Selected Reaction Monitoring Mass Spectrometry Research Articles

Gas chromatography-mass spectrometry selected ion monitoring and gas chromatography-tandem mass spectrometry selected reaction monitoring analyses of mono-, di- and tri-unsaturated C25 highly branched isoprenoid alkene biomarkers in sea ice and sediment samples: A comparative study.

The efficiency of selected ion monitoring (SIM) and selected reaction monitoring (SRM) analyses for the quantification of three mono-, di- and tri-unsaturated highly branched isoprenoid (HBI) alkenes (IP25 , IPSO25 and HBI III, respectively), often used as proxies for the occurrence of Arctic and Antarctic sea ice or the adjacent open waters, was compared. Gas chromatography (GC)-mass spectrometry (MS)/SIM and GC/MS/MS/SRM analyses were carried out on dilute solutions made from purified standards of these three HBIs, and then on hydrocarbon fractions of several sediment and sea ice sample extracts. More efficient and specific SRM transitions were selected after collision-induced dissociation of each precursor ion at different collision energies. SRM analysis avoided any overestimation of IP25 resulting from the contribution of the coeluting 13 C mass isotopomer of IPSO25 (M+ ˙ + 2) to the SIM target ion. In contrast, SRM analysis is less reliable for IPSO25 quantification in cases where several regio-isomers are present, likely due to intense double bond migrations following electron impact. In the case of HBI III, SRM analysis constitutes a potentially suitable alternative to SIM analysis, especially in terms of improving limit of detection. Despite the intense migrations of HBI double bonds under electron ionization, the selected SRM transitions should be more suitable than SIM target ions for IP25 and HBI III quantification in complex hydrocarbon fractions of natural samples. However, the advantage is less evident for IPSO25 due to the presence of numerous regio-isomers.

Infrared Laser-Based Selected Reaction Monitoring Mass Spectrometry Imaging of Banana (Musa spp.) Tissue—New Method for Detection and Spatial Localization of Metabolites in Food

In this study, for the first time, we present the application of an infrared (IR) laser ablation-remote-electrospray ionization (LARESI) platform coupled to a tandem mass spectrometer (MS/MS) operated in selected reaction monitoring (SRM) mode for targeted metabolite imaging in intact plant tissues. We examined the distribution of specific metabolites in two banana varieties: Red Dacca and Cavendish. To support MSI results, an extensive analysis of banana tissue extracts was conducted using ultra-high-performance liquid chromatography and ultra-high-resolution mass spectrometry (UHPLC-UHRMS). In the Cavendish banana, 12 metabolites were successfully identified, while Red Dacca bananas were found to contain 16 amino acids. The spatial distribution of some of these compounds found in bananas was presented for the first time. This approach eliminates the need for high vacuum conditions and the pretreatment of biological materials, making it an efficient and promising tool for studying metabolites in plant tissues.

A protein panel in cerebrospinal fluid for diagnostic and predictive assessment of Alzheimer's disease.

Alzheimer's disease (AD) is a neurodegenerative disease with heterogenous pathophysiological changes that develop years before the onset of clinical symptoms. These preclinical changes have generated considerable interest in identifying markers for the pathophysiological mechanisms linked to AD and AD-related disorders (ADRD). On the basis of our prior work integrating cerebrospinal fluid (CSF) and brain proteome networks, we developed a reliable and high-throughput mass spectrometry-selected reaction monitoring assay that targets 48 key proteins altered in CSF. To test the diagnostic utility of these proteins and compare them with existing AD biomarkers, CSF collected at baseline visits was assayed from 706 participants recruited from the Alzheimer's Disease Neuroimaging Initiative. We found that the targeted CSF panel of 48 proteins (CSF 48 panel) performed at least as well as existing AD CSF biomarkers (Aβ42, tTau, and pTau181) for predicting clinical diagnosis, FDG PET, hippocampal volume, and measures of cognitive and dementia severity. In addition, for each of those outcomes, the CSF 48 panel plus the existing AD CSF biomarkers significantly improved diagnostic performance. Furthermore, the CSF 48 panel plus existing AD CSF biomarkers significantly improved predictions for changes in FDG PET, hippocampal volume, and measures of cognitive decline and dementia severity compared with either measure alone. A potential reason for these improvements is that the CSF 48 panel reflects a range of altered biology observed in AD/ADRD. In conclusion, we show that the CSF 48 panel complements existing AD CSF biomarkers to improve diagnosis and predict future cognitive decline and dementia severity.

A comparative study of gastric adenocarcinoma HER2 IHC phenotype and mass spectrometry-based quantification.

Gastric cancer is a highly heterogeneous malignant tumor of the digestive system. Anti-HER2 treatment can inhibit downstream signaling pathways and improve clinical treatment and outcomes in patients with HER2 protein overexpression. Currently, two standard methods for evaluating HER2 expression status are immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). However, these low-throughput assays often produce discordant or equivocal results. In this study, we presented a new HER2 protein detection method based on mass spectrometry selected reaction monitoring (MS-SRM) and validated the method. We conducted a retrospective study on 118 formalin-fixed paraffin-embedded (FFPE) tissues from patients with advanced gastric adenocarcinoma in northern China, and we compared the MS-SRM results with those from IHC and correlated them with FISH. We established and validated the upper and lower detection limits (300-700 amol/μg) for abnormal HER2 protein expression in advanced gastric cancer. We also found that, among samples with mixed Lauren subtypes, those with a high level of HER2 expression had typical intestinal type features in pathology. This study demonstrated that the MS-SRM method can overcome the limitations and deficiencies of IHC, directly quantify the expression of HER2 protein in tumor cells and be used as a supplement to IHC. It has the potential to be used as a companion diagnosis for new drugs used to treat advanced gastric cancer. Large-scale clinical validation is required.

Personalized therapy for head and neck squamous carcinoma (HNSCC) utilizing tissue proteomics profiling.

6045 Background: Chemotherapy is widely used in the treatment of HNSCC, yet no biomarkers for chemotherapy is used for selection of the chemo agent in the treatment of HNSCC. We examined 143 HNSCC cancer using targeted proteomics for the protein expression levels of several chemo agents. These include markers of resistance to platinum agents (ERCC1), anti-tubulin inhibitors (TUBB3) and sensitivity markers for topoisomerase inhibitors (Topo1 – irinotecan, topotecan; Topo2A – doxorubicin, etoposide). We also measured markers for several antibody-drug conjugates (EGFR, Her2, Trop2, FR-alpha, Mesothelin). Methods: Tumor areas from Formalin-fixed, paraffin-embedded (FFPE) tumor tissues from clinical samples of HNSCC that were received at our CLIA certified laboratory were microdissected and a selected reaction monitoring mass spectrometry (SRM-MS) quantitative proteomic analysis of 72 protein biomarkers were conducted concurrently from 2-3 sections of FFPE tissue. Results: Platinum agents are widely agent in HNSCC cancer. ERCC1, a resistance marker for platinum agents was expressed in 44% of HNSCC. Similarly, TUBB3, a resistance marker for Paclitaxel, docetaxel was also expressed in ~45% of HNSCC. These indicate that ~45% of HNSCC could potentially be refractory to platinum and paclitaxel-based therapy. Additionally, ALDH1A1, a marker for resistance of cyclophosphamide, was expressed in 78% of HNSCC. Temozolomide, an alkylating agent used in other cancer type could be beneficial in 14% of HNSCC because of the lack of resistance marker MGMT. On the other hand, 88% of HNSCC expressed Topo1, which is a sensitivity marker for irinotecan or topotecan based therapy. Additionally, Top1 is also the target for the payload of several ADCs (e.g. trastuzumab deruxtecan and sacituzumab govitecan). Similarly, 55% of HNSCC expressed Topo2A, a target for etoposide and doxorubicin. Additionally, 57% of HNSCC expressed hENT1, a transporter of gemcitabine. HNSCC also expressed various targets for targeted and ADC agents. These include EGFR (86% detected with 37x range of distribution), Her3 (11%), IGF1R (16%), MET (13%), Folate receptor- alpha (18%), Mesothelin (13%), and Trop2 (89% with 134x range of distribution). Her2 was overexpressed ( > 750 amol/ug) in 11% of HNSCC, however, it was observed in 46% of HNSCC with a 53x range (276 – 14705 amol/ug), indicating that a significant population of HNSCC might be eligible for low Her2 clinical trials. Conclusions: Every cancer is unique, and the ability to analyze 72 protein biomarkers from 2-3 FFPE sections simultaneously at the same time provides a wealth of actionable information for clinical treatment or patient stratification for clinical trials.

Quantitative Mass Spectrometry Analysis of Cerebrospinal Fluid Protein Biomarkers in Alzheimer’s Disease

Alzheimer’s disease (AD) is the most common form of dementia, with cerebrospinal fluid (CSF) β-amyloid (Aβ), total Tau, and phosphorylated Tau (pTau) providing the most sensitive and specific biomarkers for diagnosis. However, these diagnostic biomarkers do not reflect the complex changes in AD brain beyond amyloid (A) and Tau (T) pathologies. Here, we report a selected reaction monitoring mass spectrometry (SRM-MS) method with isotopically labeled standards for relative protein quantification in CSF. Biomarker positive (AT+) and negative (AT−) CSF pools were used as quality controls (QCs) to assess assay precision. We detected 62 peptides (51 proteins) with an average coefficient of variation (CV) of ~13% across 30 QCs and 133 controls (cognitively normal, AT−), 127 asymptomatic (cognitively normal, AT+) and 130 symptomatic AD (cognitively impaired, AT+). Proteins that could distinguish AT+ from AT− individuals included SMOC1, GDA, 14-3-3 proteins, and those involved in glycolysis. Proteins that could distinguish cognitive impairment were mainly neuronal proteins (VGF, NPTX2, NPTXR, and SCG2). This demonstrates the utility of SRM-MS to quantify CSF protein biomarkers across stages of AD.

Evaluation of the carotenoid and fat-soluble vitamin profile of industrial hemp inflorescence by liquid chromatography coupled to mass spectrometry and photodiode-array detection

Industrial hemp (Cannabis sativa L.) is a plant matrix whose use is recently spreading for pharmaceutical and nutraceutical purposes. Detailed characterization of hemp composition is needed for future research that further exploits the beneficial effects of hemp compounds on human health. Among minor constituents, carotenoids and fat-soluble vitamins have largely been neglected to date despite carrying out several biological activities and regulatory functions. In the present paper, 22 target carotenoids and fat-soluble vitamins were analyzed in the inflorescences of seven Italian industrial hemp varieties cultivated outdoor. The analytes were extracted by cold saponification to avoid artifacts and analyzed by high-performance liquid chromatography coupled with Selected reaction monitoring mass spectrometry. Phytoene, phytofluene, and all-trans-β-carotene were the most abundant in all analyzed samples (31–55 µg g−1, 11.6–29 µg g−1, and 7.3–53 µg g−1, respectively). Besides the target analytes, liquid chromatography coupled with photodiode-array detection allowed us to tentatively identify several other carotenoids based on their retention behavior and UV–vis spectra with the support of theoretical rules and data in the literature. To the best of our knowledge, this is the first comprehensive characterization of carotenoids and fat-soluble vitamins in industrial hemp inflorescence.

Multi-omic characterization of brain changes in the vascular endothelial growth factor family during aging and Alzheimer's disease

The vascular endothelial growth factor (VEGF) signaling family has been implicated in neuroprotection and clinical progression in Alzheimer's disease (AD). Previous work in postmortem human dorsolateral prefrontal cortex demonstrated that higher transcript levels of VEGFB, PGF, FLT1, and FLT4 are associated with AD dementia, worse cognitive outcomes, and higher AD neuropathology. To expand prior work, we leveraged bulk RNA sequencing data, single nucleus RNA (snRNA) sequencing, and both tandem mass tag and selected reaction monitoring mass spectrometry proteomic measures from the post-mortem brain. Outcomes included AD diagnosis, cognition, and AD neuropathology. We replicated previously reported VEGFB and FLT1 results, whereby higher expression was associated with worse outcomes, and snRNA results suggest microglia, oligodendrocytes, and endothelia may play a central role in these associations. Additionally, FLT4 and NRP2 expression were associated with better cognitive outcomes. This study provides a comprehensive molecular picture of the VEGF signaling family in cognitive aging and AD and critical insight towards the biomarker and therapeutic potential of VEGF family members in AD.

Comparative analysis of heat‐stress‐induced abscisic acid and heat shock protein responses among pea varieties

AbstractHeat shock proteins (HSPs) and abscisic acid (ABA) play important roles in plant heat responses but have not been extensively studied in pea (Pisum sativum L.), whose heat susceptibility is well known. In this study, four pea varieties varying in heat tolerance based on field trials were evaluated. Plants were heat stressed for 3, 6, 12, or 24 h at 38 °C before pollination. Anther and stipule RNA from the same flowering node were sampled for transcriptional profiling of PsHSP18.1 and PsHSP71.2. Additional stipules were sampled for the quantification of ABA concentration and its five key catabolites from the four major ABA catabolic pathways by ultra‐high performance liquid chromatography–selected reaction monitoring mass spectrometry (UHPLC‐SRM/MS). The transcription of both HSP genes was upregulated because of heat stress (HS). In stipules, the upregulation was greatest at 3 h HS, whereas in anthers, the induced transcription was similar among different hours of HS. Likewise, more ABA accumulated in the ABA metabolism pool because of HS, and the ABA response started rapidly after 3 h of treatment. Heat‐tolerant varieties had a higher ABA synthesis and turnover rate at 3 h HS than their respective heat‐susceptible counterparts. This study provides new insights into different heat tolerance among Canadian pea varieties regarding HSP and ABA hormone regulation.

Development of an enzymatic method for the evaluation of protein deposition on contact lenses

The aim of this study was to evaluate a new digestion method to quantify protein deposition on contact lenses. Four silicone hydrogel and one hydrogel contact lens material were incubated in lactoferrin, lysozyme, immunoglobulin A, and bovine serum albumin solutions at approximate physiological concentrations and temperature. Immobilized trypsin was used to digest the protein deposits from the contact lens surfaces. The total protein absorbed to lenses was extracted and digested using sequencing grade trypsin. The tryptic peptides were quantified using selected reaction monitoring mass spectrometry. The concentration of surface protein deposits was either lower than or the same as the total protein for all lens types and proteins. Immobilised trypsin can digest protein deposits from the surface of contact lenses. This ability to analyse the amount of protein at a contact lens surface may help in elucidating the effect of surface deposition on clinical outcomes during lens wear.

VEGF-family brain protein abundance: Associations with Alzheimer's disease pathology and cognitive decline.

Previous work has implicated associations between the angiogenic vascular endothelial growth factor (VEGF) gene family and Alzheimer's disease (AD) and associated cognitive decline. Specifically, we have shown that mRNA expression of VEGFB, PGF, FLT1, and FLT4 are associated with AD diagnosis, lower cognition prior to death, faster cognitive decline, and higher AD neuropathology at death. However, we wanted to explore whether these associations persisted at the protein level. Detailed cognitive and neuropathological data were obtained from 1,084 participants in the Religious Orders Study and Rush Memory and Aging Project. Selected reaction monitoring mass spectrometry was used to quantify VEGF protein levels in dorsolateral prefrontal cortex tissue. A total of 22 peptides representing five VEGF family proteins were available for analysis. Linear regression assessed VEGF proteomic associations with cognition adjacent to death and with amyloid and tau burden at autopsy. Mixed-effects regression quantified VEGF associations with cognitive decline. Models covaried for age at death, sex, post-mortem interval, and interval to death, with secondary models covarying for post-mortem amyloid and tau burden. P-values were corrected using the false discovery rate (fdr) procedure. Higher levels of VEGFB and FLT1 peptides were associated with lower cognition prior to death (p.fdr≤0.031), as well as with faster cognitive decline (p.fdr≤0.016), while NRP1 peptides were associated with slower cognitive decline (p.fdr=0.010). VEGFB, VEGFA, and FLT1 peptides were positively associated with higher amyloid burden (p.fdr≤0.012), while NRP1 peptides were negatively associated (p.fdr=0.003). VEGFB and FLT1 peptides were also associated with higher tau burden at death (p.fdr≤0.041). Cognitive associations remained when covarying for neuropathology burden. Finally, only FLT1 peptides were differently expressed in AD cases and controls (β≥0.12, p.fdr≤0.024). Proteomic results are highly consistent with previous mRNA findings, strengthening the hypothesis that VEGF's role in AD-related cognitive decline centers on VEGFB-FLT1 signaling. The associations remained largely significant even when covarying for pathological burden, suggesting VEGF family signaling independently contributes to the clinical manifestation of AD. Interestingly, since NRP1 amplifies VEGF family angiogenic signaling, NRP1's association with slower cognitive decline at the protein level may reflect a partially-successful attempt to rescue cognition by increasing blood flow.

Targeted Selected Reaction Monitoring Verifies Histology Specific Peptide Signatures in Epithelial Ovarian Cancer.

Simple SummaryOvarian cancer is a lethal disease due to its late phase discovery. Any steps towards improving early diagnostics will dramatically increase survival rates. To identify new ovarian cancer biomarker panels, we need to focus on early-stage disease and all histologic subtypes. In this study we have, based on prior discoveries, constructed a multiplexed targeted selected-reaction-monitoring assay to detect peptides from 177 proteins in only 20 µL of plasma. The assay was evaluated in patients with a focus on early-stages and all ovarian cancer histologies in separate groups. With multivariate analysis, we found the highest predictive value in the benign vs. low-grade serous (Q2 = 0.615) and mucinous (Q2 = 0.611) early stage compared to all malignant (Q2 = 0.226) or late stage (Q2 = 0.43) ovarian cancers. The results show that each ovarian cancer histology subgroup can be identified by a unique panel of proteins.Epithelial ovarian cancer (OC) is a disease with high mortality due to vague early clinical symptoms. Benign ovarian cysts are common and accurate diagnosis remains a challenge because of the molecular heterogeneity of OC. We set out to investigate whether the disease diversity seen in ovarian cyst fluids and tumor tissue could be detected in plasma. Using existing mass spectrometry (MS)-based proteomics data, we constructed a selected reaction monitoring (SRM) assay targeting peptides from 177 cancer-related and classical proteins associated with OC. Plasma from benign, borderline, and malignant ovarian tumors were used to verify expression (n = 74). Unsupervised and supervised multivariate analyses were used for comparisons. The peptide signatures revealed by the supervised multivariate analysis contained 55 to 77 peptides each. The predictive (Q2) values were higher for benign vs. low-grade serous Q2 = 0.615, mucinous Q2 = 0.611, endometrioid Q2 = 0.428 and high-grade serous Q2 = 0.375 (stage I–II Q2 = 0.515; stage III Q2 = 0.43) OC compared to benign vs. all malignant Q2 = 0.226. With targeted SRM MS we constructed a multiplexed assay for simultaneous detection and relative quantification of 185 peptides from 177 proteins in only 20 µL of plasma. With the approach of histology-specific peptide patterns, derived from pre-selected proteins, we may be able to detect not only high-grade serous OC but also the less common OC subtypes.

Rapid identification of plasmalogen molecular species using targeted multiplexed selected reaction monitoring mass spectrometry

Plasmalogens (Pls) levels are reported to be altered in several neurological and metabolic diseases. Identification of sn-1 fatty alcohols and sn-2 fatty acids of different Pls species is necessary to determine the roles and mechanisms of action of Pls in different diseases. Previously, full-scan tandem mass spectrometry (MS/MS) was used for this purpose but is not effective for low-abundance Pls species. Recently, multiplexed selected reaction monitoring MS (SRM/MS) was found to be more selective and sensitive than conventional full-scan MS/MS for the identification of low-abundance compounds. In the present study, we developed a liquid chromatography (LC)-targeted multiplexed SRM/MS system for the identification and quantification of different Pls choline (Pls-PC) and Pls ethanolamine (Pls-PE) species. We determined five precursor-product ion transitions to identify sn-1 and sn-2 fragments of each Pls species. Consequently, sn-1 and sn-2 fatty acyl chains of 22 Pls-PC and 55 Pls-PE species were identified in mouse brain samples. Among them, some species had C20:0 and C20:1 fatty alcohols at the sn-1 position. For quantification of Pls species in mouse brain samples, a single SRM transition was employed. Thus, our results suggest that the LC-targeted multiplexed SRM/MS system is very sensitive for the identification and quantification of low-abundance lipids such as Pls, and is thus expected to make a significant contribution to basic and clinical research in this field in the future.

Structure-specific, accurate quantitation of plasmalogen glycerophosphoethanolamine

Changes in plasmalogen glycerophosphoethanolamine (PE-P) composition (structure and abundance) are a key indicator of altered lipid metabolism. Differential changes in the levels of PE-P have been reported in different disease states, including neurodegenerative diseases. Of particular interest, traumatic brain injury (TBI) has resulted in altered expression of glycerophospholipid profiles, including PE-P. To date, most analytical assays assessing PE-P have focused on general lipidomic workflows to evaluate the relative, semi-quantitative abundance of PE-P during disease progression. This approach provides a broad evaluation of PE-P, yet often lacks specificity and sensitivity for individual PE-P structures which is a necessity for robust quantitative data. The present study highlights the development of a targeted, quantitative method using a HILIC separation and selective reaction monitoring mass spectrometry for the confident identification and accurate quantitation of PE-P. Our innovative method incorporates both the sn-1 alkyl vinyl ether and sn-2 acyl chain as product ion transitions, for specific and sensitive quantitation of 100 PE-P structures. Our method also uniquely allowed for the unambiguous assignment and quantitation of di-unsaturated sn-1 PE-P structures, which to date have not been conclusively quantified. Application of this assay to a TBI mouse model resulted in distinct temporal profiles for plasma PE-P up to 28 days post injury. Plasma PE-P were significantly increased 24 h after induced TBI, followed by a gradual reduction to sham concentrations by day 28. Overall, we established a structure-specific, quantitative assay for identification and quantitation of a comprehensive set of PE-P structures with demonstrated relevance to brain injury.

Assessing the Kinetics of Metabolite Uptake and Utilization by Isolated Mitochondria Using Selective Reaction Monitoring Mass Spectrometry (SRM-MS).

Transport of tricarboxylic acid (TCA) cycle substrates across mitochondrial membranes and their subsequent oxidative decarboxylation in the matrix provide reductants for respiration-coupled ATP synthesis. These processes are typically assessed together through the ability of mitochondria to consume oxygen or release carbon dioxide, however, this approach fails to assess or separate the complexity of transport and the subsequent metabolism of substrates and products. In this chapter, we provide a strategy for simultaneously measuring substrate transport and utilization by isolated mitochondria using a mass spectrometry-based technique. The results of cofeeding of isolated mitochondria with unlabeled malate and uniformly labeled pyruvate is used as an example. Mitochondria fed with substrates are separated from the extramitochondrial space by centrifugation through a single layer of silicone oil. Analysis of mitochondrial pellet and reaction supernatant enable quantitation of substrate import and product export. This method also allows an estimation of the contribution of different enzymatic pathways to the formation of a specific product. This assay opens opportunities to verify carrier functions in organello and to identify the substrate preferences of mitochondrial transporters of unknown function using targeted and/or untargeted metabolomics approaches.

Antibody-Free Mass Spectrometry Identification of Vascular Integrity Markers in Major Trauma.

Antibody mediated strategies for protein biomarker detection are common, but may limit discovery. We hypothesized that the use of antibody-free proteomics is feasible for detecting protein biomarkers in plasma of patients sustaining major trauma. A subset of subjects with major trauma from a prospective observational trial were analyzed. Patients were assigned to one of four groups based on their presenting Abbreviated Injury Severity Score (AIS). Sensitive, antibody-free selective reaction monitoring (SRM) mass spectrometry (MS), with spiked-in isotopically labeled synthetic peptides, was used for targeted protein quantification of a panel of 10 prospective targets. An overall tiered sensitivity analytical approach was used for peptide detection and quantification based upon plasma immunoaffinity depletion and PRISM fractionation. Forty-four patients were included in the analysis, of which 82% were men with a mean age of 50 (±19) years. Half had isolated head injury (n = 22), with the remaining patients experiencing multiple injuries or polytrauma (n = 14), isolated body injury (n = 2), or minor injury (n = 6). Peptides from 3 proteins (vascular adhesion molecule 1 [VCAM1], intercellular adhesion molecule 1 [ICAM1], and matrix metalloproteinase 9 [MMP9]) were detected and quantified in non-depleted processed plasma. Peptides from 2 proteins (angiopoietin 2 [Ang2] and plasminogen activator inhibitor-1 [PAI1]) were detected and quantification in depleted plasma, whereas the remaining 5 of the 10 prospective targets were undetected. VCAM1 (p = 0.02) and MMP9 (p = 0.03) were significantly upregulated in in the major trauma groups (1–3) versus mild injury group (4), whereas the others were not. There were no differences in protein expression between patients with traumatic brain injury (TBI; groups 1 and 2) versus those without TBI (groups 3 and 4). We detected non-specific upregulation of proteins reflecting blood–brain barrier breakdown in severely injured patients, indicating label-free MS techniques are feasible and may be informative.

Targeted Phosphoinositides Analysis Using High-Performance Ion Chromatography-Coupled Selected Reaction Monitoring Mass Spectrometry.

Phosphoinositides are minor components of cell membranes, but play crucial roles in numerous signal transduction pathways. To obtain quantitative measures of phosphoinositides, sensitive, accurate, and comprehensive methods are needed. Here, we present a quantitative targeted ion chromatography–mass spectrometry-based workflow that separates phosphoinositide isomers and increases the quantitative accuracy of measured phosphoinositides. Besides testing different analytical characteristics such as extraction and separation efficiency, the reproducibility of the developed workflow was also investigated. The workflow was verified in resting and stimulated human platelets, fat cells, and rat hippocampal brain tissue, where the LOD and LOQ for phosphoinositides were at 312.5 and 625 fmol, respectively. The robustness of the workflow is shown with different applications that confirms its suitability to analyze multiple less-abundant phosphoinositides.

Validated B vitamin quantification from lentils by selected reaction monitoring mass spectrometry

A validated method for B vitamin separation and quantification from lentil seeds using ultra high performance liquid chromatography-selected reaction monitoring mass spectrometry (UHPLC-SRM MS) was reported. The use of three enzymes (acid phosphatase, β-glucosidase, and rat serum) with a 4 h incubation was sufficient to convert bound B vitamins into their free forms. Twenty B vitamers were selected and a 5-min UHPLC-SRM MS method was optimized for rapid analysis. This method was applied to quantify B vitamin concentration during lentil seed germination over a 5-day period. Total B vitamins increased up to 1.5-fold on day 5 (from 39.2 µg/g to 60.6 µg/g of dry weight) comparing with dry seeds. Vitamin B5 (pantothenic acid) was the most abundant B vitamin in both dry seeds (34.2%) and in germinated seeds (17.7%-24.5% of total B vitamins); B8 (biotin) and B12 (cyanocobalamin) were not detected in lentil samples.

MET Exon 14-altered Lung Cancers and MET Inhibitor Resistance.

MET tyrosine kinase inhibitors (TKIs) can achieve modest clinical outcomes in MET exon 14-altered lung cancers, likely secondary to primary resistance. Mechanisms of primary resistance remain poorly characterized and comprehensive proteomic analyses have not previously been performed. We performed hybrid capture-based DNA sequencing, targeted RNA sequencing, cell-free DNA sequencing, selected reaction monitoring mass spectrometry (SRM-MS), and immunohistochemistry on patient samples of MET exon 14-altered lung cancers treated with a MET TKI. Associations between overall response rate (ORR), progression-free survival (PFS), and putative genomic alterations and MET protein expression were evaluated. Seventy-five of 168 MET exon 14-altered lung cancers received a MET TKI. Previously undescribed (zygosity, clonality, whole-genome duplication) and known (copy-number focality, tumor mutational burden, mutation region/type) genomic factors were not associated with ORR/PFS (P > 0.05). In contrast, MET expression was associated with MET TKI benefit. Only cases with detectable MET expression by SRM-MS (N = 15) or immunochemistry (N = 22) responded to MET TKI therapy, and cancers with H-score ≥ 200 had a higher PFS than cancers below this cutoff (10.4 vs. 5.5 months, respectively; HR, 3.87; P = 0.02). In MET exon 14-altered cancers treated with a MET TKI, a comprehensive analysis of previously unknown and known genomic factors did not identify a genomic mechanism of primary resistance. Instead, MET expression correlated with benefit, suggesting the potential role of interrogating the proteome in addition to the genome in confirmatory prospective trials.

Peptidomics-Driven Strategy Reveals Peptides and Predicted Proteases Associated With Oral Cancer Prognosis

AbstractProtease activity has been associated with pathological processes that can lead to cancer development and progression. However, understanding the pathological unbalance in proteolysis is challenging because changes can occur simultaneously at protease, their inhibitor, and substrate levels. Here, we present a pipeline that combines peptidomics, proteomics, and peptidase predictions for studying proteolytic events in the saliva of 79 patients and their association with oral squamous cell carcinoma (OSCC) prognosis. Our findings revealed differences in the saliva peptidome of patients with (pN+) or without (pN0) lymph-node metastasis and delivered a panel of ten endogenous peptides correlated with poor prognostic factors plus five molecules able to classify pN0 and pN+ patients (area under the receiver operating characteristic curve > 0.85). In addition, endopeptidases and exopeptidases putatively implicated in the processing of differential peptides were investigated using cancer tissue gene expression data from public repositories, reinforcing their association with poorer survival rates and prognosis in oral cancer. The dynamics of the OSCC-related proteolysis were further explored via the proteomic profiling of saliva. This revealed that peptidase/endopeptidase inhibitors exhibited reduced levels in the saliva of pN+ patients, as confirmed by selected reaction monitoring–mass spectrometry, while minor changes were detected in the level of saliva proteases. Taken together, our results indicated that proteolytic activity is accentuated in the saliva of patients with OSCC and lymph-node metastasis and, at least in part, is modulated by reduced levels of salivary peptidase inhibitors. Therefore, this integrated pipeline provided better comprehension and discovery of molecular features with implications in the oral cancer metastasis prognosis.