General overview: biomarkers in neuroscience research

Proteomic analysis of peripheral blood mononuclear cells in first episode psychosis - Protein and peptide-centered approaches to elucidate potential diagnostic biomarkers

Diagnosing patients suffering from psychotic disorders is far from being achieved with molecular support, despite all the efforts to study these disorders from different perspectives. Characterizing the proteome of easily obtainable blood specimens, such as the peripheral blood mononuclear cells (PBMCs), has particular interest in biomarker discovery and generating pathophysiological knowledge. This approach has been explored in psychiatry, and while generating valuable information, it has not translated into meaningful biomarker discovery. In this project, we report the proof-of-concept of a methodology that aims to explore further information obtained with classical proteomics approaches that is easily overlooked. PBMC samples from first-episode psychosis and control subjects were subjected to a SWATH-MS approach, and the classical protein relative quantification was performed, where 389 proteins were found to be important to distinguish the two groups. Individual analysis of the quantified peptides was also performed, highlighting peptides of unchanged proteins that were significantly altered. With the combination of protein- and peptide-centered proteomics approaches, it is possible to highlight that information about proteoforms, namely regulation at the peptide level possibly due to post-translational modifications, is routinely overlooked and that its diagnostic potential should be further explored. SIGNIFICANCE: Our exploratory findings highlight the potential of MS-based proteomics strategies, combining protein- and peptide-centered approaches, to aid clinical decision-making in first-episode psychosis, helping to establish early biomarkers for schizophrenia and other psychotic disorders. Particularly, the less popular peptide-centered approach allows the identification/measurement of overlooked modulated peptides that may have potential biomarker characteristics. The application in parallel of protein- and peptide-centered strategies is transversal to research of other diseases, potentially allowing a more comprehensive characterization of the metabolic/pathophysiological alterations related to a specific disease.

Altered lipidomics biosignatures in schizophrenia: A systematic review

Multiomics approaches have significantly aided the identification of molecular signatures in complex neuropsychiatric disorders. Lipidomics, one of the newest additions in the -omics family, sheds light on lipid profiles and is an emerging methodological tool to study schizophrenia pathobiology, as lipid dysregulation has been repeatedly observed in schizophrenia. In this review, we performed a detailed literature search for lipidomics studies in schizophrenia. Following elaborate inclusion/exclusion criteria, we focused on human studies in schizophrenia and schizophrenia-related diagnoses in brain and blood specimens, including serum plasma, platelets and red blood cells. Eighteen studies fulfilled our inclusion criteria, of which five were conducted in the brain, 12 in peripheral material and one in both. Here, we first provide background on lipidomics and the main lipid categories addressed, review in detail the included literature and look for common lipidomics patterns in brain and the periphery that emerge from these studies. Furthermore, we highlight current limitations in schizophrenia lipidomics research and underline the need for following up on lipidomics results with complementary molecular approaches.

Systematic Review and Meta-Analysis on MS-Based Proteomics Applied to Human Peripheral Fluids to Assess Potential Biomarkers of Bipolar Disorder

Bipolar disorder (BD) is a clinically heterogeneous condition, presenting a complex underlying etiopathogenesis that is not sufficiently characterized. Without molecular biomarkers being used in the clinical environment, several large screen proteomics studies have been conducted to provide valuable molecular information. Mass spectrometry (MS)-based techniques can be a powerful tool for the identification of disease biomarkers, improving prediction and diagnosis ability. Here, we evaluate the efficacy of MS proteomics applied to human peripheral fluids to assess BD biomarkers and identify relevant networks of biological pathways. Following PRISMA guidelines, we searched for studies using MS proteomics to identify proteomic differences between BD patients and healthy controls (PROSPERO database: CRD42021264955). Fourteen articles fulfilled the inclusion criteria, allowing the identification of 266 differentially expressed proteins. Gene ontology analysis identified complement and coagulation cascades, lipid and cholesterol metabolism, and focal adhesion as the main enriched biological pathways. A meta-analysis was performed for apolipoproteins (A-I, C-III, and E); however, no significant differences were found. Although the proven ability of MS proteomics to characterize BD, there are several confounding factors contributing to the heterogeneity of the findings. In the future, we encourage the scientific community to use broader samples and validation cohorts, integrating omics with bioinformatics tools towards providing a comprehensive understanding of proteome alterations, seeking biomarkers of BD, and contributing to individualized prognosis and stratification strategies, besides aiding in the differential diagnosis.

Systematic Review and Meta-Analysis of Mass Spectrometry Proteomics Applied to Human Peripheral Fluids to Assess Potential Biomarkers of Schizophrenia

Mass spectrometry (MS)-based techniques can be a powerful tool to identify neuropsychiatric disorder biomarkers, improving prediction and diagnosis ability. Here, we evaluate the efficacy of MS proteomics applied to human peripheral fluids of schizophrenia (SCZ) patients to identify disease biomarkers and relevant networks of biological pathways. Following PRISMA guidelines, a search was performed for studies that used MS proteomics approaches to identify proteomic differences between SCZ patients and healthy control groups (PROSPERO database: CRD42021274183). Nineteen articles fulfilled the inclusion criteria, allowing the identification of 217 differentially expressed proteins. Gene ontology analysis identified lipid metabolism, complement and coagulation cascades, and immune response as the main enriched biological pathways. Meta-analysis results suggest the upregulation of FCN3 and downregulation of APO1, APOA2, APOC1, and APOC3 in SCZ patients. Despite the proven ability of MS proteomics to characterize SCZ, several confounding factors contribute to the heterogeneity of the findings. In the future, we encourage the scientific community to perform studies with more extensive sampling and validation cohorts, integrating omics with bioinformatics tools to provide additional comprehension of differentially expressed proteins. The produced information could harbor potential proteomic biomarkers of SCZ, contributing to individualized prognosis and stratification strategies, besides aiding in the differential diagnosis.

TAPAS: An Open-Source Software Package for Translational Neuromodeling and Computational Psychiatry

Psychiatry faces fundamental challenges with regard to mechanistically guided differential diagnosis, as well as prediction of clinical trajectories and treatment response of individual patients. This has motivated the genesis of two closely intertwined fields: (i) Translational Neuromodeling (TN), which develops "computational assays" for inferring patient-specific disease processes from neuroimaging, electrophysiological, and behavioral data; and (ii) Computational Psychiatry (CP), with the goal of incorporating computational assays into clinical decision making in everyday practice. In order to serve as objective and reliable tools for clinical routine, computational assays require end-to-end pipelines from raw data (input) to clinically useful information (output). While these are yet to be established in clinical practice, individual components of this general end-to-end pipeline are being developed and made openly available for community use. In this paper, we present the Translational Algorithms for Psychiatry-Advancing Science (TAPAS) software package, an open-source collection of building blocks for computational assays in psychiatry. Collectively, the tools in TAPAS presently cover several important aspects of the desired end-to-end pipeline, including: (i) tailored experimental designs and optimization of measurement strategy prior to data acquisition, (ii) quality control during data acquisition, and (iii) artifact correction, statistical inference, and clinical application after data acquisition. Here, we review the different tools within TAPAS and illustrate how these may help provide a deeper understanding of neural and cognitive mechanisms of disease, with the ultimate goal of establishing automatized pipelines for predictions about individual patients. We hope that the openly available tools in TAPAS will contribute to the further development of TN/CP and facilitate the translation of advances in computational neuroscience into clinically relevant computational assays.

Alpha7 nicotinic-N-methyl-D-aspartate hypothesis in the treatment of schizophrenia and beyond

Development of novel treatments for positive, cognitive, and negative symptoms continue to be a high-priority area of schizophrenia research and a major unmet clinical need. Given that all randomized controlled trials (RCTs) conducted to date failed with one add-on medication/mechanism of action, future RCTs with the same approach are not warranted. Even if the field develops a medication for cognition, others are still needed to treat negative and positive symptoms. Therefore, fixing one domain does not completely solve the problem. Also, targeting the cholinergic system, glutamatergic system, and cholinergic plus alpha7 nicotinic and N-methyl-D-aspartate (NMDA) receptors failed independently. Hence, targeting other less important pathophysiological mechanisms/targets is unlikely to be successful. Meta-analyses of RCTs targeting major pathophysiological mechanisms have found some efficacy signal in schizophrenia; thus, combination treatments with different mechanisms of action may enhance the efficacy signal. The objective of this article is to highlight the importance of conducting RCTs with novel combination treatments in schizophrenia to develop antischizophrenia treatments. Positive RCTs with novel combination treatments that target the alpha7 nicotinic and NMDA receptors simultaneously may lead to a disease-modifying therapeutic armamentarium in schizophrenia. Novel combination treatments that concurrently improve the three domains of psychopathology and several prognostic and theranostic biomarkers may facilitate therapeutic discovery in schizophrenia.

Analysis of Cerebrospinal Fluid Extracellular Vesicles by Proximity Extension Assay: A Comparative Study of Four Isolation Kits

There is a lack of reliable biomarkers for disorders of the central nervous system (CNS), and diagnostics still heavily rely on symptoms that are both subjective and difficult to quantify. The cerebrospinal fluid (CSF) is a promising source of biomarkers due to its close connection to the CNS. Extracellular vesicles are actively secreted by cells, and proteomic analysis of CSF extracellular vesicles (EVs) and their molecular composition likely reflects changes in the CNS to a higher extent compared with total CSF, especially in the case of neuroinflammation, which could increase blood–brain barrier permeability and cause an influx of plasma proteins into the CSF. We used proximity extension assay for proteomic analysis due to its high sensitivity. We believe that this methodology could be useful for de novo biomarker discovery for several CNS diseases. We compared four commercially available kits for EV isolation: MagCapture and ExoIntact (based on magnetic beads), EVSecond L70 (size-exclusion chromatography), and exoEasy (membrane affinity). The isolated EVs were characterized by nanoparticle tracking analysis, ELISA (CD63, CD81 and albumin), and proximity extension assay (PEA) using two different panels, each consisting of 92 markers. The exoEasy samples did not pass the built-in quality controls and were excluded from downstream analysis. The number of detectable proteins in the ExoIntact samples was considerably higher (~150% for the cardiovascular III panel and ~320% for the cell regulation panel) compared with other groups. ExoIntact also showed the highest intersample correlation with an average Pearson’s correlation coefficient of 0.991 compared with 0.985 and 0.927 for MagCapture and EVSecond, respectively. The median coefficient of variation was 5%, 8%, and 22% for ExoIntact, MagCapture, and EVSecond, respectively. Comparing total CSF and ExoIntact samples revealed 70 differentially expressed proteins in the cardiovascular III panel and 17 in the cell regulation panel. To our knowledge, this is the first time that CSF EVs were analyzed by PEA. In conclusion, analysis of CSF EVs by PEA is feasible, and different isolation kits give distinct results, with ExoIntact showing the highest number of identified proteins with the lowest variability.

Current challenges and possible future developments in personalized psychiatry with an emphasis on psychotic disorders

A personalized medicine approach seems to be particularly applicable to psychiatry. Indeed, considering mental illness as deregulation, unique to each patient, of molecular pathways, governing the development and functioning of the brain, seems to be the most justified way to understand and treat disorders of this medical category. In order to extract correct information about the implicated molecular pathways, data can be drawn from sampling phenotypic and genetic biomarkers and then analyzed by a machine learning algorithm. This review describes current difficulties in the field of personalized psychiatry and gives several examples of possibly actionable biomarkers of psychotic and other psychiatric disorders, including several examples of genetic studies relevant to personalized psychiatry. Most of these biomarkers are not yet ready to be introduced in clinical practice. In a next step, a perspective on the path personalized psychiatry may take in the future is given, paying particular attention to machine learning algorithms that can be used with the goal of handling multidimensional datasets.

Heterogeneity of executive function revealed by a functional random forest approach across ADHD and ASD

BACKGROUND

Those with autism spectrum disorder (ASD) and/or attention-deficit-hyperactivity disorder (ADHD) exhibit symptoms of hyperactivity and inattention, causing significant hardships for families and society. A potential mechanism involved in these conditions is atypical executive function (EF). Inconsistent findings highlight that EF features may be shared or distinct across ADHD and ASD. With ADHD and ASD each also being heterogeneous, we hypothesized that there may be nested subgroups across disorders with shared or unique underlying mechanisms.

METHODS

Participants (N = 130) included adolescents aged 7-16 with ASD (n = 64) and ADHD (n = 66). Typically developing (TD) participants (n = 28) were included for a comparative secondary sub-group analysis. Parents completed the K-SADS and youth completed an extended battery of executive and other cognitive measures. A two stage hybrid machine learning tool called functional random forest (FRF) was applied as a classification approach and then subsequently to subgroup identification. We input 43 EF variables to the classification step, a supervised random forest procedure in which the features estimated either hyperactive or inattentive ADHD symptoms per model. The FRF then produced proximity matrices and identified optimal subgroups via the infomap algorithm (a type of community detection derived from graph theory). Resting state functional connectivity MRI (rs-fMRI) was used to evaluate the neurobiological validity of the resulting subgroups.

RESULTS

Both hyperactive (Mean absolute error (MAE) = 0.72, Null model MAE = 0.8826, (t(58) = -4.9, p < .001) and inattentive (MAE = 0.7, Null model MAE = 0.85, t(58) = -4.4, p < .001) symptoms were predicted better than chance by the EF features selected. Subgroup identification was robust (Hyperactive: Q = 0.2356, p < .001; Inattentive: Q = 0.2350, p < .001). Two subgroups representing severe and mild symptomology were identified for each symptom domain. Neuroimaging data revealed that the subgroups and TD participants significantly differed within and between multiple functional brain networks, but no consistent "severity" patterns of over or under connectivity were observed between subgroups and TD.

CONCLUSION

The FRF estimated hyperactive/inattentive symptoms and identified 2 distinct subgroups per model, revealing distinct neurocognitive profiles of Severe and Mild EF performance per model. Differences in functional connectivity between subgroups did not appear to follow a severity pattern based on symptom expression, suggesting a more complex mechanistic interaction that cannot be attributed to symptom presentation alone.

Unraveling the Serum Metabolomic Profile of Post-partum Depression

Post-partum depression (PPD) is a severe psychiatric disorder affecting ∼15% of young mothers. Early life stressful conditions in periconceptual, fetal and early infant periods or exposure to maternal psychiatric disorders, have been linked to adverse childhood outcomes interfering with physiological, cognitive and emotional development. The molecular mechanisms of PPD are not yet fully understood. Unraveling the molecular underpinnings of PPD will allow timely detection and establishment of effective therapeutic approaches. To investigate the underlying molecular correlates of PPD in peripheral material, we compared the serum metabolomes of an in detail characterized group of mothers suffering from PPD and a control group of mothers, all from Heraklion, Crete in Greece. Serum samples were analyzed by a mass spectrometry platform for targeted metabolomics, based on selected reaction monitoring (SRM), which measures the levels of up to 300 metabolites. In the PPD group, we observed increased levels of glutathione-disulfide, adenylosuccinate, and ATP, which associate with oxidative stress, nucleotide biosynthesis and energy production pathways. We also followed up the metabolomic findings in a validation cohort of PPD mothers and controls. To the very best of our knowledge, this is the first metabolomic serum analysis in PPD. Our data show that molecular changes related to PPD are detectable in peripheral material, thus paving the way for additional studies in order to shed light on the molecular correlates of PPD.

When a duck is not a duck; a new interdisciplinary synthesis for environmental radiation protection

This consensus paper presents the results of a workshop held in Essen, Germany in September 2017, called to examine critically the current approach to radiological environmental protection. The meeting brought together participants from the field of low dose radiobiology and those working in radioecology. Both groups have a common aim of identifying radiation exposures and protecting populations and individuals from harmful effects of ionising radiation exposure, but rarely work closely together. A key question in radiobiology is to understand mechanisms triggered by low doses or dose rates, leading to adverse outcomes of individuals while in radioecology a key objective is to recognise when harm is occurring at the level of the ecosystem. The discussion provided a total of six strategic recommendations which would help to address these questions.

Generative models for clinical applications in computational psychiatry

Despite the success of modern neuroimaging techniques in furthering our understanding of cognitive and pathophysiological processes, translation of these advances into clinically relevant tools has been virtually absent until now. Neuromodeling represents a powerful framework for overcoming this translational deadlock, and the development of computational models to solve clinical problems has become a major scientific goal over the last decade, as reflected by the emergence of clinically oriented neuromodeling fields like Computational Psychiatry, Computational Neurology, and Computational Psychosomatics. Generative models of brain physiology and connectivity in the human brain play a key role in this endeavor, striving for computational assays that can be applied to neuroimaging data from individual patients for differential diagnosis and treatment prediction. In this review, we focus on dynamic causal modeling (DCM) and its use for Computational Psychiatry. DCM is a widely used generative modeling framework for functional magnetic resonance imaging (fMRI) and magneto-/electroencephalography (M/EEG) data. This article reviews the basic concepts of DCM, revisits examples where it has proven valuable for addressing clinically relevant questions, and critically discusses methodological challenges and recent methodological advances. We conclude this review with a more general discussion of the promises and pitfalls of generative models in Computational Psychiatry and highlight the path that lies ahead of us. This article is categorized under: Neuroscience > Computation Neuroscience > Clinical Neuroscience.

A Roadmap for the Development of Applied Computational Psychiatry

BACKGROUND

Computational psychiatry is a burgeoning field that utilizes mathematical approaches to investigate psychiatric disorders, derive quantitative predictions, and integrate data across multiple levels of description. Computational psychiatry has already led to many new insights into the neurobehavioral mechanisms that underlie several psychiatric disorders, but its usefulness from a clinical standpoint is only now starting to be considered.

METHODS

Examples of computational psychiatry are highlighted, and a phase-based pipeline for the development of clinical computational-psychiatry applications is proposed, similar to the phase-based pipeline used in drug development. It is proposed that each phase has unique endpoints and deliverables, which will be important milestones to move tasks, procedures, computational models, and algorithms from the laboratory to clinical practice.

RESULTS

Application of computational approaches should be tested on healthy volunteers in Phase I, transitioned to target populations in Phase IB and Phase IIA, and thoroughly evaluated using randomized clinical trials in Phase IIB and Phase III. Successful completion of these phases should be the basis of determining whether computational models are useful tools for prognosis, diagnosis, or treatment of psychiatric patients.

CONCLUSIONS

A new type of infrastructure will be necessary to implement the proposed pipeline. This infrastructure should consist of groups of investigators with diverse backgrounds collaborating to make computational psychiatry relevant for the clinic.

Blood microsampling from the ear capillary in non-human primates

Blood sampling from awake non-human primates (NHPs) is classically performed under constraint in the cephalic or saphenous vein. It is a challenging, potentially harmful and stressful procedure which may lead to biased results and raises ethical concerns. Laboratory NHPs undergo a head-restrained procedure allowing for a safer procedure of collecting blood from their ears. Using regular capillary blood collection devices 500 µL of blood can be easily withdrawn per puncture point, which is sufficient for performing most of the usual modern biological assays. This procedure has been validated by measuring total proteins, cortisol and vasopressin concentrations from concomitant blood samples taken from the saphenous vein and the ear capillary vessels of macaques (n = 16). We observed strong correlations between the blood concentrations of total proteins, cortisol and vasopressin (r = 0.72, r = 0.63, r = 0.83, respectively; all P values <0.01) taken from the saphenous vein and from the ear capillary. There were no significant differences between blood concentrations taken from the saphenous vein and the ear capillary. Our alternative to the classical blood collection procedure is harmless and can be routinely performed, which can therefore improve scientific results while increasing animal welfare in accordance with the 3R (replacement, reduction and refinement) principles.

Can proteomics-based diagnostics aid clinical psychiatry?

Despite major advances in infrastructure and instrumentation, proteomics-driven translational applications have not yet yielded the results that the scientific community has envisaged. In this viewpoint, the perspective of proteomics-based diagnostics in the field of clinical psychiatry is explored. The challenges that proteomics faces in the context of translational approaches are outlined and directions toward a successful clinical implementation are provided. Additional challenges that psychiatric disorders pose for clinical proteomics are highlighted and the potential of proteomics-based, blood tests for psychiatric disorders is being assessed. Proteomics offers a valuable toolkit for clinical translation that needs to be handled in a pragmatic manner and with realistic expectations.

Changing requirements and resulting needs for IT-infrastructure for longitudinal research in the neurosciences

The observation of growing "difficulties" in IT-infrastructures in neuroscience research during the last years led to a search for reasons and an analysis on how this phenomenon is reflected in the scientific literature. With a retrospective analysis of nine examples of multicenter research projects in the neurosciences and a literature review the observation was systematically analyzed. Results show that the rise in complexity mainly stems from two reasons: (1) more and more need for information on quality and context of research data (metadata) and (2) long-term requirements to handle the consent and identity/pseudonyms of study participants and biomaterials in relation to legal requirements. The combination of these two aspects together with very long study times and data evaluation periods are components of the subjectively perceived "difficulties". A direct consequence of this result is that big multicenter trials are becoming part of integrated research data environments and are not standing alone for themselves anymore. This drives up the resource needs regarding the IT-infrastructure in neuroscience research. In contrast to these findings, literature on this development is scarce and the problem probably underestimated.

Biomarkers of coronary artery disease: the promise of the transcriptome

The last years have witnessed tremendous technical advances in the field of transcriptomics that enable the simultaneous assessment of nearly all transcripts expressed in a tissue at a given time. These advances harbor the potential to gain a better understanding of the complex biological systems and for the identification and development of novel biomarkers. This article will review the current knowledge of transcriptomics biomarkers in the cardiovascular field and will provide an overview about the promises and challenges of the transcriptomics approach for biomarker identification.

A decade of proteomics studies of glaucomatous neurodegeneration

Glaucoma is a leading cause of blindness; however, limited understanding of the molecular mechanisms involved in optic nerve degeneration hinders the development of improved treatment strategies. Proteomics techniques that combine the protein chemistry, MS, and bioinformatics offer the opportunity to shed light on molecular mechanisms so that new treatment strategies can be developed for immunomodulation, neuroprotection, neurorescue, neuroregeneration, and function gain in glaucoma. The proteomics technologies also hold great promise for biomarker discovery, another important goal of glaucoma research. As much as developing new treatment strategies, molecular biomarkers are strongly needed for early diagnosis of glaucoma, prediction of its prognosis, and monitoring the responses to new treatments. It is now a decade that the proteomics analysis techniques have been using to move glaucoma research forward. This review will focus on valuable applications of proteomics in the field of glaucoma research and highlight the power of this analytical toolbox in translational and clinical research toward better characterization and improved treatment of glaucomatous neurodegeneration and discovery of glaucoma-related molecular biomarkers.

Point-of-care testing and the control of infectious diseases

Point-of-care tests (POCTs) play an important role in bridging the gap between centralized laboratory diagnostics and peripheral healthcare service providers. Particularly in infectious diseases such as HIV/AIDS and TB where early detection is imperative to improve disease outcome, uptake of an accurate test that is simple, rapid and robust can significantly alter the epidemiology and control of the disease. However, a good POCT can only serve its full potential when adopted in a comprehensive programmatic context linking patients to on-site case management. Immunochromatographic lateral flow devices for detection of antibody or antigen currently dominate available POCTs, and development of such devices has relied on the discovery and optimization of definitive biomarkers suitable for such platforms. In the future, however, there will be an increasing need to develop cost-effective POCTs that address biomarkers that are well established in laboratory settings but are not currently amenable to point-of-care, such as molecular tests for drug resistance in TB and viral load in HIV and viral hepatitis.

Neuropsychiatry: where are we and where do we go from here?

Introduction:

Neuropsychiatry has generally been regarded as a hybrid discipline that lies in the borderland between the disciplines of psychiatry and neurology. There is much debate on its current and future identity and status as a discipline.

Materials and Methods:

Taking a historical perspective, the future of neuropsychiatry is placed within the context of recent developments in clinical neuroscience.

Results:

The authors argue that with the maturation of the discipline, it must define its own identity that is not dependent entirely upon the parent disciplines. The requirements for this are the claiming of neuropsychiatric territory, a strong training agenda, an emphasis on treatments that are uniquely neuropsychiatric, and a bold embrace of new developments in clinical neuroscience.

Conclusion:

The exponential growth in neuroscientific knowledge places neuropsychiatry in an excellent position to carve out a strong identity. It is imperative that the leaders of the discipline seize the moment.

A proteomics view of the molecular mechanisms and biomarkers of glaucomatous neurodegeneration

Despite improving understanding of glaucoma, key molecular players of neurodegeneration that can be targeted for treatment of glaucoma, or molecular biomarkers that can be useful for clinical testing, remain unclear. Proteomics technology offers a powerful toolbox to accomplish these important goals of the glaucoma research and is increasingly being applied to identify molecular mechanisms and biomarkers of glaucoma. Recent studies of glaucoma using proteomics analysis techniques have resulted in the lists of differentially expressed proteins in human glaucoma and animal models. The global analysis of protein expression in glaucoma has been followed by cell-specific proteome analysis of retinal ganglion cells and astrocytes. The proteomics data have also guided targeted studies to identify post-translational modifications and protein-protein interactions during glaucomatous neurodegeneration. In addition, recent applications of proteomics have provided a number of potential biomarker candidates. Proteomics technology holds great promise to move glaucoma research forward toward new treatment strategies and biomarker discovery. By reviewing the major proteomics approaches and their applications in the field of glaucoma, this article highlights the power of proteomics in translational and clinical research related to glaucoma and also provides a framework for future research to functionally test the importance of specific molecular pathways and validate candidate biomarkers.