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Routine measurement of cancer biomarkers is performed for early detection, risk classification, and treatment monitoring, among other applications, and has substantially contributed to better clinical outcomes for patients. However, there remains an unmet need for clinically validated assays of cancer protein biomarkers. Protein tumor markers are of particular interest since proteins carry out the majority of biological processes and thus dynamically reflect changes in cancer pathophysiology. Mass spectrometry-based targeted proteomics is a powerful tool for absolute peptide and protein quantification in biological matrices with numerous advantages that make it attractive for clinical applications in oncology. The use of liquid chromatography-tandem mass spectrometry (LC–MS/MS) based methodologies has allowed laboratories to overcome challenges associated with immunoassays that are more widely used for tumor marker measurements. Yet, clinical implementation of targeted proteomics methodologies has so far been limited to a few cancer markers. This is due to numerous challenges associated with paucity of robust validation studies of new biomarkers and the labor-intensive and operationally complex nature of LC–MS/MS workflows. The purpose of this review is to provide an overview of targeted proteomics applications in cancer, workflows used in targeted proteomics, and requirements for clinical validation and implementation of targeted proteomics assays. We will also discuss advantages and challenges of targeted MS-based proteomics assays for clinical cancer biomarker analysis and highlight some recent developments that will positively contribute to the implementation of this technique into clinical laboratories.

High‐throughput and streamlined workflows are essential in clinical proteomics for standardized processing of samples from a variety of sources, including fresh‐frozen tissue, FFPE tissue, or blood. To reach this goal, we have implemented single‐pot solid‐phase‐enhanced sample preparation (SP3) on a liquid handling robot for automated processing (autoSP3) of tissue lysates in a 96‐well format. AutoSP3 performs unbiased protein purification and digestion, and delivers peptides that can be directly analyzed by LCMS, thereby significantly reducing hands‐on time, reducing variability in protein quantification, and improving longitudinal reproducibility. We demonstrate the distinguishing ability of autoSP3 to process low‐input samples, reproducibly quantifying 500–1,000 proteins from 100 to 1,000 cells. Furthermore, we applied this approach to a cohort of clinical FFPE pulmonary adenocarcinoma (ADC) samples and recapitulated their separation into known histological growth patterns. Finally, we integrated autoSP3 with AFA ultrasonication for the automated end‐to‐end sample preparation and LCMS analysis of 96 intact tissue samples. Collectively, this constitutes a generic, scalable, and cost‐effective workflow with minimal manual intervention, enabling reproducible tissue proteomics in a broad range of clinical and non‐clinical applications. Synopsis The study presents an automated sample preparation pipeline for low‐input proteomics based on the SP3 method. The seamless integration of tissue lysis with autoSP3 in a 96‐well format features low variability, high sensitivity and longitudinal reproducibility for clinical studies. An automated, scalable, and cost‐effective workflow (autoSP3) allows reproducible tissue proteomics in a broad range of clinical and non‐clinical applications. Automated tissue lysis is integrated with autoSP3 for an end‐to‐end workflow with minimal manual interference. The workflow allows reduced variability in protein quantification and increased longitudinal reproducibility. Minimal sample losses facilitate low‐input applications in a standardized workflow. Graphical Abstract The study presents an automated sample preparation pipeline for low‐input proteomics based on the SP3 method. The seamless integration of tissue lysis with autoSP3 in a 96‐well format features low variability, high sensitivity and longitudinal reproducibility for clinical studies.

Deeper understanding of liver pathophysiology would benefit from a comprehensive quantitative proteome resource at cell type resolution to predict outcome and design therapy. Here, we quantify more than 150,000 sequence‐unique peptides aggregated into 10,000 proteins across total liver, the major liver cell types, time course of primary cell cultures, and liver disease states. Bioinformatic analysis reveals that half of hepatocyte protein mass is comprised of enzymes and 23% of mitochondrial proteins, twice the proportion of other liver cell types. Using primary cell cultures, we capture dynamic proteome remodeling from tissue states to cell line states, providing useful information for biological or pharmaceutical research. Our extensive data serve as spectral library to characterize a human cohort of non‐alcoholic steatohepatitis and cirrhosis. Dramatic proteome changes in liver tissue include signatures of hepatic stellate cell activation resembling liver cirrhosis and providing functional insights. We built a web‐based dashboard application for the interactive exploration of our resource ( www.liverproteome.org ). Synopsis In‐depth acquisition and analysis of quantitative human liver proteome reveals proteome differences between liver cell types, proteome dynamics during primary cell culture and proteome changes in liver cirrhosis and NASH. This resource can be explored at www.liverproteome.org . The study presents a cell‐type resolved liver proteome with copy numbers for 10,500 proteins. Time‐course analysis of human liver primary cells uncovers functional proteome shifts. A human cohort study reveals liver proteome changes in NASH and cirrhosis. An interactive web portal ( www.liverproteome.org ) integrates the results for easy exploration. Graphical Abstract In‐depth acquisition and analysis of quantitative human liver proteome reveals proteome differences between liver cell types, proteome dynamics during primary cell culture and proteome changes in liver cirrhosis and NASH. This resource can be explored at www.liverproteome.org .

Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit. This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time. Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.

Mass spectrometry (MS), a core technology for proteomics and metabolomics, is currently being developed for clinical applications. The identification of microorganisms in clinical samples using matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry (MALDI-TOF MS) is a representative MS-based proteomics application that is relevant to daily clinical practice. This technology has the advantages of convenience, speed, and accuracy when compared with conventional biochemical methods. MALDI-TOF MS can shorten the time used for microbial identification by about 1 day in routine workflows. Sample preparation from microbial colonies has been improved, increasing the accuracy and speed of identification. MALDI-TOF MS is also used for testing blood, cerebrospinal fluid, and urine, because it can directly identify the microorganisms in these liquid samples without prior culture or subculture. Thus, MALDI-TOF MS has the potential to improve patient prognosis and decrease the length of hospitalization and is therefore currently considered an essential tool in clinical microbiology. Furthermore, MALDI-TOF MS is currently being combined with other technologies, such as flow cytometry, to expand the scope of clinical applications.

Oxygen glucose deprivation (OGD) of brain cells is the commonest in vitro model of ischemic stroke that is used extensively for basic and preclinical stroke research. Protein mass spectrometry is one of the most promising and rapidly evolving technologies in biomedical research. A systems-level understanding of cell-type-specific responses to oxygen and glucose deprivation without systemic influence is a prerequisite to delineate the response of the neurovascular unit following ischemic stroke. In this systematic review, we summarize the proteomics studies done on different OGD models. These studies have followed an expression or interaction proteomics approach. They have been primarily used to understand the cellular pathophysiology of ischemia-reperfusion injury or to assess the efficacy of interventions as potential treatment options. We compile the limitations of OGD model and downstream proteomics experiment. We further show that despite having limitations, several proteins shortlisted as altered in in vitro OGD-proteomics studies showed comparable regulation in ischemic stroke patients. This showcases the translational potential of this approach for therapeutic target and biomarker discovery. We next discuss the approaches that can be adopted for cell-type-specific validation of OGD-proteomics results in the future. Finally, we briefly present the research questions that can be addressed by OGD-proteomics studies using emerging techniques of protein mass spectrometry. We have also created a web resource compiling information from OGD-proteomics studies to facilitate data sharing for community usage. This review intends to encourage preclinical stroke community to adopt a hypothesis-free proteomics approach to understand cell-type-specific responses following ischemic stroke.

Most human tumor tissues that are obtained for pathology and diagnostic purposes are formalin-fixed and paraffin-embedded (FFPE). To perform quantitative proteomics of FFPE samples, paraffin has to be removed and formalin-induced crosslinks have to be reversed prior to proteolytic digestion. A central component of almost all deparaffinization protocols is xylene, a toxic and highly flammable solvent that has been reported to negatively affect protein extraction and quantitative proteome analysis. Here, we present a ‘green’ xylene-free protocol for accelerated sample preparation of FFPE tissues based on paraffin-removal with hot water. Combined with tissue homogenization using disposable micropestles and a modified protein aggregation capture (PAC) digestion protocol, our workflow enables streamlined and reproducible quantitative proteomic profiling of FFPE tissue. Label-free quantitation of FFPE cores from human ductal breast carcinoma in situ (DCIS) xenografts with a volume of only 0.79 mm3 showed a high correlation between replicates (r2 = 0.992) with a median %CV of 16.9%. Importantly, this small volume is already compatible with tissue micro array (TMA) cores and core needle biopsies, while our results and its ease-of-use indicate that further downsizing is feasible. Finally, our FFPE workflow does not require costly equipment and can be established in every standard clinical laboratory.

In order to effectively develop personalized medicine for kidney diseases we urgently need to develop highly accurate biomarkers for use in the clinic, since current biomarkers of kidney damage (changes in serum creatinine and/or urine albumin excretion) apply to a later stage of disease, lack accuracy, and are not connected with molecular pathophysiology. Analysis of urine peptide content (urinary peptidomics) has emerged as one of the most attractive areas in disease biomarker discovery. Urinary peptidome analysis allows the detection of short and long-term physiological or pathological changes occurring within the kidney. Urinary peptidomics has been applied extensively for several years now in renal patients, and may greatly improve kidney disease management by supporting earlier and more accurate detection, prognostic assessment, and prediction of response to treatment. It also promises better understanding of kidney disease pathophysiology, and has been proposed as a “liquid biopsy” to discriminate various types of renal disorders. Furthermore, proteins being the major drug targets, peptidome analysis may allow one to evaluate the effects of therapies at the protein signaling pathway level. We here review the most recent findings on urinary peptidomics in the setting of the most common kidney diseases.

Two-dimensional gel electrophoresis was instrumental in the birth of proteomics in the late 1980s. However, it is now often considered as an outdated technique for proteomics—a thing of the past. Although this opinion may be true for some biological questions, e.g., when analysis depth is of critical importance, for many others, two-dimensional gel electrophoresis-based proteomics still has a lot to offer. This is because of its robustness, its ability to separate proteoforms, and its easy interface with many powerful biochemistry techniques (including western blotting). This paper reviews where and why two-dimensional gel electrophoresis-based proteomics can still be profitably used. It emerges that, rather than being a thing of the past, two-dimensional gel electrophoresis-based proteomics is still highly valuable for many studies. Thus, its use cannot be dismissed on simple fashion arguments and, as usual, in science, the tree is to be judged by the fruit.

Miscarriages affect 50-70% of all gestations and 15-20% of clinically recognized pregnancies. Recurrent pregnancy loss (RPL) occurs in 1-5% of clinical pregnancies and has an enormous demographic impact. However, the etiologies and molecular pathways of RPL are scarcely understood, and therefore, reliable diagnostic and preventive methods are not yet available. Here, we aimed to discover novel biomarkers for RPL using next-generation proteomics technology to help develop early and effective diagnostic tools. First-trimester blood samples were collected from women with RPL ( =11) and controls with elective termination of pregnancy ( =11) between 6-13 weeks of gestation. After immunodepleting 14 highly abundant proteins, plasma samples were reduced, alkylated, and trypsin digested. For the separation of peptides, nano-flow reversed-phase chromatography was applied, and then mass spectrometric analysis was performed. Differentially abundant (DA) proteins were identified using strict criteria and analyzed by protein network and Gene Ontology (GO) enrichment analyses, and two biomarker candidates (CGB and PAPPA) were validated by immunoassay. Biomarker predictive properties were demonstrated using Receiver Operating Characteristic (ROC) curves. Assessments were performed for all cases and then for two gestational age groups, before and after the start of placental circulation [\"early RPL\": gestational weeks (GW) 6-9, \"late RPL\": GW 9 13]. Altogether, 651 proteins were identified and quantified across all samples. When comparing \"early control\" and \"late control\" samples, 60 proteins [11 predominantly placenta-expressed (PPE)] were DA. When analyzing all cases, 50 DA proteins were found in RPL (top 3 down: PZP, PSG9, CGB; top 3 up: C4BPA, HBA, HBB), among which 11 PPE proteins were found, all downregulated. Enriched GO terms included 'placental function', 'oxidative processes', 'immune function', and 'blood coagulation' related biological processes. When cases were split into early and late RPL groups, 40 DA proteins were identified in early RPL (top 3 down: SHBG, CGB, CGA; top 3 up: C4BPA, SAMP, C4BPB) and 90 in late RPL (top 3 down: PZP, PAPPA, PSG9; top 3 up: THBS1, ECM1, HBB), among which only 15 were shared by both RPL groups. In early RPL, only 'placental function' and 'immune function' related biological processes were enriched, while in late RPL the top enriched GO terms included 'placental function', 'oxidative processes', 'immune function', 'blood coagulation', 'angiogenesis', 'cell migration', and 'blood circulation' related biological processes. Among GO terms, only 'placental function' related biological processes were enriched when early- and late RPL DA proteins were analyzed together. Furthermore, the areas under the ROC curves were >0.9 for two protein candidates in all RPL, for five proteins in early RPL, and for ten proteins in late RPL. Among these candidates, CGB and PAPPA were validated by immunoassay which showed a good correlation with MS data (R =0.795 and R =0.965). We discovered distinct as well as shared molecular pathways associated with RPL pathogenesis before and after the start of placental circulation and identified novel biomarkers for these pathways which have outstanding discriminative properties. Our results may facilitate a better understanding of the molecular pathways of RPL. However, larger clinical studies are needed to investigate whether the identified biomarkers also have predictive power for RPL before pregnancies fail and to test drugs for the modulation of the identified disease pathways and the prevention of RPL. Our findings highlight the importance of the maternal immune system in maintaining successful pregnancy and suggest that targeting immune pathways may offer novel therapeutic approaches for RPL.