High throughput and accurate serum proteome profiling by integrated sample preparation technology and single-run data independent mass spectrometry analysis

Lin, Lin; Zheng, Jiaxin; Yu, Quan; Chen, Wendong; Xing, Jinchun; Chen, Chenxi; Tian, Ruijun

doi:10.1016/j.jprot.2017.12.014

Cited by 69 publications

(60 citation statements)

References 41 publications

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“…For LC-MS workflows, nano-LC chromatography is often used to obtain maximum sensitivity for peptide analytes, using analytical columns that are approximately 50-150 microns in diameter, with a typical recommended binding capacity of only 1.0-3.0 micrograms of total soluble digested protein (from a tissue, biofluid, or cell digest). Liquid biopsy samples, including serum and plasma, have a wide and dynamic range of endogenous proteins, with a small number of proteins representing a large fraction of the total protein mass [54]. For example, the top twenty proteins in serum/plasma represent 95% of the total protein mass.…”

Section: Affi-bams Sensitivity and Reproducibilitymentioning

confidence: 99%

Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics

Hamza

Bergo

Mamaev

et al. 2020

IJMS

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The ability to quantitatively probe diverse panels of proteins and their post-translational modifications (PTMs) across multiple samples would aid a broad spectrum of biological, biochemical and pharmacological studies. We report a novel, microarray analytical technology that combines immuno-affinity capture with Matrix Assisted Laser Desorption Ionization Mass Spectrometry (MALDI MS), which is capable of supporting highly multiplexed, targeted proteomic assays. Termed “Affinity-Bead Assisted Mass Spectrometry” (Affi-BAMS), this LC-free technology enables development of highly specific and customizable assay panels for simultaneous profiling of multiple proteins and PTMs. While affinity beads have been used previously in combination with MS, the Affi-BAMS workflow uses enrichment on a single bead that contains one type of antibody, generally capturing a single analyte (protein or PTM) while having enough binding capacity to enable quantification within approximately 3 orders of magnitude. The multiplexing capability is achieved by combining Affi-BAMS beads with different protein specificities. To enable screening of bead-captured analytes by MS, we further developed a novel method of performing spatially localized elution of targets from individual beads arrayed on a microscope slide. The resulting arrays of micro spots contain highly concentrated analytes localized within 0.5 mm diameter spots that can be directly measured using MALDI MS. While both intact proteins and protein fragments can be monitored by Affi-BAMS, we initially focused on applying this technology for bottom-up proteomics to enable screening of hundreds of samples per day by combining the robust magnetic bead-based workflow with the high throughput nature of MALDI MS acquisition. To demonstrate the variety of applications and robustness of Affi-BAMS, several studies are presented that focus on the response of 4EBP1, RPS6, ERK1/ERK2, mTOR, Histone H3 and C-MET to stimuli including rapamycin, H2O2, EPO, SU11274, Staurosporine and Vorinostat.

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Section: Affi-bams Sensitivity and Reproducibilitymentioning

confidence: 99%

Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics

Hamza

Bergo

Mamaev

et al. 2020

IJMS

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“…During the process of bone remodeling, biochemical products are produced and can be detected in the blood and/or urine, which are considered to be biomarkers. Plasma and serum are rich sources of information regarding an individual's health state, and protein tests inform medical decision making (Geyer et al, 2019;Lin et al, 2018). Biomedical substances that are involved in metabolic activities are tied to an individual's biological or metabolic status; thus, circulating proteins are considered sensitive and specific markers of certain pathological states, including abnormal bone metabolism (Brosseron et al, 2018;Shao et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Proteomic profiling analysis of postmenopausal osteoporosis and osteopenia identifies potential proteins associated with low bone mineral density

Huang

Wang

et al. 2020

PeerJ

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Postmenopausal osteoporosis (PMOP) is a major global public health concern and older women are more susceptible to experiencing fragility fractures. Our study investigated the associations between circulating proteins with bone mineral density (BMD) in postmenopausal women with or without low BMD (osteoporosis and osteopenia) using a tandem mass tag (TMT) labeling proteomic experiment and parallel reaction monitoring testing. Across all plasma samples, we quantitatively measured 1,092 proteins, and the OP and normal control (NC) samples were differentiated by principal component analysis and a partial least squares-discrimination analysis model based on the protein profiling data. The differentially abundant proteins between the low BMD and NC samples mostly exhibited binding, molecular function regulator, transporter and molecular transducer activity, and were involved in metabolic and cellular processes, stimulus response, biological regulation, immune system processes and so forth. TMT analysis and RRM validation indicated that the expression of protein Lysozyme C (P61626) was negatively related to BMD, while the expression of proteins Glucosidase (A0A024R592) and Protein disulfideisomerase A5 (Q14554) was positively related to BMD values. Collectively, our results suggest that postmenopausal women with low BMD have a different proteomic profile or signature. Protein alterations may play an important role in the pathogenesis of PMOP, and they may act as novel biomarkers and targets of therapeutic agents for this disease.

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“…[ 4 ] Mass spectrometry (MS) is one of the rapidly developing bio‐analytical techniques in recent years, which has been used to identify and validate protein biomarkers for clinical application. [ 5 ] As a method of detecting biological active molecules, MS has many advantages, [ 6 ] such as sensitivity, rapidity, specificity, and so on.…”

Section: Introductionmentioning

confidence: 99%

The Influence of Blood Collection Tubes in Biomarkers’ Screening by Mass Spectrometry

Zhang

Zhao

Duan

et al. 2020

Proteomics Clinical Apps

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Purpose Mass spectrometry is one of the rapidly developing bio‐analytical techniques in recent years, and it shows that the results of biomarkers’ screening can be influenced by pre‐analytical process. The selection of the blood collection tubes is one of the most significant steps of pre‐analytical process which is often neglected by researchers. So, it is urgent to define the influence of blood collection tubes clearly in biomarkers’ screening. Experimental Design Two types of blood collection tubes, non‐additive tubes and coagulant activator tubes, are used to collect serum samples from patients and healthy controls. All samples are analyzed using matrix‐assisted laser desorption ionization‐time of flight mass spectrum in this study. Results The serum protein profile changes while using coagulant tubes whether for patients or healthy controls. It is found that the effect of coagulant on serum protein of patients is smaller than that of control group. There are 27 significantly different peaks between the control group and the control coagulant group. However, between patient group and patient coagulant group, only one differential peak is obtained. Coagulant changes the expression differences between patients and healthy controls, making the differences expand, shrink or reverse, and most of the polypeptides are small molecule, which will change the results of biomarker's screening. Conclusions and Clinical Relevance This research suggested that different types of blood collection tubes would influence the final laboratory results. So it's important for clinicians to choose the proper tubes to detect biomarkers and make correct diagnoses.

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High throughput and accurate serum proteome profiling by integrated sample preparation technology and single-run data independent mass spectrometry analysis

Cited by 69 publications

References 41 publications

Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics

Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics

Proteomic profiling analysis of postmenopausal osteoporosis and osteopenia identifies potential proteins associated with low bone mineral density

The Influence of Blood Collection Tubes in Biomarkers’ Screening by Mass Spectrometry

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