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Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development

ABSTRACT: Jaffe JD, Keshishian H, Chang B, Addona TA, Gillette MA, Carr SA. Mol Cell Proteomics, 2008, 7, 1952-62. Tranche_hash:XQmp4fY8N3eYKVAoPWzjkrpNr0Pe4QuyNoPVdDo0UTq2JIdui2Z//aQ4jMZnat7dDuAkhiHdErfyMgBrvWT4dQRmutgAAAAAAAA0KQ==

PROVIDER: MSV000078504 | MassIVE | Fri Nov 22 16:50:00 GMT 2013

REPOSITORIES: MassIVE

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Directed sample interrogation utilizing an accurate mass exclusion-based acquisition strategy (AMEx)

Project description:Rudomin EL, Carr SA, Jaffe JD. J Proteome Res. 2009, 8, 3154-60. Tranche_hash:CGM1ky5e8D3BWT6cGfP1WouN+VbVZr5TGdHdlLB11iQDEcPieFWbdNrKPxmtVCbUvMmSN81c334ZZPWS69GX4e1H8gIAAAAAAAAMUQ==

2013-11-22 | MSV000078503 | MassIVE

A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease

Project description:Addona TA, Shi X, Keshishian H, Mani DR, Burgess M, Gillette MA, Clauser KR, Shen D, Lewis GD, Farrell LA, Fifer MA, Sabatine MS, Gerszten RE, Carr SA. Nat Biotechnol. 2011, 29(7):635-43. doi: 10.1038/nbt.1899. PMCID:PMC3366591. Discovery, AIMS, and MRM datasets Discovery_Tranche_hash: b/quYtp/Q8fY6EdnRMoUEe5Jme2WHwYKLj50kWO/JvsNdVnQV6UCgTixEFP9uQiBYJo9emQVc2lRzbDQLKURot4mEXEAAAAAAAGNYQ== AIMS_Tranche_hash: dzovoZTeT+kY0bQ4/NxPDI912ib+Z0/7UM/QS+Tzn1p0qdljLshY74okkmbLgCkQLbK8/CqwnSwPYciLSQqNc70hDuEAAAAAAACjIg== MRM_Tranche_hash: WNWMJg68D/CjrNnR26osMAfjmCNGbxEMweFdZJTps7AUv8Aw9pIhsfbMehM4lGYJSIKVx6CbZS/pBCftDf8XvDuKidMAAAAAAABCMg==

2013-12-19 | MSV000078513 | MassIVE

Quantitative, Multiplexed Assays for Low Abundance Proteins in Plasma by MRM with Stable Isotopes

Project description:Keshishian H, Addona T, Burgess M, Kuhn E, Carr SA. Mol Cell Proteomics. 2007, 12, 2212-29. Tranche_hash:LMMCbszGGFZm9e+7M2H8xf9Jvcg0KtznGn7M5VC39/NuKFK51ka/nc19AL44H2dE+FqMakaKLX6mIGEyPQ4Q7bfp92gAAAAAAAAT4A==

2013-11-21 | MSV000078502 | MassIVE

iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics

Project description:Mertins P, Udeshi ND, Clauser KR, Mani DR, Patel J, Ong, SE, Jaffe JD, Carr SA. Mol Cell Proteomics 2012, mcp.M111.014423. doi:10.1074/mcp.M111.014423. Tranche_hash:5cHw5Rj36vYNshNpy8k4nojtPyW27N/FHcImna3+zw4QV6KIlLOg3i6zesWBdWkEX608MEgdxWuVyKvvdOgB9BAanesAAAAAAACEzw==

2013-11-20 | MSV000078495 | MassIVE

A whole-blood RNA transcript based prognostic model in castration-resistant prostate cancer

Project description:Peripheral blood from 62 men with castration resistant prostate cancer was collected between 8/2006 and 6/2008. A panel of 168 inflammation-related and prostate cancer related genes was assessed with quantitative PCR to assess biomarkers predictive of survival.

2013-04-02 | GSE45705 | GEO

Integrated proteomic analysis of post-translational modifications by serial enrichment.

Project description:Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA. Nat Methods 2013, 10, 634-7. doi: 10.1038/nmeth.2518.

2013-12-10 | MSV000078509 | MassIVE

A whole-blood RNA transcript based prognostic model in castration-resistant prostate cancer

2013-04-02 | E-GEOD-45705 | biostudies-arrayexpress

Toward accurate screening in computer-aided enzyme design.

Project description:The ability to design effective enzymes is one of the most fundamental challenges in biotechnology and in some respects in biochemistry. In fact, such ability would be one of the most convincing manifestations of a full understanding of the origin of enzyme catalysis. In this work, we explore the reliability of different simulation approaches, in terms of their ability to rank different possible active site constructs. This validation is done by comparing the ability of different approaches to evaluate the catalytic contributions of various residues in chorismate mutase. It is demonstrated that the empirical valence bond (EVB) model can serve as a practical yet accurate tool in the final stages of computer-aided enzyme design (CAED). Other approaches for fast screening are also examined and found to be less accurate and mainly useful for qualitative screening of ionized residues. It is pointed out that accurate ranking of different options for enzyme design cannot be accomplished by approaches that cannot capture the electrostatic preorganization effect. This is in particular true with regard to current design approaches that use gas phase or small cluster calculations and then estimate the interaction between the enzyme and the transition state (TS) model rather than the TS binding free energy or the relevant activation free energy. The ability of the EVB model to provide a tool for quantitative ranking in the final stage of CAED may help in progressing toward the design of enzymes whose catalytic power is closer to that of native enzymes than to that of the current generation of designer enzymes.

| S-EPMC2832760 | biostudies-literature

A serum-based DNA methylation assay provides accurate detection of glioma.

Project description:BackgroundThe detection of somatic mutations in cell-free DNA (cfDNA) from liquid biopsy has emerged as a noninvasive tool to monitor the follow-up of cancer patients. However, the significance of cfDNA clinical utility remains uncertain in patients with brain tumors, primarily because of the limited sensitivity cfDNA has to detect real tumor-specific somatic mutations. This unresolved challenge has prevented accurate follow-up of glioma patients with noninvasive approaches.MethodsGenome-wide DNA methylation profiling of tumor tissue and serum cfDNA of glioma patients.ResultsHere, we developed a noninvasive approach to profile the DNA methylation status in the serum of patients with gliomas and identified a cfDNA-derived methylation signature that is associated with the presence of gliomas and related immune features. By testing the signature in an independent discovery and validation cohorts, we developed and verified a score metric (the "glioma-epigenetic liquid biopsy score" or GeLB) that optimally distinguished patients with or without glioma (sensitivity: 100%, specificity: 97.78%). Furthermore, we found that changes in GeLB score reflected clinicopathological changes during surveillance (eg, progression, pseudoprogression, and response to standard or experimental treatment).ConclusionsOur results suggest that the GeLB score can be used as a complementary approach to diagnose and follow up patients with glioma.

| S-EPMC8408843 | biostudies-literature

Genome-wide CRISPR screening combined with ATAC-see assay

Project description:Cas9 expressing eHAP cells were transduced with human sgRNA lentivirus library (Doench, 2016 Nature biotech, Addgene, #73178). The cells were selected with 1 µg/ml of puromycin for 2 days, and then used for ATAC-see at 5 and 7 days post-transduction, respectively. Cells in the G2 phase were specifically gated to sort th 5% of the cells with the highest and lowest ATAC-see signal intensity(“high” or “low” population) . The sgRNA enrichment in each population was analysed by high-throughput sequencing and computationally compared by using the MAGeCK program (Li et al., Genome Biology 2014).

2022-05-01 | GSE144450 | GEO

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