcriptome. We thus investigated whether matched datasets of transcriptomes and proteomes from bacteria under diverse conditions could be modularized in the same way to reveal novel relationships between their compositions. We found that; 1) the modules of the proteome and the transcriptome are comprised of a similar list of gene products, 2) the modules in the proteome often represent combinations of modules from the transcriptome, 3) known transcriptional and post-translational regulation is reflected in differences between two sets of modules, allowing for knowledge-mapping when interpreting module functions, and 4) through statistical modeling, absolute proteome allocation can be inferred from the transcriptome alone. Quantitative and knowledge-based relationships can thus be found at the genome-scale between the proteome and transcriptome in bacteria.

A MALDI-TOF mass spectrometry-based haemoglobin chain quantification method for rapid screen of thalassaemia

BACKGROUND

Thalassaemia is one of the most common inherited monogenic diseases worldwide with a heavy global health burden. Considering its high prevalence in low and middle-income countries, a cheap, accurate and high-throughput screening test of thalassaemia prior to a more expensive confirmatory diagnostic test is urgently needed.

METHODS

In this study, we constructed a machine learning model based on MALDI-TOF mass spectrometry quantification of haemoglobin chains in blood, and for the first time, evaluated its diagnostic efficacy in 674 thalassaemia (including both asymptomatic carriers and symptomatic patients) and control samples collected in three hospitals. Parameters related to haemoglobin imbalance (α-globin, β-globin, γ-globin, α/β and α-β) were used for feature selection before classification model construction with 8 machine learning methods in cohort 1 and further model efficiency validation in cohort 2.

RESULTS

The logistic regression model with 5 haemoglobin peak features achieved good classification performance in validation cohort 2 (AUC 0.99, 95% CI 0.98-1, sensitivity 98.7%, specificity 95.5%). Furthermore, the logistic regression model with 6 haemoglobin peak features was also constructed to specifically identify β-thalassaemia (AUC 0.94, 95% CI 0.91-0.97, sensitivity 96.5%, specificity 87.8% in validation cohort 2).

CONCLUSIONS

For the first time, we constructed an inexpensive, accurate and high-throughput classification model based on MALDI-TOF mass spectrometry quantification of haemoglobin chains and demonstrated its great potential in rapid screening of thalassaemia in large populations.Key messagesThalassaemia is one of the most common inherited monogenic diseases worldwide with a heavy global health burden.We constructed a machine learning model based on MALDI-TOF mass spectrometry quantification of haemoglobin chains to screen for thalassaemia.

Measurement of kinetic isotope effects on peptide hydroxylation using MALDI-MS

Primary kinetic isotope effects (KIEs) provide unique insight into enzymatic reactions, as they can reveal rate-limiting steps and detailed chemical mechanisms. HIF hydroxylases, part of a family of 2-oxoglutarate (2OG) oxygenases are central to the regulation of many crucial biological processes through O2-sensing, but present a challenge to monitor due to the large size of the protein substrate and the similarity between native and hydroxylated substrate. MALDI-TOF MS is a convenient tool to measure peptide masses, which can also be used to measure the discontinuous kinetics of peptide hydroxylation for Factor Inhibiting HIF (FIH). Using this technique, rate data can be observed from the mole-fraction of CTAD and CTAD-OH in small volumes, allowing noncompetitive H/D KIEs to be measured. Slow dCTAD substrate leads to extensive uncoupling of O2 consumption from peptide hydroxylation, leading to enzyme autohydroxylation, which is observed using UV-vis spectroscopy. Simultaneously measuring both the normal product, CTAD-OH, and the uncoupled product, autohydroxylated enzyme, the KIE on the microscopic step of hydrogen atom transfer (HAT) can be estimated. MALDI-MS analysis is a strong method for monitoring reactions that hydroxylate peptides, and can be generalized to other similar reactions, and simultaneous kinetic detection of branched products can provide valuable insight on microscopic KIEs at intermediate mechanistic steps.

Identification of Epigallocatechin-3-Gallate (EGCG) from Green Tea Using Mass Spectrometry

In an era where humanity is reinstating its lost hope and expectation on natural products, green tea occupies quite a position for what it has proven to be, in its endeavors for human welfare and health. Epigallocatechin-3-gallate (EGCG) is the key to the vast biological activities of green tea. Green tea is no longer in the backdrop; it has emerged as the most viral, trending bioactive molecule when it comes to health benefits for human beings. This review focuses on the use of various analytical techniques for the analysis of EGCG. That which has been achieved so far, in terms of in vitro, pure component analysis, as well as those spikes in biological fluids and those in vivo in animal and human samples, was surveyed and presented. The use of MS-based techniques for the analysis of EGCG is elaborately reviewed and the need for improvising the applications is explained. The review emphasizes that there is plenty of room to explore matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) applications in this subject area.

A Rapid and Affordable Screening Tool for Early-Stage Ovarian Cancer Detection Based on MALDI-ToF MS of Blood Serum

Ovarian cancer is a worldwide health issue that grows at a rate of almost 250,000 new cases every year. Its early detection is key for a good prognosis and even curative surgery. However, current medical examination methods and tests have been inefficient in detecting ovarian cancer at the early stage, leading to preventable death. So far, new screening tests based on molecular biomarker analysis techniques have not resulted in any substantial improvement in early-stage diagnosis and increased survival. Thus, whilst there remains clear potential to improve outcomes through early detection, novel approaches are needed. Here, we postulated that MALDI-ToF-mass-spectrometry-based tests can be a solution for effective screening of ovarian cancer. In this retrospective cohort study, we generated and analyzed the mass spectra of 181 serum samples of women with and without ovarian cancer. Using bioinformatics pipelines for analysis, including predictive modeling and machine learning, we found distinct mass spectral patterns composed of 9–20 key combinations of peak intensity or peak enrichment features for each stage of ovarian cancer. Based on a scoring algorithm and obtained patterns, the optimal sensitivity for detecting each stage of cancer was 95–97% with a specificity of 97%. Scoring all algorithms simultaneously could detect all stages of ovarian cancer at 99% sensitivity and 92% specificity. The results further demonstrate that the matrix and mass range analyzed played a key role in improving the mass spectral data quality and diagnostic power. Altogether, with the results reported here and increasing evidence of the MS assay’s diagnostic accuracy and instrument robustness, it has become imminent to consider MS in the clinical application for ovarian cancer screening.

The application of mass spectrometry imaging in traditional Chinese medicine: a review

Mass spectrometry imaging is a frontier technique which connects classical mass spectrometry with ion imaging. Various types of chemicals could be visualized in their native tissues using mass spectrometry imaging. Up to now, the most commonly applied mass spectrometry imaging techniques are matrix assisted laser desorption ionization mass spectrometry imaging, desorption electrospray ionization mass spectrometry imaging and secondary ion mass spectrometry imaging. This review gives an introduction to the principles, development and applications of commonly applied mass spectrometry imaging techniques, and then illustrates the application of mass spectrometry imaging in the investigation of traditional Chinese medicine. Recently, mass spectrometry imaging has been adopted to explore the spatial distribution of endogenous metabolites in traditional Chinese medicine. Data collected from mass spectrometry imaging can be further utilized to search for marker components of traditional Chinese medicine, discover new compounds from traditional herbs, and differentiate between medicinal plants that are similar in botanical features. Moreover, mass spectrometry imaging also plays a role in revealing the pharmacological and toxicological mechanisms of traditional Chinese medicine.

MALDI-TOF-MS analysis in low molecular weight serum peptidome biomarkers for NSCLC

Objects

Lung cancer is one of the leading causes of death from cancer in the world. Screening new serum biomarkers is important for the early detection of lung cancer. The purpose of this study was to investigate the serum peptide model between non‐small cell lung cancer (NSCLC) patients and healthy controls, as well as between paired pre‐ and postoperative NSCLC patients, and to find the low molecular weight (LMW) potential tumor markers for NSCLC.

Methods

56 serum samples from NSCLC patients, 56 controls, and 20 matched pre‐ and postoperative patients were analyzed using magnetic‐bead (MB)‐based purification technique combined with MALDI‐TOF‐MS. To distinguish NSCLC from cancer‐free controls, three models were established. Finally, comparing the three groups of serum protein fingerprints, nano‐liquid chromatography–electrospray ionization tandem mass spectrometry was used to further identify the differential peptides.

Results

Among the three models constructed, the GA model had the best diagnostic efficacy. Five differential peaks were screened by combining the case group, healthy controls, and postoperative group analysis, which were up‐regulated in the case group and showed a tendency to return to healthy control values after surgery. The protein matching the mass spectrometry peak m/z 2953.73 was identified as fibrinogen α chain.

Conclusion

This study shows that the application of MALDI‐TOF‐MS is a promising approach for the identification of potential serum biomarkers for NSCLC, which is potentially valuable for establishing a new diagnostic method for lung cancer. In addition, we found that fibrinogen α chain may be an auxiliary diagnostic indicator for NSCLC.

Laser Ablation Synthesis in Solution and Nebulization of Silver-109 Nanoparticles for Mass Spectrometry and Mass Spectrometry Imaging

Preparation of monoisotopic silver-109 nanoparticles (¹⁰⁹AgNPs) by pulsed fiber laser (PFL) ablation synthesis in solution (LASiS) with the use of a 2D galvoscanner (2D GS) is described. The procedure of covering of custom-made stainless-steel MALDI targets containing studied objects via nebulization is also presented. Examples of application of the new method (PFL-2D GS LASiS and nebulization) in mass spectrometry (MS) analyses and MS imaging (MSI) are shown. These include tests with a nonionic nucleoside and saccharide, ionic amino acids, and also a low-molecular-weight polymer. Fingerprint MS imaging is shown as an example of a fast and simple MSI procedure.

Matrix enrichment by black phosphorus improves ionization and reproducibility of mass spectrometry of intact cells, peptides, and amino acids

Intact (whole) cell matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) is an established method for biotyping in clinical microbiology as well as for revealing phenotypic shifts in cultured eukaryotic cells. Intact cell MALDI-TOF MS has recently been introduced as a quality control tool for long-term cultures of pluripotent stem cells. Despite the potential this method holds for revealing minute changes in cells, there is still a need for improving the ionization efficiency or peak reproducibility. Here we report for the first time that supplementation by fine particles of black phosphorus to the standard MALDI matrices, such as sinapinic and α-cyano-4-hydroxycinnamic acids enhance intensities of mass spectra of particular amino acids and peptides, presumably by interactions with aromatic groups within the molecules. In addition, the particles of black phosphorus induce the formation of small and regularly dispersed crystals of sinapinic acid and α-cyano-4-hydroxycinnamic acid with the analyte on a steel MALDI target plate. Patterns of mass spectra recorded from intact cells using black phosphorus-enriched matrix were more reproducible and contained peaks of higher intensities when compared to matrix without black phosphorus supplementation. In summary, enrichment of common organic matrices by black phosphorus can improve discrimination data analysis by enhancing peak intensity and reproducibility of mass spectra acquired from intact cells.

Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging of Tissues via the Formation of Reproducible Matrix Crystals by the Fluorescence-Assisted Spraying Method: A Quantification Approach

The application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) imaging to quantitative analyses is restricted by the variability of MS intensity of the analytes in nonreproducible matrix crystals of tissues. To overcome this challenge, a fluorescence-assisted spraying method was developed for a constant matrix amount employing an MS-detectable fluorescent reagent, rhodamine 6G (R6G), which was sprayed with the matrix. To form a homogeneous matrix crystal on the tissue section, a matrix solution, 1,5-diaminonaphthalene (10 mg/mL), containing R6G (40 μg/mL) and O-dinitrobenzene (O-DNB, 10 mg/mL) was sprayed until the desired constant fluorescence intensity was achieved. Compared with that obtained via conventional cycle-number-fixed spraying [relative standard deviation (RSD) = 31.1%], the reproducibility of the relative MS intensity of the analyte [ferulic acid (FA), RSD = 3.1%] to R6G was significantly improved by the fluorescence-assisted matrix spraying. This result indicated that R6G could be employed as an index of the matrix amount and an MS normalizing standard. The proposed matrix spraying successfully quantified nifedipine (0.5-40 pmol/mm² in the positive mode, R² = 0.965) and FA (0.5-75 pmol/mm² in the negative mode, R² = 0.9972) in the kidney section of a rat. Employing the quantitative MALDI-MS imaging assay, FA, which accumulated in the kidney of the rat after 50 mg/kg was orally administered, was visually determined to be 3.5, 3.0, and 0.2 μmol/g tissue at 15, 30, and 60 min, respectively.

Facile "one-pot" preparation of phosphonate functional polythiophene based microsphere via Friedel-Crafts reaction for selective enrichment of phosphopeptides from milk

A novel kind of phosphonate functionalized polythiophene microsphere was designed and fabricated via Friedel-Crafts reaction. Diethyl (thiophen-2-ylmethyl) phosphonate (DTYP) and thiophene were co-polymerized by Fe (III) catalysis, without any surfactant, stabilizer and initiator. Functional phosphonate group was directly introduced into the microsphere without redundant modification steps. The adsorption amount of the as-synthesized microsphere, Ti-poly(Th-co-DTYP), was as high as 66.7 mg/g, which was higher than that of commercial Ti⁴⁺-IMAC microsphere (49.7 mg/g). The microsphere was explored on the specific capture of phosphopeptides from either tryptic digests of milk or HeLa cell protein. As a result, 88 of unique phosphopeptides mapping to 21 phosphoproteins were identified from 150 μg of milk tryptic digest after enrichment, and a total of 2534 unique phosphopeptides mapping to 1087 phosphoproteins was identified from HeLa cell. It is expected that such a robust and facile approach will be explored in other functional microspheres to be commercialized in the future.

Toward improvement of screening through mass spectrometry-based proteomics: ovarian cancer as a case study

Ovarian cancer is one of the leading causes of cancer related deaths affecting United States women. Early-stage detection of ovarian cancer has been linked to increased survival, however, current screening methods, such as biomarker testing, have proven to be ineffective in doing so. Therefore, further developments are necessary to be able to achieve positive patient prognosis. Ongoing efforts are being made in biomarker discovery towards clinical applications in screening for early-stage ovarian cancer. In this perspective, we discuss and provide examples for several workflows employing mass spectrometry-based proteomics towards protein biomarker discovery and characterization in the context of ovarian cancer; workflows include protein identification and characterization as well as intact protein profiling. We also discuss the opportunities to merge these workflows for a multiplexed approach for biomarkers. Lastly, we provide our insight as to future developments that may serve to enhance biomarker discovery workflows while also considering translational potential.

Matrix-assisted laser desorption ionisation (MALDI) mass spectrometry (MS): basics and clinical applications

Background Matrix-assisted laser desorption ionisation (MALDI) mass spectrometry (MS) has been used for more than 30 years. Compared with other analytical techniques, it offers ease of use, high throughput, robustness, cost-effectiveness, rapid analysis and sensitivity. As advantages, current clinical techniques (e.g. immunoassays) are unable to directly measure the biomarker; rather, they measure secondary signals. MALDI-MS has been extensively researched for clinical applications, and it is set for a breakthrough as a routine tool for clinical diagnostics. Content This review reports on the principles of MALDI-MS and discusses current clinical applications and the future clinical prospects for MALDI-MS. Furthermore, the review assesses the limitations currently experienced in clinical assays, the advantages and the impact of MALDI-MS to transform clinical laboratories. Summary MALDI-MS is widely used in clinical microbiology for the screening of microbial isolates; however, there is scope to apply MALDI-MS in the diagnosis, prognosis, therapeutic drug monitoring and biopsy imaging in many diseases. Outlook There is considerable potential for MALDI-MS in clinic as a tool for screening, profiling and imaging because of its high sensitivity and specificity over alternative techniques.

Electroblotting through Enzymatic Membranes to Enhance Molecular Tissue Imaging

MALDI-TOF mass spectrometry imaging (MSI) is a powerful tool for studying biomolecule localization in tissue. Protein distributions in tissue provide important histological information; however, large proteins exhibit a high limit of detection in MALDI-MS when compared to their corresponding smaller proteolytic peptides. As a result, several techniques have emerged to digest proteins into more detectable peptides for imaging. Digestion is typically accomplished through trypsin deposition on the tissue, but this technique increases the complexity of the tissue microenvironment, which can limit the number of detectable species. This proof-of-principle study explores tryptic tissue digestion during electroblotting through a trypsin-containing membrane. This approach actively extracts and enzymatically digests proteins from mouse brain tissue sections while simultaneously reducing the complexity of the tissue microenvironment (compared to trypsin deposition on the surface) to obtain an increased number of detectable peptide fragments. The method does not greatly compromise spatial location or require expensive devices to uniformly deposit trypsin on tissue. Using electrodigestion through membranes, we detected and tentatively identified several tryptic peptides that were not observed after on-tissue digestion. Moreover, the use of pepsin rather than trypsin in digestion membranes allows extraction and digestion at low pH to detect peptides from a complementary subset of tissue proteins. Future studies will aim to further improve the method, including changing the substrate membrane to increase spatial resolution and the number of detected peptides.

Pyrene Tags for the Detection of Carbohydrates by Label-Assisted Laser Desorption/Ionisation Mass Spectrometry*

Matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-MS) is widely used for the analysis of biomolecules. Label-assisted laser desorption/ionisation mass spectrometry (LALDI-MS) is a matrix-free variant of MALDI-MS, in which only analytes covalently attached to a laser desorption/ionisation (LDI) enhancer are detected. LALDI-MS has shown promise in overcoming the limitations of MALDI-MS in terms of sample preparation and MS analysis. In this work, we have developed a series of pyrene-based LDI reagents (LALDI tags) that can be used for labelling and LALDI-MS analysis of reducing carbohydrates from complex (biological) samples without the need for additional chemical derivatisation or purification. We have systematically explored the suitability of four pyrene-based LDI enhancers and three aldehyde-reactive handles, optimised sample preparation, and demonstrated the use of LALDI tags for the detection of lactose. We have also exemplified the potential of LALDI tags for labelling carbohydrates in biological samples by direct detection of lactose in cow's milk. These results demonstrate that LALDI-MS is a promising technique for the analysis of reducing carbohydrates in biological samples, and pave the way for the development of LALDI-MS for glycomics and diagnostics.

Rapid Isolation, Propagation, and Online Analysis of a Small Number of Therapeutic Staphylococcal Bacteriophages from a Complex Matrix

A method for the fast isolation, propagation, and characterization of very low count bacteriophages active against pathogenic bacterial strains is described in this study. Bacteriophages with a count of 10² phage particles were dynamically adhered from the maximum 10 mL blood plasma sample onto the nanostructured part of the fused silica capillary. One-step propagation of phage particles of genus Kayvirus inside the etched capillary on 10⁴ Staphylococcus aureus host cells increased their number to 6 × 10⁴ phage particles. Phage particles were concentrated online and separated by capillary electrophoretic methods. No phage replication occurred when the phage-resistant S. aureus or Escherichia coli cells were used. Two-step phage propagation in the capillary allowed an increase in the total virion count to up to 6 × 10⁵ phage particles and subsequent off-line matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis of the phage zone collected after capillary electrophoresis. Relative standard deviations of the phage peak area were at most 2.3%. We expect that the method of isolating bacteriophages from blood plasma and their simultaneous identification will facilitate clinical studies of phage preparations and contribute to pharmacokinetics studies during phage therapy. This approach is also suitable for capturing and enriching new phages from the environment when a susceptible indicator strain is available.

The Effect of Bee Venom Peptides Melittin, Tertiapin, and Apamin on the Human Erythrocytes Ghosts: A Preliminary Study

Red blood cells (RBCs) are the most abundant cells in the human blood that have been extensively studied under morphology, ultrastructure, biochemical and molecular functions. Therefore, RBCs are excellent cell models in the study of biologically active compounds like drugs and toxins on the structure and function of the cell membrane. The aim of the present study was to explore erythrocyte ghost’s proteome to identify changes occurring under the influence of three bee venom peptides-melittin, tertiapin, and apamin. We conducted preliminary experiments on the erythrocyte ghosts incubated with these peptides at their non-hemolytic concentrations. Such preparations were analyzed using liquid chromatography coupled with tandem mass spectrometry. It was found that when higher concentrations of melittin and apamin were used, fewer proteins were identified. Moreover, the results clearly indicated that apamin demonstrates the greatest influence on the RBCs ghosts proteome. Interestingly, the data also suggest that tertiapin exerted a stabilizing effect on the erythrocyte membrane. The experiments carried out show the great potential of proteomic research in the projects focused on the toxin’s properties as membrane active agents. However, to determine the specificity of the effect of selected bee venom peptides on the erythrocyte ghosts, further proteomic research should be focused on the quantitative analysis.

Rapid diagnosis of periodontitis, a feasibility study using MALDI-TOF mass spectrometry

AIM

The aim of the present study was to assess the feasibility and diagnostic contribution of protein profiling using MALDI-TOF mass spectrometry applied to saliva, gingival crevicular fluid (GCF) and dental plaque from periodontitis and healthy subjects. We hypothesized that rapid routine and blinded MALDI-TOF analysis could accurately classify these three types of samples according to periodontal state.

MATERIALS AND METHODS

Unstimulated saliva, GCF and dental plaque, collected from periodontitis subjects and healthy controls, were analyzed by MALDI-TOF MS. Based on the differentially expressed peaks between the two groups, diagnostic decision trees were built for each sample.

RESULTS

Among 141 patients (67 periodontitis and 74 healthy controls), the decision trees diagnosed periodontitis with a sensitivity = 70.3% (± 0.211) and a specificity = 77.8% (± 0.165) for saliva, a sensitivity = 79.6% (± 0.188) and a specificity = 75.7% (± 0.195) for GCF, and a sensitivity = 72.1% (± 0.202) and a specificity = 72.2% (± 0.195) for dental plaque. The sensitivity and specificity of the tests were improved to 100% (CI 95% = [0.91;1]) and 100% (CI 95% = [0.92;1]), respectively, when two samples were tested.

CONCLUSION

We developed, for the first time, diagnostic tests based on protein profiles of saliva, GCF and dental plaque between periodontitis patients and healthy subjects. When at least 2 of these samples were tested, the best results were obtained.

Extending the information content of the MALDI analysis of biological fluids via multi-million shot analysis

INTRODUCTION

Reliable measurements of the protein content of biological fluids like serum or plasma can provide valuable input for the development of personalized medicine tests. Standard MALDI analysis typically only shows high abundance proteins, which limits its utility for test development. It also exhibits reproducibility issues with respect to quantitative measurements. In this paper we show how the sensitivity of MALDI profiling of intact proteins in unfractionated human serum can be substantially increased by exposing a sample to many more laser shots than are commonly used. Analytical reproducibility is also improved.

METHODS

To assess what is theoretically achievable we utilized spectra from the same samples obtained over many years and combined them to generate MALDI spectral averages of up to 100,000,000 shots for a single sample, and up to 8,000,000 shots for a set of 40 different serum samples. Spectral attributes, such as number of peaks and spectral noise of such averaged spectra were investigated together with analytical reproducibility as a function of the number of shots. We confirmed that results were similar on MALDI instruments from different manufacturers.

RESULTS

We observed an expected decrease of noise, roughly proportional to the square root of the number of shots, over the whole investigated range of the number of shots (5 orders of magnitude), resulting in an increase in the number of reliably detected peaks. The reproducibility of the amplitude of these peaks, measured by CV and concordance analysis also improves with very similar dependence on shot number, reaching median CVs below 2% for shot numbers > 4 million. Measures of analytical information content and association with biological processes increase with increasing number of shots.

CONCLUSIONS

We demonstrate that substantially increasing the number of laser shots in a MALDI-TOF analysis leads to more informative and reliable data on the protein content of unfractionated serum. This approach has already been used in the development of clinical tests in oncology.

What did we learn from multiple omics studies in asthma?

More than a decade has passed since the finalization of the Human Genome Project. Omics technologies made a huge leap from trendy and very expensive to routinely executed and relatively cheap assays. Simultaneously, we understood that omics is not a panacea for every problem in the area of human health and personalized medicine. Whilst in some areas of research omics showed immediate results, in other fields, including asthma, it only allowed us to identify the incredibly complicated molecular processes. Along with their possibilities, omics technologies also bring many issues connected to sample collection, analyses and interpretation. It is often impossible to separate the intrinsic imperfection of omics from asthma heterogeneity. Still, many insights and directions from applied omics were acquired-presumable phenotypic clusters of patients, plausible biomarkers and potential pathways involved. Omics technologies develop rapidly, bringing improvements also to asthma research. These improvements, together with our growing understanding of asthma subphenotypes and underlying cellular processes, will likely play a role in asthma management strategies.

Assessment of temperature-dependent proteomes of Pythium insidiosum by using the SWISS-PROT database

Pythium insidiosum causes the life-threatening disease, called pythiosis. Information on microbial pathogenesis could lead to an effective method of infection control. This study aims at assessing temperature-dependent proteomes, and identifying putative virulence factors of P. insidiosum. Protein extracts from growths at 25°C and 37°C were analyzed by mass spectrometry and SWISS-PROT database. A total of 1052 proteins were identified. Upon exposure to increased temperature, 219 proteins were markedly expressed, eight of which were putative virulence factors of P. insidiosum. These temperature-dependent proteins should be further investigated for their roles in pathogenesis, and some of which could be potential therapeutic targets.

The Reliable, Automatic Classification of Neonates in First-Tier MALDI-MS Screening for Sickle Cell Disease

Previous research has shown that a MALDI-MS technique can be used to screen for sickle cell disease (SCD), and that a system combining automated sample preparation, MALDI-MS analysis and classification software is a relevant approach for first-line, high-throughput SCD screening. In order to achieve a high-throughput "plug and play" approach while detecting "non-standard" profiles that might prompt the misclassification of a sample, we have incorporated various sets of alerts into the decision support software. These included "biological alert" indicators of a newborn's clinical status (e. g., detecting samples with no or low HbA), and "technical alerts" indicators for the most common non-standard profiles, i.e., those which might otherwise lead to sample misclassification. We evaluated these alerts by applying them to two datasets (produced by different laboratories). Despite the random generation of abnormal spectra by one-off technical faults or due to the nature and quality of the samples, the use of alerts fully secured the process of automatic sample classification. Firstly, cases of β-thalassemia were detected. Secondly, after a visual check on the tagged profiles and reanalysis of the corresponding biological samples, all the samples were correctly reclassified without prompting further alerts. All of the samples for which the results were not tagged were well classified (i.e., sensitivity and specificity = 1). The alerts were mainly designed for detecting false-negative classifications; all the FAS samples misclassified by the software as FA (a false negative) were marked with an alert. The implementation of alerts in the NeoScreening^® Laboratory Information Management System's decision support software opens up perspectives for the safe, reliable, automated classification of samples, with a visual check solely on abnormal results or samples. It should now be possible to evaluate the combination of the NeoSickle^® analytical solution and the NeoScreening^® Laboratory Information Management System in a real-life, prospective study of first-line SCD screening.

Systematic evaluation of repeatability of IR-MALDESI-MS and normalization strategies for correcting the analytical variation and improving image quality

Mass spectrometry imaging is a powerful tool widely used in biological, clinical, and forensic research, but its often poor repeatability limits its application for quantitative and large-scale analysis. A systematic evaluation of infrared matrix-assisted laser desorption electrospray ionization mass spectrometry (IR-MALDESI-MS) repeatability in absolute ion abundances during short- and long-term experiments was carried out on liver slices from the same rat with minimal biological variability to be expected. Results of median %RSDs ranging from 14 to 45, pooled %RMADs ranging from 11 to 33, and Pearson correlation coefficients ranging from 0.83 to 1.00 demonstrated an acceptable repeatability of IR-MALDESI-MS. Normalization is commonly applied for the purpose of accounting for analytical variability of spectra generated from different runs so as to reveal real biological differences. Nine data normalization strategies were performed on the rat liver data sets to examine their effects on reducing analytical variation, and further on a hen ovary data set containing more morphological features for the investigation of their impact on ion images. Results demonstrated that the majority of normalization approaches benefit data quality to some extent, and local normalization methods significantly outperform their global counterparts, resulting in a reduction of median %RSD up to 22. Local median normalization was found to be promisingly robust for both homogeneous and heterogeneous samples.

Matrix-Assisted Laser Desorption Time of Flight Mass Spectrometry

Matrix-assisted laser desorption time of flight mass spectrometry (MALDI-TOF MS), adapted for use in clinical microbiology laboratories, challenges current standards of microbial detection and identification. This article summarizes the capabilities of MALDI-TOF MS in diagnostic clinical microbiology laboratories and describes the underpinnings of the technology, highlighting topics such as sample preparation, spectral analysis, and accuracy. The use of MALDI-TOF MS in the clinical microbiology laboratory is growing, and, when properly deployed, can accelerate diagnosis and improve patient care.

Complementarity of Matrix- and Nanostructure-Assisted Laser Desorption/Ionization Approaches

In recent years, matrix-assisted laser desorption/ionization (MALDI) has become the main tool for the study of biological macromolecules, such as protein nano-machines, especially in the determination of their molecular masses, structure, and post-translational modifications. A key role in the classical process of desorption and ionization of the sample is played by a matrix, usually a low-molecular weight weak organic acid. Unfortunately, the interpretation of mass spectra in the mass range of below m/z 500 is difficult, and hence the analysis of low molecular weight compounds in a matrix-assisted system is an analytical challenge. Replacing the classical matrix with nanomaterials, e.g., silver nanoparticles, allows improvement of the selectivity and sensitivity of spectrometric measurement of biologically important small molecules. Nowadays, the nanostructure-assisted laser desorption/ionization (NALDI) approach complements the classic MALDI in the field of modern bioanalytics. In particular, the aim of this work is to review the recent advances in MALDI and NALDI approaches.

Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for the Rapid Detection of Antimicrobial Resistance Mechanisms and Beyond

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been successfully applied in recent years for first-line identification of pathogens in clinical microbiology because it is simple to use, rapid, and accurate and has economic benefits in hospital management. The range of clinical applications of MALDI-TOF MS for bacterial isolates is increasing constantly, from species identification to the two most promising applications in the near future: detection of antimicrobial resistance and strain typing for epidemiological studies. The aim of this review is to outline the contribution of previous MALDI-TOF MS studies in relation to detection of antimicrobial resistance and to discuss potential future challenges in this field. Three main approaches are ready (or almost ready) for clinical use, including the detection of antibiotic modifications due to the enzymatic activity of bacteria, the detection of antimicrobial resistance by analysis of the peak patterns of bacteria or mass peak profiles, and the detection of resistance by semiquantification of bacterial growth in the presence of a given antibiotic. This review provides an expert guide for MALDI-TOF MS users to new approaches in the field of antimicrobial resistance detection, especially possible applications as a routine diagnostic tool in microbiology laboratories.

Feasibility Study for the MALDI-MSI Analysis of Thyroid Fine Needle Aspiration Biopsies: Evaluating the Morphological and Proteomic Stability Over Time

PURPOSE

MALDI-MS imaging (MALDI-MSI) is an emerging technology that enables the spatial distribution of biomolecules within tissue to be combined with the traditional morphological information familiar to clinicians. Thus, for diagnostic or prognostic purposes, along with predicting response to therapeutic treatment, it is important to properly collect and handle biological specimens in order to avoid degradation or the formation of artifacts in the morphological structure and proteomic profile.

EXPERIMENTAL DESIGN

In this work, the morphological and proteomic stability of thyroid fine needle aspiration biopsies in PreservCyt (up to 14 days) and CytoLyt (up to 7 days) solutions at 4 °C has been verified, by MALDI-MSI analysis. Moreover, a new measure has been introduced in order to assess the similarity of the obtained MALDI-MSI spectra, by equally taking into account the number of signals (fit and retrofit), and their intensities (Spearman's correlation and spectra overlap).

RESULTS

Results show no degradation of the cellular morphology and a good stability of the samples up to 14 days in PreservCyt solution.

CONCLUSIONS AND CLINICAL RELEVANCE

Moreover, this protocol can be easily implemented in pathological units, allowing simple sample collection and shipment to be used not only for the proteomic MALDI-MSI analysis of thyroid FNABs but also for other biological liquid based specimens.

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.

Assessment by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry of the Effects of Preanalytical Variables on Serum Peptidome Profiles Following Long-Term Sample Storage

PURPOSE

Human serum and plasma are often used as clinical specimens in proteomics analyses, and peptidome profiling of human serum is a promising tool for identifying novel disease-associated biomarkers. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is widely used for peptidomic biomarker discovery. Careful sample collection and handling are required as either can have a profound impact on serum peptidome patterns, yet the effects of preanalytical variables on serum peptidome profiles have not been completely elucidated. The present study investigated the effects of preanalytical variables, including storage temperature, duration (up to 12 months), and thawing methods, on MALDI-TOF MS-based serum peptidome patterns.

EXPERIMENTAL DESIGN

Aliquots of serum samples were pretreated with weak cation exchanger magnetic beads using an automated ClinProtRobot system and then analyzed by MALDI-TOF MS.

RESULTS

A number of significant differences in peak intensities were observed depending on sample processing variables.

CONCLUSIONS AND CLINICAL RELEVANCE

These peaks can be used as sample quality markers to assess the effects of long-term storage on serum peptidome profiles using MALDI-TOF MS.

Detection and Identification of Serum Peptides Biomarker in Papillary Thyroid Cancer

Background

Papillary thyroid cancer (PTC) is currently the most commonly diagnosed endocrine malignancy. In addition, the sex- and age-adjusted incidence of PTC has exhibited a greater increase over the last 2 decades than in many other malignancies. Thus, discovering noninvasive specific serum biomarker to distinguish PTC from cancer-free controls in its early stages remains an important goal.

Material/Methods

Serum samples from 88 PTC patients and 80 cancer-free controls were randomly allocated into training or validation sets. Serum peptide profiling was performed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS) after using weak cation exchange magnetic beads (WCX-MB), and the results were evaluated by use of ClinProTools™ Software. To distinguish PTC from cancer-free controls, quick classifier (QC), supervised neural network (SNN), and genetic algorithm (GA) models were established. The models were blindly validated to verify their diagnostic capabilities. The most discriminative peaks were subsequently identified with a nano-liquid chromatography-electrospray ionization-tandem mass spectrometry system.

Results

Six peptide ions were identified as the most discriminative peaks between the PTC and cancer-free control samples. The QC model exhibited satisfactory sensitivity and specificity among the 3 models that were validated. Two peaks, at m/z 2671.17 and m/z 1464.68, were identified as fragments of the alpha chain of fibrinogen, while a peak at m/z 1738.92 was a fragment of complement component 4A/B.

Conclusions

MS combined with ClinProTools™ software was able to detect peptide biomarkers in PTC patients. In addition, the constructed classification models provided a serum peptidome pattern for distinguishing PTC from cancer-free controls. Both fibrinogen α and complement C4A/B were identified as potential markers for diagnosis of PTC.

How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota

INTRODUCTION

Describing the human hut gut microbiota is one the most exciting challenges of the 21^st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions. Areas covered: This review first underlines how mass spectrometric approaches have revolutionized clinical microbiology. It then highlights the contribution of MS-based methods to culturomics studies, paying particular attention to the extension of the human gut microbiota repertoire through the discovery of new bacterial species. Expert commentary: MS-based approaches have enabled cultivation methods to be resuscitated to study the human gut microbiota and thus to fill in the blanks left by high-throughput sequencing methods in terms of culturing minority populations. Continued efforts to recover new taxa using culture methods, combined with their rapid implementation in genomic databases, would allow for an exhaustive analysis of the gut microbiota through the use of a comprehensive approach.

Origins, Technological Development, and Applications of Peptidomics

Peptidomics is the comprehensive characterization of peptides from biological sources mainly by HPLC and mass spectrometry. Mass spectrometry allows the detection of a multitude of single peptides in complex mixtures. The term first appeared in full papers in the year 2001, after over 100 years of peptide research with a main focus on one or a few specific peptides. Within the last 15 years, this new field has grown to over 1200 publications. Mass spectrometry techniques, in combination with other analytical methods, were developed for the fast and comprehensive analysis of peptides in proteomics and specifically adjusted to implement peptidomics technologies. Although peptidomics is closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. The development of peptidomics is described, including the most important implementations for its technological basis. Different strategies are covered which are applied to several important applications, such as neuropeptidomics and discovery of bioactive peptides or biomarkers. This overview includes links to all other chapters in the book as well as recent developments of separation, mass spectrometric, and data processing technologies. Additionally, some new applications in food and plant peptidomics as well as immunopeptidomics are introduced.

Optimizing High-Resolution Mass Spectrometry for the Identification of Low-Abundance Post-Translational Modifications of Intact Proteins

Intact protein analysis by liquid chromatography-mass spectrometry (LC-MS) is now possible due to the improved capabilities of mass spectrometers yielding greater resolution, mass accuracy, and extended mass ranges. Concurrent measurement of post-translational modifications (PTMs) during LC-MS of intact proteins is advantageous while monitoring critical proteoform status, such as for clinical samples or during production of reference materials. However, difficulties exist for PTM identification when the protein is large or contains multiple modification sites. In this work, analyses of low-abundance proteoforms of proteins of clinical or therapeutic interest, including C-reactive protein, vitamin D-binding protein, transferrin, and immunoglobulin G (NISTmAb), were performed on an Orbitrap Elite mass spectrometer. This work investigated the effect of various instrument parameters including source temperatures, in-source CID, microscan type and quantity, resolution, and automatic gain control on spectral quality. The signal-to-noise ratio was found to be a suitable spectral attribute which facilitated identification of low abundance PTMs. Source temperature and CID voltage were found to require specific optimization for each protein. This study identifies key instrumental parameters requiring optimization for improved detection of a variety of PTMs by LC-MS and establishes a methodological framework to ensure robust proteoform identifications, the first step in their ultimate quantification.

A rapid differential display analysis of nasal swab fingerprints to distinguish allergic from non-allergic rhinitis subjects by mesoporous silica particles and MALDI-TOF mass spectrometry

Discriminating different rhinitis cases can sometimes be difficult as the diagnostic criteria used to identify the various subgroups are not always unambiguous. The nasal fluid (NF) highly reflects the pathophysiology of these inflammatory diseases. However, its collection, as nasal lavage fluid, may cause discomfort. Due to the non-invasiveness and rapidity of collection, nasal swab might represent an alternative to overcome these problems and also an ideal source of biomarkers. In this study, we demonstrate that the combined use of mesoporous silica (MPS) with MALDI-TOF MS allows the rapid detection of differential nasal peptide profiles from nasal swabs of healthy (H), allergic rhinitis (AR) and non-allergic rhinitis (NAR) subjects. NF peptides from nasal swabs were captured by the mean of MPS then profiled by MALDI-TOF MS. As a proof-of-principle, we also explored the ability of our platform to discriminate between nasal swabs of patients with AR and NAR, and between these groups and H controls. Four peaks resulted differentially expressed between NAR and AR, two peaks discriminated AR from H while one peak segregated NAR from H group. Therefore, peptides selected and enriched by our platform could form a part of a diagnostic ''rhinomic'' profile of the allergic and non-allergic patients.

Informed baseline subtraction of proteomic mass spectrometry data aided by a novel sliding window algorithm

Background

Proteomic matrix-assisted laser desorption/ionisation (MALDI) linear time-of-flight (TOF) mass spectrometry (MS) may be used to produce protein profiles from biological samples with the aim of discovering biomarkers for disease. However, the raw protein profiles suffer from several sources of bias or systematic variation which need to be removed via pre-processing before meaningful downstream analysis of the data can be undertaken. Baseline subtraction, an early pre-processing step that removes the non-peptide signal from the spectra, is complicated by the following: (i) each spectrum has, on average, wider peaks for peptides with higher mass-to-charge ratios (m/z), and (ii) the time-consuming and error-prone trial-and-error process for optimising the baseline subtraction input arguments. With reference to the aforementioned complications, we present an automated pipeline that includes (i) a novel ‘continuous’ line segment algorithm that efficiently operates over data with a transformed m/z-axis to remove the relationship between peptide mass and peak width, and (ii) an input-free algorithm to estimate peak widths on the transformed m/z scale.

Results

The automated baseline subtraction method was deployed on six publicly available proteomic MS datasets using six different m/z-axis transformations. Optimality of the automated baseline subtraction pipeline was assessed quantitatively using the mean absolute scaled error (MASE) when compared to a gold-standard baseline subtracted signal. Several of the transformations investigated were able to reduce, if not entirely remove, the peak width and peak location relationship resulting in near-optimal baseline subtraction using the automated pipeline. The proposed novel ‘continuous’ line segment algorithm is shown to far outperform naive sliding window algorithms with regard to the computational time required. The improvement in computational time was at least four-fold on real MALDI TOF-MS data and at least an order of magnitude on many simulated datasets.

Conclusions

The advantages of the proposed pipeline include informed and data specific input arguments for baseline subtraction methods, the avoidance of time-intensive and subjective piecewise baseline subtraction, and the ability to automate baseline subtraction completely. Moreover, individual steps can be adopted as stand-alone routines.

Electronic supplementary material

The online version of this article (doi:10.1186/s12953-016-0107-8) contains supplementary material, which is available to authorized users.

Critical factors determining the quantification capability of matrix-assisted laser desorption/ionization- time-of-flight mass spectrometry

Quantitative analysis with mass spectrometry (MS) is important but challenging. Matrix-assisted laser desorption/ionization (MALDI) coupled with time-of-flight (TOF) MS offers superior sensitivity, resolution and speed, but such techniques have numerous disadvantages that hinder quantitative analyses. This review summarizes essential obstacles to analyte quantification with MALDI-TOF MS, including the complex ionization mechanism of MALDI, sensitive characteristics of the applied electric fields and the mass-dependent detection efficiency of ion detectors. General quantitative ionization and desorption interpretations of ion production are described. Important instrument parameters and available methods of MALDI-TOF MS used for quantitative analysis are also reviewed.This article is part of the themed issue 'Quantitative mass spectrometry'.

Salivary peptidome profiling for diagnosis of severe early childhood caries

BACKGROUND

Severe early childhood caries (s-ECC), which has quite high prevalence among children, is a widespread problem with significant impacts among both developing and developed countries. At present, it is widely known that no early detective techniques and diagnostic tests could have high sensitivity and specificity when using for clinical screening of s-ECC. In this study, we had applied magnetic bead (MB)-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to screen distinctive candidate biomarkers of this disease, so as to establish protein profiles and diagnostic models of s-ECC.

METHODS

Firstly, we used the technique mentioned above to detect specifically expressed peptides in saliva samples from ten children with s-ECC, separately at the time point of before, 1 and 4 weeks after dental treatment. Then a diagnostic model for s-ECC was established with the K nearest-neighbour method, which was validated in another six children in the next stage of study. After that, linear ion trap-orbitrap-mass spectrometry (LTQ-Orbitrap-MS) was performed to identify which of the proteins in saliva might be the origination of these peptides.

RESULTS

We found that seven peptide peaks were significantly different when comparing the three time points, among them two were higher, while other five were lower in the pre-treatment s-ECC group compared with post-treatment. The sensitivity and specificity of the diagnostic model we built were both 83.3 %. Two of these peptides were identified to be segments of histatin-1, which was one important secretory protein in saliva.

CONCLUSIONS

Hereby we confirmed that MB-based MALDI-TOF MS is an effective method for screening distinctive peptides from the saliva of junior patients with s-ECC, and histatin-1 may probably be one important candidate biomarker of this common dental disease. These findings might have bright prospect in future in establishing new diagnostic methods for s-ECC.

Targeted Treatment for Bacterial Infections: Prospects for Pathogen-Specific Antibiotics Coupled with Rapid Diagnostics

Antibiotics are a cornerstone of modern medicine and have significantly reduced the burden of infectious diseases. However, commonly used broad-spectrum antibiotics can cause major collateral damage to the human microbiome, causing complications ranging from antibiotic-associated colitis to the rapid spread of resistance. Employing narrower spectrum antibiotics targeting specific pathogens may alleviate this predicament as well as provide additional tools to expand an antibiotic repertoire threatened by the inevitability of resistance. Improvements in clinical diagnosis will be required to effectively utilize pathogen-specific antibiotics and new molecular diagnostics are poised to fulfill this need. Here we review recent trends and the future prospects of deploying narrower spectrum antibiotics coupled with rapid diagnostics. Further, we discuss the theoretical advantages and limitations of this emerging approach to controlling bacterial infectious diseases.

Development of a MALDI MS-based platform for early detection of acute kidney injury

PURPOSE

Septic acute kidney injury (AKI) is associated with poor outcome. This can partly be attributed to delayed diagnosis and incomplete understanding of the underlying pathophysiology. Our aim was to develop an early predictive test for AKI based on the analysis of urinary peptide biomarkers by MALDI-MS.

EXPERIMENTAL DESIGN

Urine samples from 95 patients with sepsis were analyzed by MALDI-MS. Marker search and multimarker model establishment were performed using the peptide profiles from 17 patients with existing or within the next 5 days developing AKI and 17 with no change in renal function. Replicates of urine sample pools from the AKI and non-AKI patient groups and normal controls were also included to select the analytically most robust AKI markers.

RESULTS

Thirty-nine urinary peptides were selected by cross-validated variable selection to generate a support vector machine multidimensional AKI classifier. Prognostic performance of the AKI classifier on an independent validation set including the remaining 61 patients of the study population (17 controls and 44 cases) was good with an area under the receiver operating characteristics curve of 0.82 and a sensitivity and specificity of 86% and 76%, respectively.

CONCLUSION AND CLINICAL RELEVANCE

A urinary peptide marker model detects onset of AKI with acceptable accuracy in septic patients. Such a platform can eventually be transferred to the clinic as fast MALDI-MS test format.

Challenges in biomarker discovery with MALDI-TOF MS

MALDI-TOF MS technique is commonly used in system biology and clinical studies to search for new potential markers associated with pathological conditions. Despite numerous concerns regarding a sample preparation or processing of complex data, this strategy is still recognized as a popular tool and its awareness has risen in the proteomic community over the last decade. In this review, we present comprehensive application of MALDI mass spectrometry with special focus on profiling research. We also discuss major advantages and disadvantages of universal sample preparation methods such as micro-SPE columns, immunodepletion or magnetic beads, and we show the potential of nanostructured materials in capturing low molecular weight subproteomes. Furthermore, as the general protocol considerably affects spectra quality and interpretation, an alternative solution for improved ion detection, including hydrophobic constituents, data processing and statistical analysis is being considered in up-to-date profiling pattern. In conclusion, many reports involving MALDI-TOF MS indicated highly abundant proteins as valuable indicators, and at the same time showed the inaccuracy of available methods in the detection of low abundant proteome that is the most interesting from the clinical perspective. Therefore, the analytical aspects of sample preparation methods should be standardized to provide a reproducible, low sample handling and credible procedure.