Orbitrap Fusion Mass Spectrometer Research Articles

Investigating the Neuroprotective Effect of Withaferin-A in a Parkinsonian Mouse Model

Parkinson's disease (PD) is an enduring and advancing neurodegenerative disorder that impacts millions worldwide. While options to manage its symptoms are available, a definitive cure remains elusive. To enhance the quality of life for PD patients and to alleviate symptoms, various classes of medications are employed including Levodopa (L-Dopa), Dopamine Agonists and Dopamine Agonists. Within this investigation, we investigated the neuroprotective potential of Withaferin-A within a mouse model of Parkinsonism, utilizing a proteomics methodology. Withaferin A, a natural compound extracted from the plant Withania somnifera, colloquially known as ashwagandha, has been explored for its therapeutic attributes across several conditions including PD. To assess the neuroprotective capacity of Withaferin A (WA), we employed a quantitative proteomics strategy to pinpoint proteins with distinct expression patterns in mouse models of Parkinson's disease (PD) treated with WA and 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). The experimental setup encompassed four groups of mice: Group I as control, group II administered MPTP, group III treated with Withaferin A and group IV receiving Withaferin A treatment. After humane termination and intracardial infusion, the substantia nigra (SN) region of the mice brains was collected. Employing tandem mass tags, quantitative proteomics was executed on the obtained brain samples through an Orbitrap Fusion Mass spectrometer (MS). The subsequent analysis of LC-MS/MS data was conducted via Proteome Discoverer and NCBI's mouse protein database using the MASCOT search engine. This comprehensive exploration unveiled a list of 6044 proteins among which alpha-synuclein was identified. Notably, 133 proteins exhibited differential expression. These differentially expressed proteins played pivotal roles in significant biological processes including cellular processes (signal transduction), metabolic processes (NADP metabolic process) and signaling (dopamine receptor signaling). Crucial pathways uncovered encompass Parkinson's disease and the dopamine receptor-mediated signaling pathway. It is our belief that the insights gleaned from this study provide a foundation for formulating targeted treatment strategies to combat Parkinson's disease, thus potentially enhancing the therapeutic landscape for individuals affected by this condition.

1620. Identification of plasma biomarkers of neurological complications in patients with congenital cytomegalovirus infection by proteome analysis

Abstract Background Congenital cytomegalovirus infection (cCMV) is the leading cause of non-hereditary sensorineural hearing loss and can cause other long-term neurodevelopmental disabilities. To consider antiviral treatment, it is important to differentiate between symptomatic and asymptomatic patients by early infancy. However, it is difficult to identify neurological complications in some cases. This study aimed to identify candidate plasma biomarkers for neurological complications of cCMV during the neonatal period using proteome analysis. Methods This study retrospectively enrolled five patients with asymptomatic cCMV and nine patients with symptomatic cCMV, including those with hearing loss and/or abnormal brain imaging. Plasma samples were obtained during the neonatal period. After extraction of 14 high-abundant proteins from the plasma, proteins were digested by trypsin. The peptides were analyzed by liquid chromatography–mass spectrometry using an Orbitrap Fusion mass spectrometer. Protein quantification was performed using Proteome Discoverer. Levels of differently expressed proteins were validated by enzyme-linked immunosorbent assay. Results In total, 456 proteins were identified and quantified. Levels of 65 proteins were significantly higher in patients with symptomatic cCMV than in those with asymptomatic cCMV. The top two enriched categories for these proteins according to pathway enrichment analysis were “complement and coagulation cascade” and “inflammatory response.” In contrast, levels of 30 proteins were significantly higher in patients with abnormal brain imaging. Plasma levels of fms-related receptor tyrosine kinase 4 (FLT4) were significantly higher in patients with symptomatic cCMV than in those with asymptomatic cCMV. Moreover, levels of plasma peptidylprolyl isomerase A (PPIA) were significantly higher in patients with abnormal brain imaging than in those without. Conclusion Proteome analysis showed that the proteins related to inflammatory response pathways were upregulated in patients with symptomatic cCMV. FLT4 and PPIA can be used as novel diagnostic biomarkers for neurological complications of cCMV to enable early therapeutic intervention with antiviral agents. Disclosures All Authors: No reported disclosures

Exploring the Active Constitutions of Peach Blossom for Amelioration of Loperamide-Induced Mice Constipation by Ultra-Performance Liquid Chromatography-Mass Spectrometry Combined with Network Pharmacology

Constipation is a multifactorial health problem resulting from systemic or neurologic disorders including medication. Peach blossom, an edible flower, could promote defecation, urination, and improve abdominal pain. However, the active components and mechanisms of action remain unclear. In the present study, we established a loperamide-induced mice constipation model to validate the anti-constipation activity of peach blossom. Some classical biomarkers for constipation, including fecal water content, gastrointestinal transit ratio, and fecal pellet weight were used to evaluate the efficacy of peach blossom. Then, the chemical compounds present in peach blossom were screened out by Ultra-performance liquid chromatography (UPLC)-Orbitrap fusion mass spectrometer combined with diagnostic ions and database searching. Finally, the potential mechanism of peach blossom for the treatment of constipation was explored by network pharmacology on a system level. Peach blossom significantly reduced the fecal water content, gastrointestinal transit ratio, and fecal pellet weight, which were increased in the model group. Histological analysis showed that peach blossom could alleviate histological changes of the colon in constipated mice. In UPLC-MS analysis, 40 compounds, mainly flavonoids and phenolic acids, were identified. Network pharmacology analysis results indicate that 27 compounds exhibited anti-constipation activity by neurotransmitter receptor activity, carboxylic acid binding, flavin adenine dinucleotide binding, adrenergic receptor, and nuclear receptor activity. In this study, we found that peach blossom might alleviate the pathological process of constipation by regulating multi-targets. Our study serves as a theoretical basis for the utilization and further development of peach blossom as a promising health food for ameliorating constipation.

Abstract 3916: Cyanobacterial natural product Sec61α inhibitors induce broad suppression of the glioma cell secretome

Abstract Coibamide A is a cyclopeptide natural product with potent antiproliferative activity against cultured human cancer cells and subcutaneous U87-MG glioblastoma tumors in mice. We have recently determined that coibamide A binds to the Sec61 translocon channel at a site that is close, but not identical, to the binding site of the peptide/polyketide natural product apratoxin A. As the majority of secreted proteins in mammalian cells are trafficked through the conventional secretory pathway via the Sec61 translocon, this raised the possibility that coibamide A and apratoxin A block import and secretion of different Sec61 client proteins. In the present study, we analyzed and compared the secretome of human U87-MG glioblastoma cells in the presence and absence of both marine natural products. U87-MG glioblastoma cells were treated with coibamide A (5 nM), apratoxin A (5 nM), or vehicle for 24 h. The growth media was then replaced with serum-free media for a further 24 h. Tryptic proteomic samples were generated from cell-free conditioned media and analyzed on a LC-coupled Orbitrap Fusion mass spectrometer. The high-resolution Orbitrap mass analyzer was used to both identify precursor ions for tandem mass (MS2) analysis in the ion trap mass analyzer and to quantitate those ions (MS1). Secreted proteins were identified from peptide–spectrum matches to the human protein database using a decoy database to assign an FDR and quantified from their MS1 ion intensities. Comparison of mass spectrometric data against the human secretome database revealed 175 proteins in the U87-MG cell secretome that were identified with high confidence. Differences between coibamide A and apratoxin A treatment were not significant, however both Sec61 inhibitors induced significant suppression of the U87-MG secretome relative to vehicle-treated cells. Treatment with coibamide A or apratoxin A resulted in the reduction of 75% of quantifiable secretome (131 proteins). Of the remaining 44 proteins, 34 are directed to intracellular organelles or contain a motif associated with retention in the endoplasmic reticulum and 10 were not suppressed with treatment but were hypothesized to be Sec61 clients. Malignant glioblastoma cells secrete proteins into the extracellular space and use complex intercellular signaling mechanisms for a survival advantage. Our results indicate that broad-acting inhibitors of Sec61-dependent co-translational translocation block the progression of a significant percentage of the U87-MG glioblastoma cell secretome including several proteins that have previously been detected as biomarkers in the cerebrospinal fluid, blood, or urine of brain tumor patients. Taken together, our work illustrates the feasibility of inducing a reversible suppression of numerous (undrugged) extracellular signals by targeting Sec61-dependent protein biogenesis in the secretory pathway with drug-like molecules. Citation Format: Daphne R. Mattos, Jeffrey D. Serrill, Philip R. Gafken, Kerry L. McPhail, Walter K. Vogel, Jane E. Ishmael. Cyanobacterial natural product Sec61α inhibitors induce broad suppression of the glioma cell secretome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3916.

Proteomic Analysis of Cardiac Adaptation to Exercise by High Resolution Mass Spectrometry.

Regular exercise has many health benefits, among which is a significant reduction of cardiovascular risk. Although many beneficial effects of exercise are well described, the exact mechanisms by which exercise confers cardiovascular benefits are yet to be fully understood. In the current study, we have used high resolution mass spectrometry to determine the proteomic responses of the heart to exercise training in mice. The impact of exercise-induced oxidative stress on modifications of cardiomyocyte proteins with lipid peroxidation biomarker 4-hydroxynonenal (4-HNE) was examined as well. Fourteen male mice were randomized into the control (sedentary) group and the exercise group that was subjected to a swim exercise training program for 5 days a week for 5 months. Proteins were isolated from the left ventricular tissue, fractionated and digested for shotgun proteomics. Peptides were separated by nanoliquid chromatography and analyzed on an Orbitrap Fusion mass spectrometer using high-energy collision–induced dissociation and electron transfer dissociation fragmentation. We identified distinct ventricular protein signatures established in response to exercise training. Comparative proteomics identified 23 proteins that were upregulated and 37 proteins that were downregulated with exercise, in addition to 65 proteins that were identified only in ventricular tissue samples of exercised mice. Most of the proteins specific to exercised mice are involved in respiratory electron transport and/or implicated in glutathione conjugation. Additionally, 10 proteins were found to be modified with 4-HNE. This study provides new data on the effects of exercise on the cardiac proteome and contributes to our understanding of the molecular mechanisms underlying the beneficial effects of exercise on the heart.

Phosphorus Deficiency Promoted Hydrolysis of Organophosphate Esters in Plants: Mechanisms and Transformation Pathways.

The biotransformation of organophosphate esters (OPEs) in white lupin (Lupinus albus) and wheat (Triticum aestivum L.) was investigated in hydroponic experiments with different phosphorus (P)-containing conditions. The hydrolysis rates of OPEs followed the order of triphenyl phosphate (TPHP) > tri-n-butyl phosphate (TnBP) > tris(1,3-dichloro-2-propyl) phosphate (TDCPP). Hydrolysis of OPEs was accelerated at P-deficient conditions, and faster hydrolysis took place in white lupin than in wheat. Coincidingly, the production of acid phosphatase (ACP) in both plants was promoted, and much higher intracellular and extracellular ACPs were observed in white lupin under P-deficient conditions. In vitro experiments revealed that ACP was a key enzyme to hydrolyze OPEs. The hydrolysis rates of OPEs were significantly correlated with the Hirshfeld charges, calculated by density functional theory, of the oxygen atom in the single P-O bond. Using ultra-high-performance liquid chromatography coupled with Orbitrap Fusion mass spectrometer, 30 metabolites were successfully identified. Some of these metabolites, such as sulfate-conjugated products, hydration of cysteine-conjugated products of TPHP, and reductively dechlorinated metabolites of TDCPP, were observed for the first time in plants. It is noteworthy that OPEs may transform into many hydroxylated metabolites, and special attention should be paid to their potential environmental effects.

Proteome of breast cancer derived microvesicles

The aim of the research. To examine the proteomic profi le of breast cancer exosomes. Material and methods. Cell lines used for this study were MDA-MB-231 female epithelial breast cancer cells (ATCC HTB-26) and MCF10A non-tumorigenic epithelial breast tissue cells. MVs were isolated using diff erential ultracentrifugation. Samples were lysed, reduced, alkylated, digested, and analyzed by an Orbitrap Fusion mass spectrometer. MS raw fi les were analyzed using MaxQuant version 1.6.12.0. Peptides were searched against the human UniProt FASTA database using the Andromeda search engine, integrated into MaxQuant. Results. MVs derived from MCF10A and MDA-MB-231 cell lines were analyzed, and 1427 and 547 proteins were identifi ed in the MDA-MB-231 and MCF10A-derived MVs, respectively. In total, 455 proteins were common to both MDA-MB-231 and MCF10A MVs. MVs derived from MCF10A and MDAMB-231 cell lines were analyzed, and 1427 and 547 proteins were identifi ed in the MDA-MB-231 and MCF10A-derived MVs, respectively. In total, 455 proteins were common to both MDA-MB-231 and MCF10A MVs. Th e unique MDA-MB-231 MV proteins were searched against the DisGeNET human diseases database. Out of 972 MDA-MB-231 MV proteins, 112 were cancer-related while 32 were specifi cally associated with BC. In the MDA-MB-231 MV proteome, 23 Wnt signaling pathway proteins were identifi ed based on their GO biological process. Proteomic analysis identifi ed enzymes OAT, TALDO1, and BLMH were only in MVs from metastatic MDA-MB-231 cell line. The specific activity of OAT and TALDO1 was higher in MV fractions of MDA-MB-231 in comparison to the non-cancerous MCF10A cell line-derived MVs. Th ese fi ndings might suggest that these enzymes might play a role in BC. In our present study, we found that some enzymes identifi ed from MV fractions were already proposed to play a role in cancer therapy as therapeutic targets (OAT, TALDO1) and resistance against chemotherapy agents (BLMH).

Synergistic optimization of Liquid Chromatography and Mass Spectrometry parameters on Orbitrap Tribrid mass spectrometer for high efficient data-dependent proteomics.

Steady improvement in Orbitrap-based mass spectrometry (MS) technologies has greatly advanced the peptide sequencing speed and depth. In-depth analysis of the performance of state-of-the-art MS and optimization of key parameters can improve sequencing efficiency. In this study, we first systematically compared the performance of two popular data-dependent acquisition approaches, with Orbitrap as the first-stage (MS1) mass analyzer and the same Orbitrap (high-high approach) or ion trap (high-low approach) as the second-stage (MS2) mass analyzer, on the Orbitrap Fusion mass spectrometer. High-high approach outperformed high-low approach in terms of better saturation of the scan cycle and higher MS2 identification rate. However, regardless of the acquisition method, there are still more than 60% of peptide features untargeted for MS2 scan. We then systematically optimized the MS parameters using the high-high approach. Increasing the isolation window in the high-high approach could facilitate faster scan speed, but decreased MS2 identification rate. On the contrary, increasing the injection time of MS2 scan could increase identification rate but decrease scan speed and the number of identified MS2 spectra. Dynamic exclusion time should be set properly according to the chromatography peak width. Furthermore, we found that the Orbitrap analyzer, rather than the analytical column, was easily saturated with higher loading amount, thus limited the dynamic range of MS1-based quantification. By using optimized parameters, 10 000 proteins and 110 000 unique peptides were identified by using 20 h of effective liquid chromatography (LC) gradient time. The study therefore illustrated the importance of synchronizing LC-MS precursor ion targeting, fragment ion detection, and chromatographic separation for high efficient data-dependent proteomics.

Xylosyl Extension of O-Glucose Glycans on the Extracellular Domain of NOTCH1 and NOTCH2 Regulates Notch Cell Surface Trafficking.

Biochemical and genetic studies have indicated that O-linked glycosylation such as O-glucose (Glc), fucose (Fuc), and N-acetylglucosamine (GlcNAc) is critical for Notch signaling; however, it is not fully understood how O-glycans regulate the Notch receptor function. Notch receptors are type-I transmembrane proteins with large extracellular domains (ECD), containing 29–36 epidermal growth factor-like (EGF) repeats. Here, we analyzed O-Glc glycans on NOTCH1 and NOTCH2 expressed in HEK293T cells using an Orbitrap Fusion mass spectrometer and successfully revealed the structures and stoichiometries of all 17 EGF repeats of NOTCH1 with the O-Glc consensus sequence (C1-X-S-X-(P/A)-C2), and 16 out of 17 EGF repeats of NOTCH2 with the same consensus sequence. High levels of O-Glc attachment and xylosyl elongation were detected on most NOTCH1 and NOTCH2 EGF repeats. When both glucoside xylosyltransferases, GXYLT1 and GXYLT2, responsible for the xylosyl elongation of O-glucose, were genetically deleted, the expression of endogenous NOTCH1 and NOTCH2 on the surface of HEK293T cells did not change, but the cell surface expression of overexpressed NOTCH1 and NOTCH2 decreased compared with that in the wild type cells. In vitro secretion assays consistently showed a reduced secretion of both the NOTCH1 and NOTCH2 ECDs in GXYLT1 and GXYLT2 double knockout cells compared with the wild type cells, suggesting a significant role of the elongation of O-Glc glycans on the Notch ECDs in the quality control of Notch receptors.

Protein corona formation on particles in bovine synovial fluid and in a rat knee model of osteoarthritis

Purpose: In osteoarthritis (OA), molecular changes occur throughout the joint, causing changes in the joint milieu. Micro- and nanoparticles can be used to characterize these molecular changes. Specifically, proteins within the synovial fluid non-specifically adsorb onto the surface of particles. As such, changes in the protein corona formation on the particle surface may relate to molecular changes in OA. While protein corona formation is commonly studied in serum and cell culture media, it has not been assessed in OA animal models. In this study, protein corona formation was assessed in bovine synovial fluid and in a rat OA model. Methods: First, commercially available, magnetic microparticles (Dynabeads) were placed in bovine synovial fluid and separated using magnetic separation or centrifugation. The resulting protein corona was characterized using mass spectrometry. Then, 12 male and 12 female Lewis rats (9 weeks old) received a unilateral, simulated medial collateral ligament and meniscal injury. At 2, 5, or 8 weeks post-surgery, operated and contralateral limbs were injected with magnetic particles (n=4 per sex). After a 4-hour incubation, animals were euthanized, particles were recovered from the joint, and the protein corona was characterized using an Orbitrap Fusion Mass Spectrometer. Results: In bovine synovial fluid, a total of 116 proteins were identified, of which 35 were different between magnetic separation and centrifugation. In the rat OA model, 454, 464, and 342 proteins were identified at 2, 5, and 8 weeks post-surgery, respectively. Of the identified proteins on the particle surface, 35, 59, and 13 were different between the operated and contralateral limbs at 2, 5, and 8 weeks, respectively (p < 0.05, see Figure 1). Using principal component analysis, changes in the protein corona were found to relate with OA progression. Conclusions: Data from the bovine synovial fluid demonstrated that the protein corona that forms on the particle surface varies based on the method of particle separation from synovial fluid. Moreover, the in vivo data demonstrates that the protein corona layer on a particle surface changes at various stages of OA progression. Understanding how the particle-protein interface changes as a function of disease progression may be useful for biomarker discovery and informing the design of intra-articular drug delivery vehicles.

Abstract 3741: Identification of RNA binding proteins influenced by ionizing radiation through RNA interactome capture

Abstract Cells respond to ionizing radiation (IR) through the activities of constitutively expressed proteins and through changes in gene expression. Constitutively expressed proteins play well-defined roles in major components of the cellular radioresponse, such as DNA repair and cell cycle. However, the contribution of changes in gene expression to the radioresponse is less understood. We have previously demonstrated through polysome profiling and microarray analysis that translational control is a key component of radiation-induced changes in gene expression. In response to IR, specific transcripts are recruited to or away from polysomes without affecting the global polysome profile of the cells. One mechanistic explanation for this observation is that IR influences the activity of RNA binding proteins (RBPs), which regulate the inclusion or exclusion of transcripts from polysomes. Here, we utilized RNA interactome capture (RIC) to identify RBPs bound to transcripts in control and irradiated human cancer cells. Cells were either mock irradiated or treated with 2Gy. One hour post-IR, RNA and protein complexes were crosslinked with 254 nm UV light. mRNA was isolated from cell lysates with oligo(dT) magnetic beads followed by several rounds of highly stringent washes to remove non-specific interactors. RNA was removed from crosslinked proteins by RNase digestion. The proteins were separated on SDS-PAGE gels and subjected to in-gel trypsin digestion, and the subsequent peptides were analyzed by label-free quantification mass spectrometry using an Orbitrap Fusion mass spectrometer. Proteome Discoverer 2.2 was used to search the data against human proteins from the UniProt database using SequestHT with a 1% false discovery rate. We found that we were able to efficiently pull down RNA:protein complexes with a crosslinking dose of 150 mJ/cm2. As determined by silver staining, the protein pattern of crosslinked samples differed greatly from protein isolated from whole cell lysates. By western blot, this method highly enriched for known RBPs, such as PTBP1 and CUGBP1, while contamination from non-RBPs, such as actin and tubulin, was not detected. By mass spectrometry, we identified hundreds of RBPs in each replicate above the no crosslinking background control for both untreated and irradiated cells. However, more RBPs were consistently detected in the control cells. Examples of RBPs preferentially binding in control cells include SSB, a protein involved in a variety of RNA metabolic processes, and U2AF2, a protein involved in RNA splicing. Overall, these data demonstrate that RIC is a sensitive and rigorous method to identify RBPs and that RBPs may play a role in radiation-induced post-transcriptional gene regulation. Preferential binders identified by this method may provide further insight into pathways regulating tumor cell radiosensitivity. Citation Format: Stacey L. Lehman, Theresa Wechsler, Gaelyn C. Lyons, Lisa M. Jenkins, Kevin Camphausen, Philip J. Tofilon. Identification of RNA binding proteins influenced by ionizing radiation through RNA interactome capture [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3741.

In-Depth Proteomic Analysis of Human Bronchoalveolar Lavage Fluid toward the Biomarker Discovery for Lung Cancers.

Lung cancer is among the most common cancers. Bronchoalveolar lavage fluid (BALF) can be easily obtained from patients with lung cancers. The aim is to develop a novel proteomic method of the molecule-based sensitive detection of biomarkers from BALF. BALF samples are collected from segmental bronchus of 14 patients with lung cancers from Kyung Hee University Hospital. First, BALF proteome is depleted using a depletion column, and then peptides are prepared from the enriched low abundant proteins and fractionated by high pH reverse phase liquid chromatography prior to LC-MS/MS. Data are available via ProteomeXchange with identifier PXD012645. A novel method is developed for in-depth proteomic analysis of BALF by combining antibody-based depletion of high abundant proteins from BALF with high pH peptide fractionation. Peptides are analyzed on a high resolution Orbitrap Fusion mass spectrometer. MaxQuant search result in the identification of 4615 protein groups mapped to 4534 genes. It is found that the method outperformed conventional BALF proteomic methods and it is believed that this method will facilitate the biomarker research for lung cancer. In addition, it is shown that BALF will be a great source of biomarkers of lung diseases.

Exploratory proteomics of human synovial fluid in knee osteoarthritis: towards biomarker identification

Purpose: There is a lack of valid and robust biomarkers in the field of OA diagnosis, prognosis, and treatment evaluation. Thus, our aim was to perform mass spectrometry (MS) of human synovial fluid using a global discovery approach, to identify biomarker candidates associated with meniscus degradation and/or knee OA. Methods: Synovial fluid was sampled from 3 different subject groups: i) end-stage medial compartment knee OA patients undergoing arthroplasty (n=11, 3 men, 8 women; age range 55-80 years), ii) knee arthroscopy patients who had knee symptoms but no or only minor knee trauma, typically having a degenerative meniscal tear (n=7, 3 men, 5 women; age range 50-64 years), and iii) deceased human donors (within 48 hours post mortem) without known chronic knee disease (n=13, 8 men, 5 women; age range 19-79 years). These 3 groups were roughly assumed to represent i) end-stage knee OA, ii) early knee OA, and iii) healthy controls, respectively. For all 3 groups, we required no visual signs of blood contamination to be present in the synovial fluid. For the cadaver knee tissues (controls), we further required the meniscus and the weight-bearing femoral surface of cartilage/bone to be macroscopically intact. All synovial fluids were centrifuged and freshly frozen and stored at -80°C. For the analysis, 50 μL of synovial fluid from each sample was mixed with MS-safe proteinase inhibitor cocktail and hyaluronidase, and further depleted of the 7 most abundant proteins with the multiple affinity removal system (MARS Hu7 spin cartridge). After reduction and alkylation, the samples were precipitated and the pellets were further digested with sequencing grade trypsin (Promega. Following digestion, samples were cleaned with a 30kDa filter and desalted. The samples were further spiked with iRT peptides before analysis by MS. The samples were analyzed with an EASY-nLC 1000 coupled to an Orbitrap Fusion mass spectrometer. The samples were analyzed with data-independent acquisition settings. The raw MS data were further analyzed with Spectronaut™ software for protein identification and quant data extraction. The quant data extracted using Spectronaut™ were further imported into the R environment (http://www.R-project.org/) to facilitate data analysis and visualization. Differences in protein levels between the 3 different groups were analyzed using the limma package and multiple logistic regression analysis. Differentially expressed proteins between the groups were clustered by hierarchical clustering using Pearson correlation coefficient as the distance metric. For each cluster, the enriched Gene Ontology terms and Reactome pathway names were identified and the most representative ones were annotated. Results: In total, 529 proteins were identified in the 31 different synovial fluid samples. Principal component analysis suggested a profound difference between the protein profiles of synovial fluid from controls vs arthroplasty patients, while the arthroscopy group had a protein profile that was in-between controls and the arthroplasty group (Figure 1). Statistical differential analysis yielded significant differences in the levels of 45 proteins comparing controls vs arthroplasty patients, 43 proteins for controls vs arthroscopy patients, and 58 proteins for arthroplasty vs arthroscopy patients. Extracellular matrix proteins like collagens and aggrecan showed higher expression in controls than in arthroplasty patients. Collagen on the other hand was higher in arthroscopy patients compared to controls. Decorin, a previously suggested biomarker candidate for OA, was significantly higher in controls compared to both arthroscopy and arthroplasty patients. The differentially expressed proteins associated with the acute inflammatory response (Table 1) were higher in the arthroscopy group compared to both controls and arthroplasty patients. Generally, extracellular matrix proteins were negatively correlated with immune system proteins and positively correlated with proteins involved in wound healing (Figure 2). Conclusions: There is a profound difference in the protein profile of human synovial fluid in knee-healthy controls vs knee OA patients. The inflammatory response seems to be higher in the early stages of OA than in later stages of the disease. Our findings emphasize the importance of OA staging in the development and use of biomarkers.View Large Image Figure ViewerDownload Hi-res image Download (PPT)View Large Image Figure ViewerDownload Hi-res image Download (PPT)

Discovering Protein Biomarkers from Clinical Peripheral Blood Mononuclear Cells Using Data-Independent Acquisition Mass Spectrometry.

Global proteomics analyses are traditionally performed in data-dependent acquisition (DDA) mode, which results in inadequate reproducibility across large sample cohorts due to the under-sampling inherent to shotgun proteomics. Recently, data-independent acquisition (DIA) strategies were introduced to allow reproducible detection and quantification of thousands of proteins with consistent sensitivity across samples. Here, we present an approach to analyze changes to the protein network in human peripheral blood mononuclear cells (PBMCs) from clinical blood samples, using DIA as a unique platform for biomarker discovery. We describe how to generate spectral PBMC proteome libraries by applying peptide fractionation followed by DDA analysis, and then how to apply DIA methods to PBMC samples from individual patients using a high-resolution Orbitrap Fusion mass spectrometer.

Proteomic Investigation of Murine Neuronal α7-Nicotinic Acetylcholine Receptor Interacting Proteins.

The α7-nicotinic acetylcholine receptor (α7-nAChR) is a ligand-gated ion channel that is expressed widely in vertebrates and is the principal high-affinity α-bungarotoxin (α-bgtx) binding protein in the mammalian CNS. α7-nAChRs associate with proteins that can modulate its properties. The α7-nAChR interactome is the summation of proteins interacting or associating with α7-nAChRs in a protein complex. To identify an α7-nAChR interactome in neural tissue, we isolated α-bgtx-affinity protein complexes from wild-type and α7-nAChR knockout (α7 KO) mouse whole brain tissue homogenates using α-bgtx-affinity beads. Affinity precipitated proteins were trypsinized and analyzed with an Orbitrap Fusion mass spectrometer. Proteins isolated with the α7-nAChR specific ligand, α-bgtx, were determined to be α7-nAChR associated proteins. The α7-nAChR subunit and 120 additional proteins were identified. Additionally, 369 proteins were identified as binding to α-bgtx in the absence of α7-nAChR expression, thereby identifying nonspecific proteins for α7-nAChR investigations using α-bgtx enrichment. These results expand on our previous investigations of α7-nAChR interacting proteins using α-bgtx-affinity bead isolation by controlling for differences between α7-nAChR and α-bgtx-specific proteins, developing an improved protein isolation methodology, and incorporating the latest technology in mass spectrometry. The α7-nAChR interactome identified in this study includes proteins associated with the expression, localization, function, or modulation of α7-nAChRs, and it provides a foundation for future studies to elucidate how these interactions contribute to human disease.

Evaluation of the High-Field Orbitrap Fusion for Compound Annotation in Metabolomics.

Annotation of signals of interest represents a key point in mass spectrometry-based metabolomics studies. The first level of investigation is the elemental composition, which can be deduced from accurately measured masses and isotope patterns. However, accuracy of these two parameters remains to be evaluated on last generation mass spectrometers to determine the level of confidence that can be used during the annotation process. In this context, we evaluated the performance of the Orbitrap Fusion mass spectrometer for the first time and demonstrated huge potential for metabolite annotation via elemental composition determination. This work was performed using a set of 50 standard compounds analyzed under LC/MS conditions in solvent and biological media. Accurate control of the number of trapped ions proved mandatory to avoid space charge effects, ensure sub-ppm mass accuracy (using external calibration), and reliable measurement of isotopic patterns at 500,000 resolution. On the basis of the results, we propose standard optimized experimental conditions for performing robust and accurate untargeted metabolomics on the Orbitrap Fusion at high mass measurement and mass spectral accuracy.

LC/MS-based Intact IgG and Released Glycan Analysis for Bioprocessing Applications.

Robust plate based antibody glycan analysis platforms are urgently needed for biopharmaceutical development and manufacturing as well as for clinical biomarker research. A 96-well plate based workflow has been developed to analyze both intact IgG antibodies and released N-glycans using an Orbitrap Fusion Mass Spectrometer and an LC/MS method on the Waters UNIFI platform. Here, such a workflow including protein A purification, PNGaseF digestion, 2-AB labeling, and SPE clean-up is described. The measured IgG glycan profile is consistent with that obtained from non-plate based method and commercial kit and has the advantage of less hands-on time. Also the application of the workflow in cell culture monitoring and clonal selection work is demonstrated. Apart from checking the major glycan structure changes among clones, post translational modifications (PTMs) such as C-terminal lysine residue clipping and N-terminal pyroglutamic acid formation can also be deduced from the workflow.

Direct Measurement of S-Nitrosothiols with an Orbitrap Fusion Mass Spectrometer: S-Nitrosoglutathione Reductase as a Model Protein.

Recent studies suggest cysteine S-nitrosation of S-nitrosoglutathione reductase (GSNOR) could regulate protein redox homeostasis. "Switch" assays enable discovery of putatively S-nitrosated proteins. However, with few exceptions, researchers have not examined the kinetics and biophysical consequences of S-nitrosation. Methods to quantify protein S-nitrosothiol (SNO) abundance and formation kinetics would bridge this mechanistic gap and allow interpretation of the consequences of specific modifications, as well as facilitate development of specific S-nitrosation inhibitors. Here, we describe a rapid assay to estimate protein SNO abundance with intact protein electrospray ionization mass spectrometry. Originally designed using recombinant GSNOR, these methods are applicable to any purified protein to test for or further study nitrosatable cysteines.

The extracellular metaproteome of soils under semiarid climate: A methodological comparison of extraction buffers

We compare the protein extraction efficiencies, as well as the phylogenetic and functional information provided, of two extraction protocols in soils that differ mainly in their organic matter and clay contents, the main factors limiting protein extraction in semiarid soils. These protocols utilise extractants commonly used for the assay of extracellular enzyme activities. The first method was based on the utilisation of the modified universal buffer (MUB). The second was based on the extraction of humic substances with sodium pyrophosphate. When compared to the total amount of proteins in soil, the results indicate a very-low extraction efficiency for both protocols. Analysis in an Orbitrap Fusion mass spectrometer and further searching against an “ad hoc” metagenome evidenced that the phylogenetic and functional information retrieved from the extracellular soil metaproteome can be biased by the extraction buffer.

Comparative proteomics of cancer stem cells in osteosarcoma using ultra-high-performance liquid chromatography and Orbitrap Fusion mass spectrometer

Osteosarcoma is the most common malignant tumour found in bones, and it has a poor prognosis. For improved therapy, it is significant to have a deep understanding of the proteomics changes in the cancer stem cells (CSCs) of osteosarcoma. Therefore, a comparative proteomics approach based on ultra-high-performance liquid chromatography coupled to an Orbitrap Fusion mass spectrometer (UHPLC-Orbitrap Fusion MS) was established to investigate the key molecular changes between CSCs and non-CSCs in human osteosarcoma HOS cells. A proteomic analysis was performed on these samples and a total of more than 6600 proteins were identified in each run. Moreover, most of the correlation coefficients between three biological repeats were more than 0.9 in each group. That finding demonstrated not only that the reproducibility of the test is good but also that the stability of this MS is excellent. A label-free quantitative method was applied to analyse differentially expressed proteins. Using the criteria of greater than 1.5-fold changes and a p value < 0.05, 124 proteins were identified as being significantly different between HOS-CSCs and non-CSCs. A pathway analysis of differentially expressed proteins by Ingenuity Pathway Analysis (IPA) revealed the potential molecular regulatory networks that may regulate CSCs. Selected differential α-actinin 4 (ACTN4) proteins were validated by Western blot assay. These findings enhance our understanding of the molecular changes in CSCs and may provide additional improvements in therapy for treating osteosarcoma. Moreover, the UHPLC-Orbitrap Fusion MS-based proteomics method is helpful in cancer research.