SWATH Method Research Articles

Investigating the pathogenesis of vitreous in postmortem COVID patients via untargeted metabolomics based bioinformatics model

SARS-CoV-2 virus has become a worldwide pandemic causing millions of death. This severe disaster lead to a immense panic and stress all over the world. Several studies were dedicated to understand its mechanism, pathogenesis and spreading characteristics. By this way, scientists try to develop different therapy and diagnose strategies. For these reasons, several metabolomics, proteomics and genomics studies were also carried out to improve knowledge in this newly identified virus. In this study, we are aimed to explain the pathogenesis of SARS-CoV-2 exposure on postmortem COVID (+) patients via untargeted metabolomics analysis. To carry out this study, a Data Independent Acquisition SWATH method is optimized and performed. Vitreous samples were analyzed in both MS1 and MS2 ESI(+) mode. An orthogonal Partial Least Square Discriminant Analysis were performed for classification. It was observed that lipid metabolism, several amino acids and oxidative stress biomarkers were strongly affected due to high inflammation and possible cytokine storm.

Characterization of proteome profile data of chemicals based on data-independent acquisition MS with SWATH method.

Transcriptomic data of cultured cells treated with a chemical are widely recognized as useful numeric information that describes the effects of the chemical. This property is due to the high coverage and low arbitrariness of the transcriptomic data as profiles of chemicals. Considering the importance of posttranslational regulation, proteomic profiles could provide insights into the unrecognized aspects of the effects of chemicals. Therefore, this study aimed to address the question of how well the proteomic profiles obtained using data-independent acquisition (DIA) with the sequential window acquisition of all theoretical mass spectra, which can achieve comprehensive and arbitrariness-free protein quantification, can describe chemical effects. We demonstrated that the proteomic data obtained using DIA-MS exhibited favorable properties as profile data, such as being able to discriminate chemicals like the transcriptomic profiles. Furthermore, we revealed a new mode of action of a natural compound, harmine, through profile data analysis using the proteomic profile data. To our knowledge, this is the first study to investigate the properties of proteomic data obtained using DIA-MS as the profiles of chemicals. Our 54 (samples) × 2831 (proteins) data matrix would be an important source for further analyses to understand the effects of chemicals in a data-driven manner.

BIOM-20. IDENTIFICATION OF BLOOD BIOMARKERS FOR DIFFERENTIATING PSEUDOPROGRESSION FROM RECURRENCE IN GLIOBLASTOMA

Abstract After the initial treatment of glioblastoma, we occasionally encounter difficulty in distinguishing between pseudoprogression and recurrence. Observation without obtaining a pathological diagnosis is a common strategy in clinical practice. If the differentiation can be achieved easily, and reliably, early treatment can be introduced appropriately, leading to the benefits of early glioblastoma treatment. In this study, we attempted to identify blood biomarkers that help distinguish between recurrence and pseudoprogression. Blood samples were collected in 25 cases of primary glioblastoma, IDH wild type, at three time points: before treatment, after standard treatment: operation and temozolomide chemotherapy with concomitant radiation therapy, and when an enhancing lesion was recognized (21 cases of recurrence, 4 cases of pseudoprogression). Gelsolin (GSN), Apolipoprotein A-IV, Osteopontin, SERPINA3, ITIH2/4 Ceruloplasmin, LRG1, Collagen-1A2, which we previously extracted as diagnostic markers, using the comprehensive proteomics SWATH method, in blood samples of healthy volunteers and patients with glioblastoma (PLoS One. 2018, J Proteome Res. 2020), were analyzed. Absolute quantitative values of candidate molecules in the blood were obtained using a commercially available enzyme-linked immunoassay. Among the candidate molecules, GSN was significantly lower in pseudoprogression than in recurrence (p = 0.0032), and ROC analysis showed sensitivity of 95%, specificity of 100%, and an AUC = 0.98, which makes GSN a useful molecule to consider as a differential marker. We previously reported that GSN, actin binding protein, and inflammation markers are downregulated in glioblastoma (Cancer Sci. 2020). In summary, GSN was extracted as a candidate blood biomarker for the diagnosis of pseudoprogression. We are planning to validate the research with nationwide multi-institutional studies.

Optimization of Microflow LC Coupled with Scanning SWATH and Its Application in Hepatocellular Carcinoma Tissues.

Scanning SWATH coupled with normal-flow LC has been recently introduced for high-content, high-throughput proteomics analysis, which requires a relatively large amount of sample injection. Here we established the microflow LC coupled with Scanning SWATH for samples with relatively small quantities. First, we optimized several key parameters of the LC and MS settings, including C18 particle size for the analytical column, LC gradient and flow rate, as well as effective ion accumulation time and isolation window width for MS acquisition. We then compared the optimized Scanning SWATH method with the conventional variable window SWATH (referred to as SWATH) method. Results showed that the total ion chromatogram signals in Scanning SWATH were 10 times higher than that of SWATH, and Scanning SWATH identified 12.2-22.2% more peptides than SWATH. Finally, we employed 120 min Scanning SWATH to acquire the proteomes of 62 formalin-fixed, paraffin-embedded (FFPE) tissue samples from 31 patients with hepatocellular carcinoma (HCC). Altogether, 92 334 peptides and 8516 proteins were quantified. Besides the reported biomarkers, including ANXA2, MCM7, SUOX, and AKR1B10, we identified new potential HCC biomarkers such as CST5, TP53, CEBPB, and E2F4. Taken together, we present an optimal workflow integrating microflow LC and Scanning SWATH that effectively improves the protein identification and quantitation.

Activation of Annexin A2 signaling at the blood-brain barrier in a mouse model of multiple sclerosis.

Blood-brain barrier (BBB) dysfunction is a fundamental cause of multiple sclerosis and identifying the molecules that are responsible is an urgent matter. Protein expression was comprehensively quantified at the BBB of experimental autoimmune encephalomyelitis (EAE) mice, a model of multiple sclerosis, using the SWATH method. Concerning tight junction molecules, the level of expression of Claudin-5, which, in a previous immunohistochemical analysis, was confirmed to be down-regulated by EAE, remained unchanged, but the expression of Claudin-11 and Occludin was decreased by 0.69- and 0.62-fold, respectively, in brain capillaries isolated from EAE mice. A number of other cell-cell junctional molecules including ESAM, CADM1, CADM2, CADM3, CADM4, and HEPACAM were also down-regulated. The levels of expression of intercellular adhesion molecule 1 (ICAM1) and vascular cell adhesion molecule 1 (VCAM1), which directly mediate the infiltration of lymphocytes across the BBB, were increased in EAE mice by 3.3- and 2.6-fold, respectively. The expression of CXADR, which possibly facilitates the adhesion of migrating cells, was also increased by 3.5-fold. Interestingly, various members of the Annexin A (ANXA) family were also up-regulated in brain capillaries that were isolated from EAE mice. In a pathway associated with cell infiltration and tight junction disruption, a series of molecules that are involved in ANXA2 signaling (ANXA2, PTP1B, Ahnak, S100A11, CD44, Kindlin2, Integrin α5, Fibronectin, Fibrinogen) were up-regulated. ANXA2 is selectively and abundantly expressed in endothelial cells in the brain. The daily administration of an ANXA2 inhibitor (LCKLSL peptide) significantly suppressed the development of EAE in mice. In summary, the activation of ANXA2 signaling at the BBB appear to play an important role in the pathogenesis of EAE.

Leveraging homologies for cross-species plasma proteomics in ungulates using data-independent acquisition

The collection of blood plasma is minimally invasive, and the fluid is a rich source of proteins for biomarker studies in both humans and animals. Plasma protein analysis by mass spectrometry (MS) can be challenging, though modern data acquisition strategies, such as sequential window acquisition of all theoretical fragment ion spectra (SWATH), enable reproducible quantitation of hundreds of proteins in non-depleted plasma from humans and laboratory model animals. Although there is strong potential to enhance veterinary and translational research, SWATH-based plasma proteomics in non-laboratory animals is virtually non-existent. One limitation to date is the lack of comprehensively annotated genomes to aid protein identification. The current study established plasma peptide spectral repositories for sheep and cattle that enabled quantification of over 200 proteins in non-depleted plasma using SWATH approach. Moreover, bioinformatics pipeline was developed to leverage inter-species homologies to enhance the depth of baseline libraries and plasma protein quantification in bovids. Finally, the practical utility of using bovid libraries for SWATH data extraction in taxonomically related non-domestic ungulate species (giraffe) has been demonstrated. SignificanceAbility to quickly generate comprehensive spectral libraries is limiting the applicability of data-independent acquisition, such as SWATH, to study proteomes of non-laboratory animals. We describe an approach to obtain relatively shallow foundational plasma repositories from domestic ruminants and employ homology searches to increase the depth of data, which we subsequently extend to unsequenced ungulates using SWATH method. When applied to cross-species proteomics, the number of proteins quantified by our approach far exceeds what is traditionally used in plasma protein tests.

Combined proteomic and lipidomic studies in Pompe disease allow a better disease mechanism understanding.

Pompe disease (PD) is caused by deficiency of the enzyme acid α-glucosidase resulting in glycogen accumulation in lysosomes. Clinical symptoms include skeletal myopathy, respiratory failure, and cardiac hypertrophy. We studied plasma proteomic and lipidomic profiles in 12 PD patients compared to age-matched controls. The proteomic profiles were analyzed by nLC-MS/MS SWATH method. Wide-targeted lipidomic analysis was performed by LC-IMS/MS, allowing to quantify >1100 lipid species, spanning 13 classes. Significant differences were found for 16 proteins, with four showing the most relevant changes (GPLD1, PON1, LDHB, PKM). Lipidomic analysis showed elevated levels of three phosphatidylcholines and of the free fatty acid 22:4, and reduced levels of six lysophosphatidylcholines. Up-regulated glycolytic enzymes (LDHB and PKM) are involved in autophagy and glycogen metabolism, while down-regulated PON1 and GPLD1 combined with lipidomic data indicate an abnormal phospholipid metabolism. Reduced GPLD1 and dysregulation of lipids with acyl-chains characteristic of GPI-anchor structure suggest the potential involvement of GPI-anchor system in PD. Results of proteomic analysis displayed the involvement of multiple cellular functions affecting inflammatory, immune and antioxidant responses, autophagy, Ca2+ -homeostasis, and cell adhesion. The combined multi-omic approach revealed new biosignatures in PD, providing novel insights in disease pathophysiology with potential future clinical application.

Data-Independent Acquisition for the Quantification and Identification of Metabolites in Plasma.

A popular fragmentation technique for non-targeted analysis is called data-independent acquisition (DIA), because it provides fragmentation data for all analytes in a specific mass range. In this work, we demonstrated the strengths and weaknesses of DIA. Two types of chromatography (fractionation/3 min and hydrophilic interaction liquid chromatography (HILIC)/18 min) and three DIA protocols (variable sequential window acquisition of all theoretical mass spectra (SWATH), fixed SWATH and MSALL) were used to evaluate the performance of DIA. Our results show that fast chromatography and MSALL often results in product ion overlap and complex MS/MS spectra, which reduces the quantitative and qualitative power of these DIA protocols. The combination of SWATH and HILIC allowed for the correct identification of 20 metabolites using the NIST library. After SWATH window customization (i.e., variable SWATH), we were able to quantify ten structural isomers with a mean accuracy of 103% (91–113%). The robustness of the variable SWATH and HILIC method was demonstrated by the accurate quantification of these structural isomers in 10 highly diverse blood samples. Since the combination of variable SWATH and HILIC results in good quantitative and qualitative fragmentation data, it is promising for both targeted and untargeted platforms. This should decrease the number of platforms needed in metabolomics and increase the value of a single analysis.

Accelerated Protein Biomarker Discovery from FFPE Tissue Samples Using Single-Shot, Short Gradient Microflow SWATH MS.

We reported and evaluated a microflow, single-shot, short gradient SWATH MS method intended to accelerate the discovery and verification of protein biomarkers in preclassified clinical specimens. The method uses a 15 min gradient microflow-LC peptide separation, an optimized SWATH MS window configuration, and OpenSWATH software for data analysis. We applied the method to a cohort containing 204 FFPE tissue samples from 58 prostate cancer patients and 10 benign prostatic hyperplasia patients. Altogether we identified 27,975 proteotypic peptides and 4037 SwissProt proteins from these 204 samples. Compared to a reference SWATH method with a 2 h gradient, we found 3800 proteins were quantified by the two methods on two different instruments with relatively high consistency (r = 0.77). The accelerated method consumed only 17% instrument time, while quantifying 80% of proteins compared to the 2 h gradient SWATH. Although the missing value rate increased by 20%, batch effects reduced by 21%. 75 deregulated proteins measured by the accelerated method were selected for further validation. A shortlist of 134 selected peptide precursors from the 75 proteins were analyzed using MRM-HR, and the results exhibited high quantitative consistency with the 15 min SWATH method (r = 0.89) in the same sample set. We further verified the applicability of these 75 proteins in separating benign and malignant tissues (AUC = 0.99) in an independent prostate cancer cohort (n = 154). Altogether, the results showed that the 15 min gradient microflow SWATH accelerated large-scale data acquisition by 6 times, reduced batch effect by 21%, introduced 20% more missing values, and exhibited comparable ability to separate disease groups.

Optimization and Comparison of Information-Dependent Acquisition (IDA) to Sequential Window Acquisition of All Theoretical Fragment Ion Spectra (SWATH) for High-Resolution Mass Spectrometry in Clinical Toxicology.

Untargeted data acquisition on high-resolution mass spectrometers (HRMSs) has been used in clinical toxicology for screening and identifying unknown compounds in patient samples. A common modality for untargeted HRMS data acquisition is information-dependent acquisition (IDA), which analyzes the most abundant small molecules within an acquisition cycle. This process can potentially lead to false negatives of clinically relevant compounds at low concentrations. Sequential window acquisition of all theoretical fragment ion spectra (SWATH) has emerged as a method of unbiased, untargeted HRMS data acquisition in which no spectral data are lost. SWATH has yet to be optimized and assessed for use in clinical toxicology. We developed a variable-window SWATH method (vSWATH) and compared it to IDA by limit of detection studies in drug-supplemented urine (81 compounds) and against a retrospective cohort of 50 clinical urine samples characterized by LC-MS/MS. vSWATH had a lower limit of detection than IDA for 33 (41%) drugs and metabolites added into urine samples. Both IDA and vSWATH were equivalent in discovering compounds from clinical urine samples and confirmed 26 additional compounds not previously discovered by targeted LC-MS/MS. Lastly, the unbiased acquisition of spectra in vSWATH allowed for identification of 5 low-abundance compounds missed by IDA. This vSWATH method for clinical toxicology demonstrated equivalent analytical sensitivity and specificity for untargeted drug screening and identification in urine samples. vSWATH provided the additional benefit of collecting all tandem mass spectrometry spectra in a sample, which could be useful in discovering low-abundance compounds not discovered by IDA.

ANALISIS POTENSI JENIS POHON LOKAL GUNA REVEGETASI LAHAN TAMBANG EMAS (PT. J-Resources Bolaang Mongondow Site Lanut)

The purposes of this study are (1) to know the local trees which growing at area before mining operation began and when mining operation by PT. J Resource Bolaang Mongondow has started, (2) to know the kind of local trees which is appropriate with revegetation land, (3) to know technical planning the use of local tree for revegetation gold mine area. This study is use line swath method. This method is as the modification of dual swaths method or track method which with through one or more swaths in the track so that in every line path should have many swaths in some distance. The sampling intensity which use in this study is 10 %. The variables (data) of the study are consists by primary data and secondary data. To collect the data the researcher use a literature study which to collect the first data from many literatures about the analysis of local trees and revegetation land, direct observation, and identify kind of local trees by using work sheet data. The result of the study at the PT. J Resources Bolaang Mongondow Lanut-Site forest area, the researcher have found that (1) 29 species of vegetation tree level with the total number 50 individual trees and vegetation of local trees consist of 8 species and those are Matoa (Pometia pinnata), kitchen wood (Dryobalanops aromatic), Gopasa (Vitex cofassus), Sengon (Albazia moluccana), Benuang (Octomeles sumatrana), Trembesi (Albizia saman), Candlenut (Aleurites moluccana), and Durian (Durio spp). From all of the total number of individual trees which is in 6 swaths examples (plot), (2) it has founded 10 species trees level with the level of dominance (level of mastery) in the vegetation community are: Diangow (Anarcadium Sp), Dongiat/Matoa (Pometia Pinnata), Dau’/Dao (Dracontomelon dao), Toraut/Gopasa (Vitex cofassus), Biluk (Aegle marmefes), Nutmeg (Myristica sp), Dongkat/Stone wood (Irvingia malayana oliv), Atul/Kitchen wood (Dryobalanops aromatic), Tagoy (Laportea sinuate), and tula-tula (Floribundus muel). (3) For the revegetation area planning should be formulated that the revegetation area in gold mine must effective and efficient, because the area with slope and difference contour will have different way to handling (land with <300 slope have different slope >300).

SWATH enables precise label-free quantification on proteome scale.

MS-based proteomics has emerged as a powerful tool in biological studies. The shotgun proteomics strategy, in which proteolytic peptides are analyzed in data-dependent mode, enables a detection of the most comprehensive proteome (>10000 proteins from whole-cell lysate). The quantitative proteomics uses stable isotopes or label-free method to measure relative protein abundance. The isotope labeling strategies are more precise and accurate compared to label-free methods, but labeling procedures are complicated and expensive, and the sample number and types are also limited. Sequential window acquisition of all theoretical mass spectra (SWATH) is a recently developed technique, in which data-independent acquisition is coupled with peptide spectral library match. In principle SWATH method is able to do label-free quantification in an MRM-like manner, which has higher quantification accuracy and precision. Previous data have demonstrated that SWATH can be used to quantify less complex systems, such as spiked-in peptide mixture or protein complex. Our study first time assessed the quantification performance of SWATH method on proteome scale using a complex mouse-cell lysate sample. In total 3600 proteins got identified and quantified without sample prefractionation. The SWATH method shows outstanding quantification precision, whereas the quantification accuracy becomes less perfect when protein abundances differ greatly. However, this inaccuracy does not prevent discovering biological correlates, because the measured signal intensities had linear relationship to the sample loading amounts; thus the SWATH method can predict precisely the significance of a protein. Our results prove that SWATH can provide precise label-free quantification on proteome scale.

SWATH-based Comparative Proteomic Analysis of the Mycobacterium bovis BCG-Korea Strain

A derivative of Mycobacterium bovis Bacillus Calmette-Guerin (BCG) has been used for the preparation of tuberculosis vaccines. To establish a Korean tuberculosis vaccine derived from BCG-Pasteur 1173P2, genome sequencing of a BCG-Korea strain was completed by Joung and coworkers. 1 A comparison analysis of the genome sequences of the BCG-Pasteur 1173P2 and BCG-Korea strains showed marginal increases in the total genome length (~0.05%) and the number of genes (~4%) in the BCG-Korea genome. However, how the genomic changes affect the BCG-Korea protein expression levels remains unknown. Here, we provide evidence of the proteomic alterations in the BCG-Korea strain by using a SWATH-based mass spectrometric approach (Sequential Window Acquisition of all THeoretical mass spectra). Twenty BCG proteins were selected by top-rank identification in the BCG proteome analysis and the proteins were quantified by the SWATH method. Thirteen of 20 proteins showing significant changes were enough to discriminate between the two BCG proteomes. The SWATH method is very straightforward and provides a promising approach owing to its strong reliability and reproducibility during the proteomic analysis.

Comparison of Information-Dependent Acquisition, SWATH, and MSAll Techniques in Metabolite Identification Study Employing Ultrahigh-Performance Liquid Chromatography–Quadrupole Time-of-Flight Mass Spectrometry

Sensitive and selective liquid chromatography-mass spectrometry (LC-MS) analysis is a powerful and essential tool for metabolite identification in drug discovery and development. An MS(2) (or tandem, MS/MS) mass spectrum is acquired from the fragmentation of a precursor ion by multiple methods including information-dependent acquisition (IDA), SWATH (sequential window acquisition of all theoretical fragment-ion spectra), and MS(All) (also called MS(E)) techniques. We compared these three techniques in their capabilities to produce comprehensive MS(2) data by assessing both metabolite MS(2) acquisition hit rate and the quality of MS(2) spectra. Rat liver microsomal incubations from eight test compounds were analyzed with four methods (IDA, MMDF (multiple mass defect filters)-IDA, SWATH, or MS(All)) using an ultrahigh-performance liquid chromatography-qudrupole time-of-flight mass spectrometry (UHPLC-Q-TOF MS) platform. A combined total of 227 drug-related materials (DRM) were detected from all eight test article incubations, and among those, 5% and 4% of DRM were not triggered for MS(2) acquisition with IDA and MMDF-IDA methods, respectively. When the same samples were spiked to an equal volume of blank rat urine (urine sample), the DRM without MS(2) acquisition increased to 29% and 18%, correspondingly. In contrast, 100% of DRM in both matrixes were subjected to MS(2) acquisition with either the SWATH or MS(All) method. However, the quality of the acquired MS(2) spectra decreased in the order of IDA, SWATH, and MS(All) methods. An average of 10, 9, and 6 out of 10 most abundant ions in MS(2) spectra were the real product ions of DRM detected in microsomal samples from IDA, SWATH, and MS(All) methods, respectively. The corresponding numbers declined to 9, 6, and 3 in the urine samples. Overall, IDA-based methods acquired qualitatively better MS(2) spectra but with a lower MS(2) acquisition hit rate than the other two methods. SWATH outperformed the MS(All) method given its better quality of MS(2) spectra with an identical MS(2) acquisition hit rate.

On the complexity of point-in-polygon algorithms

Point-in-polygon is one of the fundamental operations of Geographic Information Systems. A number of algorithms can be applied. Different algorithms lead to different running efficiencies. In the study, the complexities of eight point-in-polygon algorithms were analyzed. General and specific examples are studied. In the general example, an unlimited number of nodes are assumed; whereas in the second example, eight nodes are specified. For convex polygons, the sum of area method, the sign of offset method, and the orientation method is well suited for a single point query. For possibly concave polygons, the ray intersection method and the swath method should be selected. For eight node polygons, the ray intersection method with bounding rectangles is faster.