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Article: An IROA Workflow for correction and normalization of ion suppression in mass spectrometry-based metabolomic profiling data.

Mahmud, Iqbal / Wei, Bo / Veillon, Lucas / Tan, Lin / Martinez, Sara / Tran, Bao / Raskind, Alexander / de Jong, Felice / Akbani, Rehan / Weinstein, John N / Beecher, Chris / Lorenzi, Philip L

Research square

2024

Abstract: Ion suppression is a major problem in mass spectrometry (MS)-based metabolomics; it can dramatically decrease measurement accuracy, precision, and signal-to-noise sensitivity. Here we report a new method, the IROA TruQuant Workflow, that uses a stable ... ...

Abstract	Ion suppression is a major problem in mass spectrometry (MS)-based metabolomics; it can dramatically decrease measurement accuracy, precision, and signal-to-noise sensitivity. Here we report a new method, the IROA TruQuant Workflow, that uses a stable isotope-labeled internal standard (IROA-IS) plus novel companion algorithms to 1) measure and correct for ion suppression, and 2) perform Dual MSTUS normalization of MS metabolomic data. We have evaluated the method across ion chromatography (IC), hydrophilic interaction liquid chromatography (HILIC), and reverse phase liquid chromatography (RPLC)-MS systems in both positive and negative ionization modes, with clean and unclean ion sources, and across different biological matrices. Across the broad range of conditions tested, all detected metabolites exhibited ion suppression ranging from 1% to 90+% and coefficient of variations ranging from 1% to 20%, but the Workflow and companion algorithms were highly effective at nulling out that suppression and error. Overall, the Workflow corrects ion suppression across diverse analytical conditions and produces robust normalization of non-targeted metabolomic data.
Language	English
Publishing date	2024-02-01
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-3914827/v1
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Article ; Online: N-Glycan Profile of Cerebrospinal Fluids from Alzheimer's Disease Patients Using Liquid Chromatography with Mass Spectrometry.

Cho, Byeong Gwan / Veillon, Lucas / Mechref, Yehia

Journal of proteome research

2019 Volume 18, Issue 10, Page(s) 3770–3779

Abstract: Glycosylation, an essential post-translational protein modification, is known to be altered in a variety of diseases, including neurodegenerative diseases such as Alzheimer's disease (AD), which is one of the most common neurodegenerative disorders that ... ...

Abstract	Glycosylation, an essential post-translational protein modification, is known to be altered in a variety of diseases, including neurodegenerative diseases such as Alzheimer's disease (AD), which is one of the most common neurodegenerative disorders that results in cognitive and memory impairments. To investigate the progression of such a condition, cerebrospinal fluid (CSF), a unique biofluid that may possess significant biochemical and neurochemical changes due to the disease, is utilized. However, due to the low concentration of proteins in CSF, a large volume of the biofluid is often required to comprehensively characterize the glycome in CSF. In this work, a glycomic study of CSF was performed using as little as 10 μL of CSF. This approach was executed with permethylation of released N-glycans with minimal sample cleanup, in conjunction with an online purification system attached to liquid chromatography and a high-resolution mass spectrometer. This technique was then applied to clinical samples. Preliminary data suggest that fucosylated and bisecting GlcNAc structures were higher in abundances in females with AD, while both females and males exhibited lower abundances of high-mannose structures. Although there seems to be statistically significant differences between disease state and disease-free CSF, due to the lack of number of samples, further validation study should be conducted.
MeSH term(s)	Alzheimer Disease/cerebrospinal fluid ; Chromatography, Liquid/methods ; Female ; Fucose ; Glucose ; Glycomics/methods ; Glycosylation ; Humans ; Male ; Mass Spectrometry/methods ; Polysaccharides/cerebrospinal fluid ; Sex Factors
Chemical Substances	Polysaccharides ; Fucose (28RYY2IV3F) ; Glucose (IY9XDZ35W2)
Language	English
Publishing date	2019-09-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.9b00504
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Zs.A 6189: Show issues

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Article ; Online: The bacterial microbiota regulates normal hematopoiesis via metabolite-induced type 1 interferon signaling.

Yan, Hannah / Walker, Forrest C / Ali, Arushana / Han, Hyojeong / Tan, Lin / Veillon, Lucas / Lorenzi, Philip L / Baldridge, Megan T / King, Katherine Y

Blood advances

2022 Volume 6, Issue 6, Page(s) 1754–1765

Abstract: Antibiotic therapy, especially when administered long term, is associated with adverse hematologic effects such as cytopenia. Signals from the intestinal microbiota are critical to maintain normal hematopoiesis, and antibiotics can cause bone marrow ... ...

Abstract	Antibiotic therapy, especially when administered long term, is associated with adverse hematologic effects such as cytopenia. Signals from the intestinal microbiota are critical to maintain normal hematopoiesis, and antibiotics can cause bone marrow suppression through depletion of the microbiota. We reported previously that STAT1 signaling is necessary for microbiota-dependent hematopoiesis, but the precise mechanisms by which the gut microbiota signals to the host bone marrow to regulate hematopoiesis remain undefined. We sought to identify the cell type(s) through which STAT1 promotes microbiota-mediated hematopoiesis and to elucidate which upstream signaling pathways trigger STAT1 signaling. Using conditional knockout and chimeric mice, we found that the microbiota induced STAT1 signaling in non-myeloid hematopoietic cells to support hematopoiesis and that STAT1 signaling was specifically dependent on type I interferons (IFNs). Indeed, basal type I IFN signaling was reduced in hematopoietic progenitor cells with antibiotic treatment. In addition, we discovered that oral administration of a commensal-derived product, NOD1 ligand, rescues the hematopoietic defects induced by antibiotics in mice. Using metabolomics, we identified additional microbially produced candidates that can stimulate type I IFN signaling to potentially rescue the hematopoietic defects induced by antibiotics, including phosphatidylcholine and γ-glutamylalanine. Overall, our studies define a signaling pathway through which microbiota promotes normal hematopoiesis and identify microbial metabolites that may serve as therapeutic agents to ameliorate antibiotic-induced bone marrow suppression and cytopenia.
MeSH term(s)	Animals ; Hematopoiesis ; Hematopoietic Stem Cells ; Interferon Type I/pharmacology ; Mice ; Microbiota ; Signal Transduction
Chemical Substances	Interferon Type I
Language	English
Publishing date	2022-02-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2915908-8
ISSN	2473-9537 ; 2473-9529
ISSN (online)	2473-9537
ISSN	2473-9529
DOI	10.1182/bloodadvances.2021006816
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Zs.A 7153: Show issues

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Article ; Online: Carbon Nanoparticles and Graphene Nanosheets as MALDI Matrices in Glycomics: a New Approach to Improve Glycan Profiling in Biological Samples.

Banazadeh, Alireza / Peng, Wenjing / Veillon, Lucas / Mechref, Yehia

Journal of the American Society for Mass Spectrometry

2018 Volume 29, Issue 9, Page(s) 1892–1900

Abstract: Glycomics continues to be a highly dynamic and interesting research area due to the need to comprehensively understand the biological attributes of glycosylation in many important biological functions such as the immune response, cell development, cell ... ...

Abstract	Glycomics continues to be a highly dynamic and interesting research area due to the need to comprehensively understand the biological attributes of glycosylation in many important biological functions such as the immune response, cell development, cell differentiation/adhesion, and host-pathogen interactions. Although matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) has proven to be suitable for glycomic profiling studies, there is a need for improved sensitivity in the detection of native glycans, which ionize inefficiently. In this study, we investigated the efficiencies of graphene nanosheets (GNs) and carbon nanoparticles (CNPs) as MALDI matrices and co-matrices in glycan profiling. Our results indicated an enhancement of signal intensity by several orders of magnitude upon using GNs and CNPs in MALDI analysis of N-glycans derived from a variety of biological samples. Interestingly, increasing the amounts of CNPs and GNs improved not only the signal intensities but also prompted in-source decay (ISD) fragmentations, which produced extensive glycosidic and cross-ring cleavages. Our results indicated that the extent of ISD fragmentation could be modulated by CNP and GN concentrations, to obtain MS
MeSH term(s)	Glycomics/methods ; Graphite/chemistry ; Nanoparticles/chemistry ; Polysaccharides/analysis ; Polysaccharides/chemistry ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
Chemical Substances	Polysaccharides ; Graphite (7782-42-5)
Language	English
Publishing date	2018-06-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1007/s13361-018-1985-z
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Zs.A 4618: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 241: Show issues

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Article ; Online: Adipose tissue-specific ablation of Ces1d causes metabolic dysregulation in mice.

Li, Gang / Li, Xin / Yang, Li / Wang, Shuyue / Dai, Yulin / Fekry, Baharan / Veillon, Lucas / Tan, Lin / Berdeaux, Rebecca / Eckel-Mahan, Kristin / Lorenzi, Philip L / Zhao, Zhongming / Lehner, Richard / Sun, Kai

Life science alliance

2022 Volume 5, Issue 8

Abstract: Carboxylesterase 1d (Ces1d) is a crucial enzyme with a wide range of activities in multiple tissues. It has been reported to localize predominantly in ER. Here, we found that Ces1d levels are significantly increased in obese patients with type 2 diabetes. ...

Abstract	Carboxylesterase 1d (Ces1d) is a crucial enzyme with a wide range of activities in multiple tissues. It has been reported to localize predominantly in ER. Here, we found that Ces1d levels are significantly increased in obese patients with type 2 diabetes. Intriguingly, a high level of Ces1d translocates onto lipid droplets where it digests the lipids to produce a unique set of fatty acids. We further revealed that adipose tissue-specific Ces1d knock-out (FKO) mice gained more body weight with increased fat mass during a high fat-diet challenge. The FKO mice exhibited impaired glucose and lipid metabolism and developed exacerbated liver steatosis. Mechanistically, deficiency of Ces1d induced abnormally large lipid droplet deposition in the adipocytes, causing ectopic accumulation of triglycerides in other peripheral tissues. Furthermore, loss of Ces1d diminished the circulating free fatty acids serving as signaling molecules to trigger the epigenetic regulations of energy metabolism via lipid-sensing transcriptional factors, such as HNF4α. The metabolic disorders induced an unhealthy microenvironment in the metabolically active tissues, ultimately leading to systemic insulin resistance.
MeSH term(s)	Adipocytes/metabolism ; Adipose Tissue/metabolism ; Animals ; Carboxylesterase/genetics ; Carboxylesterase/metabolism ; Diabetes Mellitus, Type 2/genetics ; Diabetes Mellitus, Type 2/metabolism ; Diet, High-Fat ; Humans ; Mice
Chemical Substances	Carboxylesterase (EC 3.1.1.1) ; Ces1d protein, mouse (EC 3.1.1.1)
Language	English
Publishing date	2022-04-22
Publishing country	United States
Document type	Journal Article
ISSN	2575-1077
ISSN (online)	2575-1077
DOI	10.26508/lsa.202101209
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Article ; Online: Direct comparison of derivatization strategies for LC-MS/MS analysis of N-glycans.

Zhou, Shiyue / Veillon, Lucas / Dong, Xue / Huang, Yifan / Mechref, Yehia

The Analyst

2017 Volume 142, Issue 23, Page(s) 4446–4455

Abstract: Protein glycosylation is a common post-translational modification that has significant impacts on protein folding, lifespan, conformation, distribution and function. N-Glycans, which are attached to asparagine residues of proteins, are studied most often ...

Abstract	Protein glycosylation is a common post-translational modification that has significant impacts on protein folding, lifespan, conformation, distribution and function. N-Glycans, which are attached to asparagine residues of proteins, are studied most often due to their compatibility with enzymatic release. Despite the ease of N-glycan release, compositional and structural complexity coupled with poor ionization efficiency during liquid chromatography mass spectrometry (LC-MS) make quantitative glycomic studies a significant challenge. To overcome these challenges, glycans are almost always derivatized prior to LC-MS analyses to impart favorable characteristics, such as improved ionization efficiency, increased LC separation efficiency and the production of more informative fragments during tandem MS. There are a number of derivatization methods available for LC-MS analysis of glycans, each of which imparts different properties that affect both glycan retention on LC columns and MS analyses. To provide guidance for the proper selection of derivatizing reagents and LC columns, herein, we describe a comprehensive assessment of 2-aminobenzamide, procainamide, aminoxyTMT, RapiFluor-MS (RFMS) labeling, reduction and reduction with permethylation for N-glycan analysis. Of the derivatization strategies examined, RFMS provided the highest MS signal enhancement for neutral glycans, while permethylation significantly enhanced the MS intensity and structural stability of sialylated glycans.
MeSH term(s)	Chromatography, Liquid ; Glycoproteins/chemistry ; Glycosylation ; Polysaccharides/analysis ; Tandem Mass Spectrometry
Chemical Substances	Glycoproteins ; Polysaccharides
Language	English
Publishing date	2017-10-30
Publishing country	England
Document type	Comparative Study ; Journal Article
ZDB-ID	210747-8
ISSN	1364-5528 ; 0003-2654
ISSN (online)	1364-5528
ISSN	0003-2654
DOI	10.1039/c7an01262d
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Zs.A 2423: Show issues

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Article ; Online: LC-MS/MS analysis of permethylated N-glycans facilitating isomeric characterization.

Zhou, Shiyue / Dong, Xue / Veillon, Lucas / Huang, Yifan / Mechref, Yehia

Analytical and bioanalytical chemistry

2016 Volume 409, Issue 2, Page(s) 453–466

Abstract: The biosynthesis of glycans is a template-free process; hence compositionally identical glycans may contain highly heterogeneous structures. Meanwhile, the functions of glycans in biological processes are significantly influenced by the glycan structure. ...

Abstract	The biosynthesis of glycans is a template-free process; hence compositionally identical glycans may contain highly heterogeneous structures. Meanwhile, the functions of glycans in biological processes are significantly influenced by the glycan structure. Structural elucidation of glycans is an essential component of glycobiology. Although NMR is considered the most powerful approach for structural glycan studies, it suffers from low sensitivity and requires highly purified glycans. Although mass spectrometry (MS)-based methods have been applied in numerous glycan structure studies, there are challenges in preserving glycan structure during ionization. Permethylation is an efficient derivatization method that improves glycan structural stability. In this report, permethylated glycans are isomerically separated; thus facilitating structural analysis of a mixture of glycans by LC-MS/MS. Separation by porous graphitic carbon liquid chromatography at high temperatures in conjunction with tandem mass spectrometry (PGC-LC-MS/MS) was utilized for unequivocal characterization of glycan isomers. Glycan fucosylation sites were confidently determined by eliminating fucose rearrangement and assignment of diagnostic ions, achieved by permethylation and PGC-LC at high temperatures, respectively. Assigning monosaccharide residues to specific glycan antennae was also achieved. Galactose linkages were also distinguished from each other by CID/HCD tandem MS. This was attainable because of the different bond energies associated with monosaccharide linkages. Graphical Abstract LC-MS and tandem MS of terminal galactose isomers.
MeSH term(s)	Chromatography, Liquid ; Isomerism ; Methylation ; Polysaccharides/chemistry ; Tandem Mass Spectrometry
Chemical Substances	Polysaccharides
Language	English
Publishing date	2016-10-28
Publishing country	Germany
Document type	Journal Article
ZDB-ID	201093-8
ISSN	1618-2650 ; 0016-1152 ; 0372-7920
ISSN (online)	1618-2650
ISSN	0016-1152 ; 0372-7920
DOI	10.1007/s00216-016-9996-8
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Article: Characterization of isomeric glycan structures by LCâMS/MS

Veillon, Lucas / Yifan Huang / Wenjing Peng / Xue Dong / Byeong Gwan Cho / Yehia Mechref

Electrophoresis. 2017 Sept., v. 38, no. 17

2017

Abstract: The characterization of glycosylation is critical for obtaining a comprehensive view of the regulation and functions of glycoproteins of interest. Due to the complex nature of oligosaccharides, stemming from variable compositions and linkages, and ion ... ...

Abstract	The characterization of glycosylation is critical for obtaining a comprehensive view of the regulation and functions of glycoproteins of interest. Due to the complex nature of oligosaccharides, stemming from variable compositions and linkages, and ion suppression effects, the chromatographic separation of glycans, including isomeric structures, is necessary for exhaustive characterization by MS. This review introduces the fundamental principles underlying the techniques in LC utilized by modern day glycomics researchers. Recent advances in porous graphitized carbon, reverse phase, ion exchange, and hydrophilic interaction LC utilized in conjunction with MS, for the characterization of protein glycosylation, are described with an emphasis on methods capable of resolving isomeric glycan structures.
Keywords	carbon ; chromatography ; electrophoresis ; glycomics ; glycoproteins ; glycosylation ; ion exchange ; oligosaccharides ; polysaccharides ; researchers
Language	English
Dates of publication	2017-09
Size	p. 2100-2114.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	REVIEW
ZDB-ID	619001-7
ISSN	1522-2683 ; 0173-0835
ISSN (online)	1522-2683
ISSN	0173-0835
DOI	10.1002/elps.201700042
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Lipidomic Profiles of Plasma Exosomes Identify Candidate Biomarkers for Early Detection of Hepatocellular Carcinoma in Patients with Cirrhosis.

Sanchez, Jessica I / Jiao, Jingjing / Kwan, Suet-Ying / Veillon, Lucas / Warmoes, Marc O / Tan, Lin / Odewole, Mobolaji / Rich, Nicole E / Wei, Peng / Lorenzi, Philip L / Singal, Amit G / Beretta, Laura

Cancer prevention research (Philadelphia, Pa.)

2021 Volume 14, Issue 10, Page(s) 955–962

Abstract: Novel biomarkers for HCC surveillance in cirrhotic patients are urgently needed. Exosomes and their lipid content in particular represent potentially valuable noninvasive diagnostic biomarkers. We isolated exosomes from plasma of 72 cirrhotic patients, ... ...

Abstract	Novel biomarkers for HCC surveillance in cirrhotic patients are urgently needed. Exosomes and their lipid content in particular represent potentially valuable noninvasive diagnostic biomarkers. We isolated exosomes from plasma of 72 cirrhotic patients, including 31 with HCC. Exosomes and unfractionated plasma were processed for untargeted lipidomics using ultra-high-resolution mass spectrometry. A total of 2,864 lipid species, belonging to 52 classes, were identified. Both exosome fractionation and HCC diagnosis had significant impact on the lipid profiles. Ten lipid classes were enriched in HCC exosomes compared with non-HCC exosomes. Dilysocardiolipins were detected in 35% of the HCC exosomes but in none of the non-HCC exosomes (
MeSH term(s)	Aged ; Biomarkers, Tumor/blood ; Carcinoma, Hepatocellular/complications ; Carcinoma, Hepatocellular/diagnosis ; Carcinoma, Hepatocellular/pathology ; Case-Control Studies ; Early Detection of Cancer/methods ; Exosomes/chemistry ; Exosomes/metabolism ; Exosomes/pathology ; Female ; Humans ; Lipidomics ; Lipids/blood ; Liver Cirrhosis/blood ; Liver Cirrhosis/complications ; Liver Cirrhosis/diagnosis ; Liver Cirrhosis/pathology ; Liver Neoplasms/complications ; Liver Neoplasms/diagnosis ; Liver Neoplasms/pathology ; Male ; Middle Aged ; Predictive Value of Tests
Chemical Substances	Biomarkers, Tumor ; Lipids
Language	English
Publishing date	2021-07-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2434717-6
ISSN	1940-6215 ; 1940-6207
ISSN (online)	1940-6215
ISSN	1940-6207
DOI	10.1158/1940-6207.CAPR-20-0612
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Article ; Online: Characterization of isomeric glycan structures by LC-MS/MS.

Veillon, Lucas / Huang, Yifan / Peng, Wenjing / Dong, Xue / Cho, Byeong Gwan / Mechref, Yehia

Electrophoresis

2017 Volume 38, Issue 17, Page(s) 2100–2114

Abstract	The characterization of glycosylation is critical for obtaining a comprehensive view of the regulation and functions of glycoproteins of interest. Due to the complex nature of oligosaccharides, stemming from variable compositions and linkages, and ion suppression effects, the chromatographic separation of glycans, including isomeric structures, is necessary for exhaustive characterization by MS. This review introduces the fundamental principles underlying the techniques in LC utilized by modern day glycomics researchers. Recent advances in porous graphitized carbon, reverse phase, ion exchange, and hydrophilic interaction LC utilized in conjunction with MS, for the characterization of protein glycosylation, are described with an emphasis on methods capable of resolving isomeric glycan structures.
MeSH term(s)	Chromatography, Liquid/methods ; Isomerism ; Polysaccharides/analysis ; Polysaccharides/chemistry ; Tandem Mass Spectrometry/methods
Chemical Substances	Polysaccharides
Language	English
Publishing date	2017-05-17
Publishing country	Germany
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	619001-7
ISSN	1522-2683 ; 0173-0835
ISSN (online)	1522-2683
ISSN	0173-0835
DOI	10.1002/elps.201700042
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