Multiplexed peptide analysis using data-independent acquisition and Skyline

Target-protein degradation is an emerging field in drug discovery and development. In particular, the substrate-receptor proteins of the cullin-ubiquitin ligase system play a key role in selective protein degradation, which is an essential component of the anti-myeloma activity of immunomodulatory drugs (IMiDs), such as lenalidomide. Here, we demonstrate that a series of anticancer sulfonamides NSC 719239 (E7820), indisulam, and NSC 339004 (chloroquinoxaline sulfonamide, CQS) induce proteasomal degradation of the U2AF-related splicing factor coactivator of activating protein-1 and estrogen receptors (CAPERα) via CRL4 mediated ubiquitination in human cancer cell lines. Both CRISPR-Cas9-based knockout of DCAF15 and a single amino acid substitution of CAPERα conferred resistance against sulfonamide-induced CAPERα degradation and cell-growth inhibition. Thus, these sulfonamides represent selective chemical probes for disrupting CAPERα function and designate DCAFs as promising drug targets for promoting selective protein degradation in cancer therapy.

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“…39). Peptide spectral libraries were established based on Thermo's MSF files using Proteome Discoverer 1.4 with a cutoff score of 0.99.…”

Section: Lc-ms/ms Analysismentioning

confidence: 99%

Selective degradation of splicing factor CAPERα by anticancer sulfonamides

et al. 2017

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“…In MS E methods, all the ions generated at ionization source are transmitted to the collision cell, which alternates between high and low energy (c.a. from 15 to 55 eV), sending to the TOF analyzer, simultaneously, the precursors, and fragments of the peptides [64].…”

Section: Liquid Chromatography Coupled With Mass Spectrometry (Lc-ms)mentioning

confidence: 99%

Determination of Gluten Peptides Associated with Celiac Disease by Mass Spectrometry

Alves¹,

D’Almeida²,

Ferreira³

2017

Celiac Disease and Non-Celiac Gluten Sensitivity

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Gluten is a big protein network composed of monomeric fraction (prolamins) and polymeric fraction (glutelins), occurring in many cereal-based products, especially in those containing wheat. Gluten peptides can trigger food allergies and intolerances, including inflammatory reactions as the celiac disease, an autoimmune disorder of the small intestine characterized by mucosal degeneration and villous atrophy. The treatment is the permanent exclusion of gluten from diet. However, gluten analysis is a very difficult task, due to the high complexity of polypeptides and the lack of consensus on the most appropriate analytical method. Proteomics approaches, combining liquid chromatography and mass spectrometry in tandem (LC-MS/MS), have been pointed as the most promising nonimmunological techniques for gluten detection. LC-MS analyses associated with bioinformatics and specific-prolamin database can solve methodological limitations since it is based on the accurate molecular mass of peptide biomarkers. One of the major contributions of proteomics has been the identification of epitopes of gluten peptides responsible for wheat-related diseases. Recent works have defined grain-specific gluten peptides and also the lowest concentration at which peptides could be confidently detected. Proteomic application for gluten quantification should support not only regulatory limits in processed foods, but also the safety of consumers about food labeled as gluten-free.

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“…On the other hand, acquiring a narrow DIA mass range, instead of a conventional full scan, improves the Orbitrap-based detection sensitivity. The reason for the improvement in sensitivity is due to the less intense ion beam, which permits longer ion injection times into the C-trap and, therefore, increases absolute sensitivity [13,14].…”

Section: Introductionmentioning

confidence: 98%

Nested data independent MS/MS acquisition

Kaufmann¹,

Walker²

2016

Anal Bioanal Chem

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Data independent acquisition (DIA) attempts to provide comprehensive MS/MS data while providing a cycle time that is capable of following the elution profile of chromatographic peaks. Currently available MS technology is not yet fully capable of fulfilling these expectations. This paper suggests a new multiplex-based approach to more closely achieve this objective. Customized scans have been programmed for a Q Orbitrap instrument. Multiple nonadjacent mass range segments are sequentially collected (cut out) by the quadrupole. These combined mass ranges undergo fragmentation, and the resulting product ions are analyzed as a whole by the Orbitrap analyzer. The systematical variation of the mass range segments (nested design) permits the mathematical assignment of the observed product ions within a narrow precursor mass range. The proposed approach allows the use of mass windows that are narrower than those in conventional DIA (SWATH). A unique aspect of the proposed approach is the fact that halving the mass window width requires the addition of only a single multiplexed scan. This is different from conventional DIA, which requires the number of mass windows to be doubled in order to achieve the same objective. This paper shows that for a given cycle time, the proposed nested DIA technique produces significantly less chimeric product ion spectra than conventional DIA. However, further improvements from the programming, and most likely the hardware side, are still required in order to achieve the aim of comprehensive MS/MS. Graphical Abstract Schematic of nested design.

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Multiplexed peptide analysis using data-independent acquisition and Skyline

Cited by 182 publications

References 50 publications

Selective degradation of splicing factor CAPERα by anticancer sulfonamides

Selective degradation of splicing factor CAPERα by anticancer sulfonamides

Determination of Gluten Peptides Associated with Celiac Disease by Mass Spectrometry

Nested data independent MS/MS acquisition

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