Mixed-mode ion exchange-based integrated proteomics technology for fast and deep plasma proteome profiling

Lu, Xue; Lin, Lin; Zhou, Wenbin; Chen, Wendong; Tang, Jun; Sun, Xiujie; Huang, Peiwu; Tian, Ruijun

doi:10.1016/j.chroma.2018.06.020

Cited by 29 publications

(43 citation statements)

References 37 publications

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“…61,100 LC-MS methods are being developed to minimize protein loss and degradation, and to achieve deep proteome profiling in plasma. 101 LC-MS following immunoaffinity purification has been used to identify tumor HLA antigens in plasma of adults with glioblastoma. 102 In addition to high resolution mass spectrometry, methods such as ELISAs (enzyme linked immunosorbent assays) can quantify protein levels in blood.…”

Section: Methods Of Analysismentioning

confidence: 99%

Liquid biopsy for pediatric central nervous system tumors

et al. 2018

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Central nervous system (CNS) tumors are the most common solid tumors in children, and the leading cause of cancer-related death. Over the past decade, molecular profiling has been incorporated into treatment for pediatric CNS tumors, allowing for a more personalized approach to therapy. Through the identification of tumor-specific changes, it is now possible to diagnose, assign a prognostic subgroup, and develop targeted chemotherapeutic treatment plans for many cancer types. The successful incorporation of informative liquid biopsies, where the liquid biome is interrogated for tumor-associated molecular clues, has the potential to greatly complement the precision-based approach to treatment, and ultimately, to improve clinical outcomes for children with CNS tumors. In this article, the current application of liquid biopsy in cancer therapy will be reviewed, as will its potential for the diagnosis and therapeutic monitoring of pediatric CNS tumors.

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Section: Methods Of Analysismentioning

confidence: 99%

Liquid biopsy for pediatric central nervous system tumors

et al. 2018

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“…In this design, protein digest was fractionated with SCX/SAX mixed-mode and then with high-pH RPLC prior to low-pH RPLC-MS/MS analysis. From 1 mL of serum, 862 proteins were identified with 12 fractions in 12 h of MS/MS analysis [70]. The third dimension was low-pH RPLC coupled with MS/MS analysis.…”

Section: Offline 3d-lc Systemsmentioning

confidence: 99%

“…Several features in these two strategies comparison are listed in Table 4. Recently, with the development of some integrated devices as has been discussed, offline 3D-LC strategies could overcome their major limitations: sample loss and large sample amount requirement [69][70][71][72][73][74]. These devices, therefore, make the recent offline 3D-LC approaches more potent and applicable to clinical samples.…”

Section: Comparison Of Offline and Online Setupsmentioning

confidence: 99%

“…Generally, 3D-LC systems suffer from sample loss, an increase in time and sample consumptions. Sample loss is one of the major drawbacks when performing 3D-LC [70]. As a result, 3D-LC methods often require a large amount of sample.…”

Section: Author's Outlook and Concluding Remarksmentioning

confidence: 99%

“…However, the development of integrated devices has intensely reduced the sample amount. For example, the 3D-LC method with mixed-mode-SISPROT can be performed with~60 µg of depleted plasma [70]. One can also choose to carry out online 3D-LC for in-depth proteomic analysis in case the sample amount is limited.…”

Section: Author's Outlook and Concluding Remarksmentioning

confidence: 99%

See 2 more Smart Citations

Review of Three-Dimensional Liquid Chromatography Platforms for Bottom-Up Proteomics

Duong

Park

Lee

2020

IJMS

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Proteomics is a large-scale study of proteins, aiming at the description and characterization of all expressed proteins in biological systems. The expressed proteins are typically highly complex and large in abundance range. To fulfill high accuracy and sensitivity of proteome analysis, the hybrid platforms of multidimensional (MD) separations and mass spectrometry have provided the most powerful solution. Multidimensional separations provide enhanced peak capacity and reduce sample complexity, which enables mass spectrometry to analyze more proteins with high sensitivity. Although two-dimensional (2D) separations have been widely used since the early period of proteomics, three-dimensional (3D) separation was barely used by low reproducibility of separation, increased analysis time in mass spectrometry. With developments of novel microscale techniques such as nano-UPLC and improvements of mass spectrometry, the 3D separation becomes a reliable and practical selection. This review summarizes existing offline and online 3D-LC platforms developed for proteomics and their applications. In detail, setups and implementation of those systems as well as their advances are outlined. The performance of those platforms is also discussed and compared with the state-of-the-art 2D-LC. In addition, we provide some perspectives on the future developments and applications of 3D-LC in proteomics.

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Dual roles of drug or its metabolite−protein conjugate: Cutting‐edge strategy of drug discovery using shotgun proteomics

Gong

Chen

Sun

et al. 2022

Medicinal Research Reviews

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Many drugs can bind directly to proteins or be bioactivated by metabolizing enzymes to form reactive metabolites (RMs) that rapidly bind to proteins to form drug−protein conjugates or metabolite−protein conjugates (DMPCs). The close relationship between DMPCs and idiosyncratic adverse drug reactions (IADRs) has been recognized; drug discovery teams tend to avoid covalent interactions in drug discovery projects. Covalent interactions in DMPCs can provide high potency and long action duration and conquer the intractable targets, inspiring drug design, and development. This forms the dual role feature of DMPCs. Understanding the functional implications of DMPCs in IADR control and therapeutic applications requires precise identification of these conjugates from complex biological samples. While classical biochemical methods have contributed significantly to DMPC detection in the past decades, the low abundance and low coverage of DMPCs have become a bottleneck in this field. An emerging transformation toward shotgun proteomics is on the rise. The evolving shotgun proteomics techniques offer improved reproducibility, throughput, specificity, operability, and standardization. Here, we review recent progress in the systematic discovery of DMPCs using shotgun proteomics. Furthermore, the applications of shotgun proteomics supporting drug development, toxicity mechanism investigation, and drug repurposing processes are also reviewed and prospected.

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Mixed-mode ion exchange-based integrated proteomics technology for fast and deep plasma proteome profiling

Cited by 29 publications

References 37 publications

Liquid biopsy for pediatric central nervous system tumors

Liquid biopsy for pediatric central nervous system tumors

Review of Three-Dimensional Liquid Chromatography Platforms for Bottom-Up Proteomics

Dual roles of drug or its metabolite−protein conjugate: Cutting‐edge strategy of drug discovery using shotgun proteomics

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