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Sample data sharing application system

Platform Introduction

The mass spectrometry platform is committed to providing mass spectrometry analysis technology detection and services for biological species from small molecules to macromolecular complex systems. Main technical services include: structural determination of small molecular compounds, determination of biological macromolecule mass, nucleic acid mass spectrometry, protein identification, protein quantification, post-translational modification identification of proteins (such as phosphorylation, ubiquitination, glycosylation, etc.), discovery of biomarkers, including proteomics, metabolomics and lipomics analysis.

Instrument configuration
The large-scale analysis and detection instruments of the biological mass spectrometry platform include: THERMO Orbitrap Exploris 480, THERMO QE plus, THERMO Orbitrap Eclipse, AB SCIEX TripleTOF 5600 plus and other high resolution liquid mass spectrometry systems, Aglient 8890-7010B triple four-stage rod gas chromatograph, Aglient 7890A-5975C single four-stage rod gas chromatograph, AB SCIEX QTRAP 4500 and AB SCIEX Triple Quad 4500 triple four-stage rod liquid mass spectrometry systems, Agilent 600 MHz ultra-low temperature nuclear magnetic resonance spectrometer, Agilent 400 MHz nuclear magnetic resonance spectrometer, and DR MassARRAY time-of-flight mass spectrometry detection system.

Aglient 8890-7010B triple quadrupole gas-mass spectrometer

Aglient 8890-7010B triple quadrupole gas-mass spectrometer

AB SCIEX 4500 triple four-stage rod liquid-mass coupling system

AB SCIEX 4500 triple four-stage rod liquid-mass coupling system

AB SCIEX TripleTOF 5600 plus high resolution mass spectrometer

AB SCIEX TripleTOF 5600 plus high resolution mass spectrometer

MassARRAY time-of-flight mass spectrometry detection system

MassARRAY time-of-flight mass spectrometry detection system

Agilent 7890A/5975C

Agilent 7890A/5975C

Ultra-low temperature 600 megawatt nuclear magnetic spectrometer

Ultra-low temperature 600 megawatt nuclear magnetic spectrometer

THERMO Orbitrap Eclipse

THERMO Orbitrap Eclipse

THERMO QE plus

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Service Items

Proteomics services

Metabolomics service

Nucleic acid mass spectrometry detection service

Olink Precision Proteomics Analysis Service

Product Description With the accomplishment of human whole genome sequencing, medical research has moved from genomics to the post-genomic era. The research value of proteins as functional executors of life activities is gaining more and more attention. Protein biomarkers can serve as important features in pathophysiology, bridge the gap between genome and phenotype, and have a profound impact on improving future healthcare, especially in precision medicine. However, the progress has been stunted by the lack of technologies that can provide high specificity, sensitivity, and throughput. The emergence of Olink technology, however, can break through these obstacles and accelerate the development of proteomics in the field of precision medicine. Technology principle. Olink protein detection platform is based on the neighbor extension technology Proximity Extension Assay (PEA) for protein detection. For each protein to be detected, a pair of antibodies is designed at two adjacent antigenic epitopes, which are coupled to a specific DNA single strand with paired bases at the end of the single strand. When the pair of antibodies binds to the target protein, the two adjacent DNA single strands are hybridized and complemented and extended in an enzymatic reaction, which then forms a double-stranded template. The detection of the double-stranded template using microfluidic qPCR or NGS enables the quantitative analysis of the protein. This technique cleverly converts protein quantification to DNA quantification, solving the problem that proteins cannot be amplified, thus enabling the detection of trace amounts of proteins. Technical advantages. 1. High specificity: High specificity by using two antibodies to recognize one protein, labeling and full validation by Barcode. 2. Wide dynamic range: The entire panel spans 10 log values, allowing simultaneous consideration of proteins of different abundance. 3. High sensitivity: The detection sensitivity is as low as fg/mL level, which can detect thousands of disease-related low abundance proteins (especially low abundance biomarkers in plasma and serum samples) at the histological level. 4. High detection throughput: 96/384/3072panel, each panel can detect 88 samples at a time. By combining qPCR and NGS high throughput detection platform, it can produce millions of protein data per week. 5. Micro sample: 48-384 protein markers can be detected simultaneously in 1μL plasma, and more than 3000 protein markers can be detected in 8μL plasma. 6. High reproducibility: strict quality control, 99.8% of proteins without cross-reactivity, mature detection platform, high data quality, good reproducibility, suitable for large data analysis requirements, and the reproducibility requirements of clinical translational applications. Application areas. Biomarker research: disease risk assessment, disease typing, disease prediction, disease diagnosis and prognosis. Drug discovery: drug target discovery, clinical treatment effect evaluation, basic research.

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Protein qualitative analysis services

a. Protein full-spectrum analysis Protein full-spectrum analysis can also be called mass spectrometry shotgun analysis. which refers to the component analysis.The Objects of study are complete tissues, body fluids or their extracts, with the aim of identifying as many peptides and protein molecules as possible. The basic principle of protein mass spectrometry identification is to digest proteins into peptide mixtures by proteases, and then ionize them by electron bombardment or other means to form charged ions with different mass-to-charge ratios, and then separate the peptide ions with specific mass-to-charge ratios by a mass analyzer. The protein was identified by comparing the actual spectrogram with the primary and secondary mass spectra of protein digested by protease in theory. Schematic diagram of protein full spectrum analysis Instruments used: Orbitrap Eclipse, Orbitrap Exploris 480, Q Exactive plus; AB SCIEX: TripleTOF 5600 plus. Technical advantages: Comprehensive identification of a large number of proteins in whole cells, tissues or complex mixed samples, with 200-5000 proteins can be identified. Application areas: Identification of all expressed proteins in tissues, cells or organelles in a given physiological state. Sample requirements: Sample Sample requirements Protein solution Total protein > 500 μg, concentration > 0.1 μg/μL; Buffer solution without detergent NP40, Triton X-100, etc. Lead time（Project Cycle） Progress Time period Sample collection/Quality control 2-3 working days Sample processing 4-5 working days Mass spectrometry detection 2-3 working days Data analysis 2-3 working days Total No more than 15 working days Note: For more than 5 samples, 3 working days will be added for each additional sample. If there is an urgent need, please contact us for negotiation. b. Protein Identification LC-MS/MS technology was used to identify proteins for moderately complex samples such as single strips (i.e., SDS-PAGE samples), IP, Co-IP, and Pull-down purification solutions. 凝胶电泳条带鉴定路线图 Pull-down experiment roadmap Instruments: Orbitrap Eclipse, Orbitrap Exploris 480, Q Exactive Plus . Technical advantages: high sensitivity, high accuracy. Suitable for moderately complex protein samples, such as IP, Co-IP . Application areas: disease marker research, mechanism of action research, plant resistance research, drug target research, specific functional protein identification. Sample requirements: Sample Sample requirements SDS-PAGE bands Komas staining, silver staining (mass spectrometry compatible) bands are clearly visible Protein solution Total protein >5μg, concentration >0.1μg/μL; buffer without detergent NP40, Triton X-100, etc. Lead time（Project Cycle） Progress Time period Sample collection/Quality control 1-2 working days Sample processing 2-3 working days Mass spectrometry detection 2-3 working days Data analysis 2-3 working days Report generation 1-2 working days Total No more than 10 working days Note: For more than 10 samples, 1 working days will be added for each additional sample. If there is an urgent need, please contact us for negotiation.

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Protein Quantification Service

a.TMT™ Technology TMT™ (Tandem Mass Tag™) technology is an in vitro peptide labeling technology developed by Thermo Scientific, which is designed for the identification and quantification of proteins in different samples by tandem mass spectrometry (MS). This technique uses multiple isotope labels to label the amino groups of peptides, and after LC-MS/MS analysis, the relative amounts of proteins in 2-16 groups of different samples can be compared simultaneously. TMT™技术示意图 Instruments used:Orbitrap Eclipse, Orbitrap Exploris 480,Q Exactive Plus. Technical advantages: Simultaneous analysis of protein differences in 2-16 samples of different conditions. Suitable for a wide range of sample types: cytoplasmic proteins, membrane proteins, nuclear proteins, extracellular proteins, etc. Compared with protein quantification by gel separation, TMT mass spectrometry can detect more types of protein molecules, such as low-abundance proteins, strongly acidic (base) proteins, <10KD or >100KD protein molecules. Application areas: disease marker screening, mechanism of action research, plant resistance research, drug action target research, special functional protein screening. Sample requirements Sample Type Sample requirements (per group of samples) Protein extract Concentration >1μg/μL, total protein >300μg Cell sample Cell volume >10^7 Tissue samples Animal, microbial tissue wet weight >10mg; plant fresh tissue >100mg Body fluid sample Blood volume>500μL 　Lead time： Progress Time period Sample collection/Quality control 1-2 working days Sample processing 5-6 working days Mass spectrometry test 3-4 working days Data analysis 2-3 working days Total No more than 20 working days Note: For more than 10 samples, 1 working days will be added for each additional sample. If there is an urgent need, please contact us for negotiation. b.Label-free Label-free quantification is the mass spectrometric analysis of enzymatic protein peptides by liquid chromatography-mass spectrometry (LC-MS). Label-free定量蛋白组学实验流程 Instruments used: THERMO: Orbitrap Eclipse, Orbitrap Exploris 480,Q Exactive Plus. Technical advantages: no labeling of proteins, low cost and low volume of samples required. Application areas: disease marker screening, mechanism of action research, plant resistance research, drug target research, special function protein screening. c.SWATH/DIA SWATH/DIA is a new panoramic scanning mode for mass spectrometry. Compared with the traditional shot-gun technique, SWATH/DIA acquisition mode is able to scan all precusor peptide in the scan interval at ultra-high speed and perform secondary fragmentation, thus obtaining complete peptide information. With SWATH /DIA acquisition mode, complete quantitative and qualitative results can be obtained in a single experiment, without method optimization. SWATH/DIA mode overcomes the problem of shot-gun scan randomness, resulting in better data reproducibility. SWATH/DIA is particularly suitable for enrichment of purified samples, e.g. SWATH/DIA quantification after IP to detect proteins that interact with the target protein. SWATH技术示意图 Instruments used: THERMO: Orbitrap Eclipse, Orbitrap Exploris 480, Q Exactive plus; AB SCIEX: TripleTOF 5600 plus Technical advantages High sensitivity, which has the data acquisition mode of MRM, combined with a high-resolution mass spectrometry system with comparable sensitivity to MRM. Quantitative correlation between duplicate samples can reach above 0.99. Quantitative accuracy almost comparable to MRM technique. the quantification range can span 4 orders of magnitude The quantitative results are very good. Application areas: mechanism and regulatory mechanism research, screening of disease markers, screening of drug use and prognostic markers, molecular typing of diseases. Sample requirements： Sample Type Sample requirements (per group of samples) Protein extract Concentration >1μg/μL, total protein >300μg Cell sample Cell volume >107 Tissue samples Animal, microbial tissue wet weight >10mg; plant fresh tissue >100mg Body fluid sample Blood volume>500μL Lead time: Progress Time period Sample collection/Quality control 1-2 working day Sample processing 5-6 working days Mass spectrometry test 3-4 working days Data analysis 2-3 working days Total No more than 20 working days Note: For more than 4 samples, 5 working day will be added fo

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Protein modification analysis service

The research work of proteomics not only focuses on the changes of protein expression levels in different cell growth periods or under disease conditions, but also many vital life processes are not only controlled by the relative abundance of proteins, but also regulated by spatiotemporal and spatiotemporal distribution of reversible post-translational modifications. Therefore, revealing the rules of post-translational modifications is an important prerequisite for analyzing the complex and diverse biological functions of proteins. The molecular weight of protein will change when it is modified after translation. The molecular weight of protein or polypeptide can be accurately determined by mass spectrometry. At the same time, the content of post-translational modified protein in the sample is low and the dynamic range is wide, so it is necessary to enrich the modified protein or peptide segment before mass spectrometry detection.

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Targeted metabolomics

Targeted metabolomics analysis is the targeted and specific detection and analysis of the specified metabolites in the list by using standard samples as controls. The key points of targeted metabolomics analysis are high accuracy, high throughput and high reliability. Although this type of analysis is more routine than metabolic profiling, it can be used for very large numbers of samples. Targeted metabolomics can be applied to. (1) Validating new findings and hypotheses proposed by metabolomics experiments; (2) Conducting hypothesis-based exploratory experiments and studying metabolic models for specific metabolites. Basic Research Process The process of targeted metabolomics research can be divided into: sample collection, standard curve creation, metabolite extraction and isolation, on-line assay, and data analysis. Sample types Serum - Plasma - Urine - Cerebrospinal fluid - Saliva - Feces - Microorganisms - Cells - Plants - Tissues - Others 　 Targeted metabonomics services and cycles are shown in the following table: 靶向代谢组学服务和周期平台仪器型号代谢物化合物数目检测周期检测价格 GC-MS/MS Aglient 7890A-5975C或8890-7010B 短链脂肪酸 11种短链脂肪酸约15个工作日请询价游离脂肪酸 37种游离脂肪酸 UHPLC-QqQ MS SCIEX QTRAP 4500或Triple Quad 4500 维生素 12种水溶性约20个工作日请询价氨基酸 32种氨基酸神经递质 27种神经递质植物激素 10种植物激素胆汁酸 48种胆汁酸辅酶 18种辅酶抗生素 105种抗生素 11种短链脂肪酸绝对定性定量分析序号中文名称英文名称分子式 CAS号相对分子质量 1 乙酸 acetic acid C2H4O2 64-19-7 60.05 2 丙酸 propionic acid C3H6O2 79-09-4 74.08 3 异丁酸 isobutyric acid C4H8O2 79-31-2 88.11 4 丁酸 n-butyric acid C4H8O2 107-92-6 88.11 5 异戊酸 isovaleric acid C5H10O2 503-74-2 102.13 6 戊酸 n-valeric acid C5H10O2 109-52-4 102.13 7 4-甲基戊酸 4-methylvaleric acid C6H12O2 646-07-1 116.16 8 正己酸 hexanoic acid C6H12O2 142-62-1 116.15 9 2-甲基己酸 2-methylhexanoic acid C7H14O2 4536-23-6 130.18 10 正庚酸 n-heptylic acid C7H14O2 111-14-8 130.18 11 正辛酸 n-octanoic acid C8H16O2 124-07-2 144.21 37种游离脂肪酸绝对定性定量分析编号中文名称英文名称简写 1 丁酸 butyric acid C4:0 2 己酸 caproic acid C6:0 3 辛酸 caprylic acid C8:0 4 癸酸 capric acid C10:0 5 十一烷酸 undecanoic acid C11:0 6 月桂酸 lauric acid C12:0 7 十三烷酸 tridecanoic acid C13:0 8 十四酸 myristic acid C14:0 9 十四碳烯酸 myristoleic acid C14:1n5 10 十五烷酸 pentadecanoic acid C15:0 11 顺-10-十五碳烯酸 cis-10-pentadecenoic acid C15:1n5 12 棕榈酸 palmitic acid C16:0 13 棕榈油酸 palmitoleic acid C16:1n7 14 十七烷酸 heptadecanoic acid C17:0 15 顺-10-十七烯酸 cis-10-heptadecenoic acid C17:1n7 16 硬脂酸 stearic acid C18:0 17 反油酸 elaidic acid C18:1n9t 18 油酸 oleic acid C18:1n9c 19 反亚油酸 linolelaidic acid C18:2n6t 20 亚油酸 linoleic acid C18:2n6c 21 γ-亚麻酸 r-linolenic acid C18:3n6 22 α-亚麻酸 α-linolenic acid C1

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Non-targeted metabolomics

Non-targeted metabolomics (i.e. discovery metabolomics) is a non-hypothetical approach that aims to obtain as many metabolites as possible from a single analysis. The main purpose is to compare the metabolomes (all metabolites of a given organism) of the control and experimental groups to find out the differences in their metabolites and to explore the metabolic pathways between the differential metabolites. The analysis generally includes: a. Metabolic profiling (also called differential expression analysis): looking for metabolites of interest with statistically significant abundance changes in a set of experimental and control samples. b. Identification: After performing metabolic profiling, the chemical structure of these metabolites is determined. c. Interpretation: The final step in the research process, explaining the association between the metabolites found and the biological process or biological state. Research Process The non-targeted metabolomics research process can be mainly divided into experimental design, sample collection and processing, metabolite extraction and concentration, sample detection, data analysis, metabolite identification, and finally biological interpretation. Because the metabolome changes extremely fast, the metabolite species are various, the concentration varies greatly, the chemical properties are different, and the data information is huge, each step may have a large impact on the final results, so it is crucial to realize the standardized operation of metabolomics Technology platform The main platforms for non-targeted metabolomics are nuclear magnetic resonance (NMR), gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS), each of which has a certain bias, so researchers need to choose the appropriate platform according to the purpose of the study and the type of samples. The purpose is to achieve a more complete and comprehensive study. Table Comparison of major assay platforms for non-targeted Major Assay Platforms Advantages Disadvantages NMR 1. High throughput 2. Universality 3. Good objectivity and reproducibility 4. Fast (2~3 min/sample) 5. Simple pretreatment, no derivatization and separation required 6. Non-invasive 7. Can detect most organic compounds in the sample 8. Long instrument life 1. Detection dynamic range is narrow 2. Lower sensitivity and resolution than MS 3. The sample amount is relatively large (0.1 ~ 0.5 mL) 4. Expensive instrumentation and maintenance costs GC-MS 1. High throughput 2. High precision, sensitivity and reproducibility 3. Has a reference standard spectral database, easy to characterize 4. The sample amount is moderate (0.1~0.2 mL) 5. Can detect most organic and some inorganic molecules in the sample 1. Requires derivatization 2. Requires separation 3. Slow analysis speed (20~40 min/sample) 4. It is difficult to identify new compounds 5. Not suitable for the analysis of difficult volatile, thermally unstable substances LC-MS 1. High throughput 2. High separation rate and sensitivity 3. Wide dynamic range of detection 4. Simple sample processing, no need for derivatization 5. Small sample size (10~100 μL) 6. Applicable to thermally unstable, non-volatile, not easily derivatized and large molecular weight substances 1. Slow analysis speed (15~40 min/sample) 2. Lack of standard spectral database for reference 3. Difficult to identify new compounds 4. Higher cost 5. Short instrument life Data analysis methods The data obtained from non-targeted metabolomics are complex and multidimensional, and the chemometric methods need to be fully applied to deeply explore the information in them. The data are generally pre-processed first, and the specific process includes normalization, data transformation, centralization, and normalization steps. Only after pre-processing, simplification and dimensionality reduction of the data are realized, and reliable data models are established. The pattern recognition methods applied to metabolomics data analysis mainly include unsupervised learning methods and supervised learning methods. The unsupervised learning methods mainly include: principal component analysis (PCA), nonlinear mapping, cluster analysis, etc. Supervised learning methods are mainly based on partial least squares (PLS), neural network improvement methods, least squares-discriminant analysis (PLS-DA), orthogonal least squares (OPLS), etc., among which PCA and PLS-DA are commonly used pattern recognition methods in metabolomics. Non-targeted metabolomics data processing process Sample types Serum - Plasma - Urine - Cerebrospinal fluid - Saliva - Feces - Microorganisms - Cells - Plants - Tissues – Other Lead time

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Nucleic acid mass spectrometry detection service

MassARRAY is based on Matrix Assisted Laser Desorption /Ionization-Time of Flight (MALDI-TOF) technology, and is the global original nucleic acid mass spectrometry platform for high precision DNA qualitative analysis. This technology platform Perfectly integrates the high sensitivity of PCR technology, the high throughput of chip technology,the high accuracy of mass Spectrometry technology and the powerful function of computer Intelligent analysis, which is the best tool for large sample size Verification of a large number of candidate SNP and DNA methylation markers discovered by sequencing and chip technology.The MassARRAY system provides a unique solution for targeted gene detection using limited samples. It can meet the assay design, validation and performance needs of genomics laboratories. Technology Principle The MassARRAY time-of-flight mass spectrometry detection system consists of a matrix-assisted laser desorption ionization (MALDI) source, a time-of-flight mass analyzer (TOF), and a template preparation plate.The principle of MALDI is to irradiate a co-crystalline film formed by the sample and matrix with a laser, and the matrix absorbs energy from the laser and transmits it to the biomolecules, causing them to ionize.The principle of TOF is Biomolecules are ionized and accelerated through the flight tube by an electric field, and the mass-to-charge ratio of the ions is proportional to the ion's time of flight. The system is extremely accurate and fast, allowing multiple samples to be tested at one time. Multiplex PCR amplification is first performed, followed by single-base extension with modified ddNTP, enabling the mass spectrometry system to accurately identify differences in individual bases and report the frequency of each base according to peak area, and thus accurately analyze the frequency of allele distribution in the sample. Application scope Detection of variant types :. a.SNPs/SNVs (point mutations) b.Indels (insertion/deletion mutations) c.CNVs (copy number variants) d.Gene Fusions e.Methylations Main application areas a.Suitable for genome-wide SNP association studies and subsequent large sample size validation b. Susceptibility gene analysis and gene localization for complex diseases c.High sensitivity analysis of somatic mutations d. Population genetics studies e. Pharmacogenomics (drug development and individual drug use) f. Other: pathogenic microbial detection, health management, biological sample identification, etc. Available tests Skin type genetic test Advanced tumor susceptibility gene test for men(six items) Metabolic genetic test Advanced tumor susceptibility gene test for women (seven tests) Weight and health management gene test Deafness gene test Scientific exercise gene test Folic acid gene test Breast cancer susceptibility gene test Gene test for hypertension Basic five tumor susceptibility gene test Epilepsy gene test Cardiovascular disease gene test Project advantages a. Multiplex reactions, fast detection cycle Single reactions up to 10 to 60 assays and only simple PCR and extension reagents are required, no fluorescent probes are needed and the project lead time is within 5 working days. b.High accuracy and sensitivity Typing accuracy >99.7%, which is the gold standard for SNP detection; detection sensitivity up to 0.1% for low frequency alleles and rare mutations. c.Flexible throughput The standard 96 chips are available to meet the needs of different detection volumes, and the samples can be tested on the machine without making up samples. d. High sample compatibility Each reaction well requires only 5-10ng of genomic DNA, and supports biological samples from various sources: blood, blood collection cards, oral swabs, saliva, semen, fresh tissue, puncture tissue and FFPE samples, seeds, roots, leaves, etc. Even highly degraded samples can be tested. e. Support different types of marker detection for a wide range of applications It can detect SNP, point mutation, In/Del, CNV, gene fusion and methylation and many other variant types, which can be applied to genetic diseases, solid tumors and liquid biopsies, pharmacogenomics and many other fields.

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