Finding the Sweet Spot in ERLIC Mobile Phase for Simultaneous Enrichment of N-Glyco and Phosphopeptides

Cui, Yusi; Yang, Kuo‐Ho; Tabang, Dylan Nicholas; Huang, Junfeng; Tang, Weiping

doi:10.1007/s13361-019-02230-6

Cited by 23 publications

(25 citation statements)

References 78 publications

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“…DiLeu labeled glycopeptides were enriched using in-house packed SAX-HILIC SPE tips following previously reported procedure with minor modification 42 , 43 . 3 mg of cotton wool was inserted into a 200 µL TopTip.…”

Section: Methodsmentioning

confidence: 99%

Acetyl-CoA flux from the cytosol to the ER regulates engagement and quality of the secretory pathway

Dieterich

Cui

Braun

et al. 2021

Sci Rep

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Nε-lysine acetylation in the ER is an essential component of the quality control machinery. ER acetylation is ensured by a membrane transporter, AT-1/SLC33A1, which translocates cytosolic acetyl-CoA into the ER lumen, and two acetyltransferases, ATase1 and ATase2, which acetylate nascent polypeptides within the ER lumen. Dysfunctional AT-1, as caused by gene mutation or duplication events, results in severe disease phenotypes. Here, we used two models of AT-1 dysregulation to investigate dynamics of the secretory pathway: AT-1 sTg, a model of systemic AT-1 overexpression, and AT-1S113R/+, a model of AT-1 haploinsufficiency. The animals displayed reorganization of the ER, ERGIC, and Golgi apparatus. In particular, AT-1 sTg animals displayed a marked delay in Golgi-to-plasma membrane protein trafficking, significant alterations in Golgi-based N-glycan modification, and a marked expansion of the lysosomal network. Collectively our results indicate that AT-1 is essential to maintain proper organization and engagement of the secretory pathway.

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Section: Methodsmentioning

confidence: 99%

Acetyl-CoA flux from the cytosol to the ER regulates engagement and quality of the secretory pathway

Dieterich

Cui

Braun

et al. 2021

Sci Rep

Self Cite

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“…Third, when considering the glycosylation of exosomes, researchers have paid more attention to glycoproteins, with related technologies being developed and optimized primarily for them. 22,66 However, glycoproteins are not the only component that is glycosylated in exosomes. It must be pointed out that glycolipids also play an important role in the biological functions of exosomes.…”

Section: Discussionmentioning

confidence: 99%

“…More tissue comparative studies on the efficacy of using exosomes as biomarkers from diverse sources are also necessary. Third, when considering the glycosylation of exosomes, researchers have paid more attention to glycoproteins, with related technologies being developed and optimized primarily for them 22,66 . However, glycoproteins are not the only component that is glycosylated in exosomes.…”

Section: Discussionmentioning

confidence: 99%

The “sugar‐coated bullets” of cancer: Tumor‐derived exosome surface glycosylation from basic knowledge to applications

Lin

Zhou

Tan

2020

Clinical & Translational Med

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Scientific interest in exosomes has exploded in recent decades. In 1990 only three articles were published on exosomes, while over 1,700 have already been published halfway into 2020. 1 While researchers have shown much interest in exosomes since being discovered in 1981, an appreciation of the potential role of glycans in exosome structure and function has emerged only recently. Glycosylation is one of the most common post-translational modification, which functions in many physiological and pathological aspects of cellular function. Many components of exosomes are heavily glycosylated including proteins, lipids, among others. Thus, glycosylation undoubtedly has a great impact on exosome biosynthesis and function. Despite the importance of glycosylation in exosomes and the recent recognition of them as biomarkers for not only malignancies but also other system dysfunction and disease, the characterization of exosome glycans remains understudied. In this review, we discuss glycosylation patterns of exosomes derived from various tissues, their biological features, and potential for various clinical applications. We highlight state-of-the-art knowledge about the fine structure of exosomes, which will allow researchers to reconstruct them by surface modification. These efforts will likely lead to novel disease-related biomarker discovery, purification tagging, and targeted drug transfer for clinical applications in the future.

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“…Feature (2), MS2 Peak Filtering, similar to MS-Filter in Protein Prospector, can be used to focus attention on glycopeptide spectra by limiting the search to spectra containing glycan oxonium ions at m/z's such as 138.055, 204.087, and/or 274.092. As shown previously by Medzihradszky et al [21], ordinary and especially phospho-proteomics data sets often contain unrecognized glycopeptide spectra that can be found by filtering for oxonium ions, and it is quite feasible to enrich for both phosphorylation and glycosylation simultaneously [22]. Filtering by MS2 peaks can also be used to find all glycopeptides with the same peptide part by filtering for glycanloss peaks such as those from the bare peptide (Y0) or the bare peptide plus HexNAc (Y1) [23].…”

Section: Introductionmentioning

confidence: 90%

Peak Filtering, Peak Annotation, and Wildcard Search for Glycoproteomics

Roushan

Wilson

Kletter

et al. 2021

Molecular & Cellular Proteomics

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Glycopeptides in peptide or digested protein samples pose a number of analytical and bioinformatics challenges beyond those posed by unmodified peptides or peptides with smaller posttranslational modifications. Exact structural elucidation of glycans is generally beyond the capability of a single mass spectrometry experiment, so a reasonable level of identification for tandem mass spectrometry, taken by several glycopeptide software tools, is that of peptide sequence and glycan composition, meaning the number of monosaccharides of each distinct mass, for example HexNAc(2)Hex(5) rather than man5. Even at this level, however, glycopeptide analysis poses challenges: finding glycopeptide spectra when they are a tiny fraction of the total spectra; assigning spectra with unanticipated glycans, not in the initial glycan database; and finding, scoring, and labeling diagnostic peaks in tandem mass spectra. Here we discuss recent improvements to Byonic, a glycoproteomics search program, that address these three issues. Byonic now supports filtering spectra by m/z peaks, so that the user can limit attention to spectra with diagnostic peaks, for example, at least two out of three of 204.087 for HexNAc, 274.092 for NeuAc (with water loss), and 366.139 for HexNAc-Hex, all within a set mass tolerance, for example, ± 0.01 Daltons. Also new is glycan “wildcard” search, which allows an unspecified mass within a user-set mass range to be applied to N- or O-linked glycans and enables assignment of spectra with unanticipated glycans. Finally the next release of Byonic supports user-specified peak annotations from user-defined posttranslational modifications. We demonstrate the utility of these new software features by finding previously unrecognized glycopeptides in publicly available data, including glycosylated neuropeptides from rat brain.

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Finding the Sweet Spot in ERLIC Mobile Phase for Simultaneous Enrichment of N-Glyco and Phosphopeptides

Cited by 23 publications

References 78 publications

Acetyl-CoA flux from the cytosol to the ER regulates engagement and quality of the secretory pathway

Acetyl-CoA flux from the cytosol to the ER regulates engagement and quality of the secretory pathway

The “sugar‐coated bullets” of cancer: Tumor‐derived exosome surface glycosylation from basic knowledge to applications

Peak Filtering, Peak Annotation, and Wildcard Search for Glycoproteomics

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