N-glycoproteomics: mass spectrometry-based glycosylation site annotation

2012 ◽  
Vol 393 (4) ◽  
pp. 249-258 ◽  
Author(s):  
Yvonne Pasing ◽  
Albert Sickmann ◽  
Urs Lewandrowski
Keyword(s):  
Mass Spectrometry ◽  
Detailed Analysis ◽  
Quantitative Assessment ◽  
Large Scale ◽  
Glycosylation Site ◽  
Qualitative And Quantitative ◽  
Essential Protein ◽  
Short Overview ◽  
Wide Scale ◽  
Enrichment Techniques

Abstract Glycosylations are ubiquitous and, in many cases, essential protein modifications. Yet comprehensive and detailed analysis of glycosylations on a proteome-wide scale is a daunting and still unsolved challenge. However, a common workflow has emerged over the last decade for large-scale N-glycosylation site annotation by application of proteomic methodology. Thereby, the qualitative and quantitative assessment of hundreds or thousands of modification sites is enabled. This review presents a short overview about common enrichment techniques and glycosylation site detection for N-glycopeptides, including benefits and challenges of analysis.

scholarly journals Zirconium(IV)-IMAC for phosphopeptide enrichment in phosphoproteomics

2020 ◽  
Author(s):  
Ignacio Arribas Diez ◽  
Ireshyn Govender ◽  
Previn Naicker ◽  
Stoyan Stoychev ◽  
Justin Jordaan ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Affinity Chromatography ◽  
Metal Ion ◽  
Large Scale ◽  
Cell Signalling ◽  
Phosphopeptide Enrichment ◽  
Magnetic Microparticles ◽  
Affinity Enrichment ◽  
Metal Oxide Affinity Chromatography ◽  
Enrichment Techniques

ABSTRACTPhosphopeptide enrichment is an essential step in large-scale, quantitative phosphoproteomics studies by mass spectrometry. Several phosphopeptide affinity enrichment techniques exist, such as Immobilized Metal ion Affinity Chromatography (IMAC) and Metal Oxide Affinity Chromatography (MOAC). We compared Zirconium (IV) IMAC (Zr-IMAC) magnetic microparticles to more commonly used Titanium (IV) IMAC (Ti-IMAC) and TiO2 magnetic microparticles for phosphopeptide enrichment from simple and complex protein samples prior phosphopeptide sequencing and characterization by mass spectrometry (LC-MS/MS). We optimized sample-loading conditions to increase phosphopeptide recovery for Zr-IMAC, Ti-IMAC and TiO2 based workflows. The performance of Zr-IMAC was enhanced by 19-22% to recover up to 5173 phosphopeptides from 200 µg of protein extract from HepG2/C3A cells, making Zr-IMAC the preferred method for phosphopeptide enrichment in this study. Ti-IMAC and TiO2 performance were also optimized to improve phosphopeptide numbers by 28% and 35%, respectively. Furthermore, Zr-IMAC based phosphoproteomics in the magnetic microsphere format identified 23% more phosphopeptides than HPLC-based Fe(III)-IMAC for same sample amount (200 µg), thereby adding 37% more uniquely identified phosphopeptides. We conclude that Zr-IMAC improves phosphoproteome coverage and recommend that this affinity enrichment method should be more widely used in biological and biomedical studies of cell signalling and in the search for disease-biomarkers.

Algorithm of combining chromatography mass spectrometry-untargeted profiling and multivariate analysis for identification of marker-substances in samples of complex composition

2020 ◽  
Vol 86 (7) ◽  
pp. 12-19
Author(s):  
I. V. Plyushchenko ◽  
D. G. Shakhmatov ◽  
I. A. Rodin
Keyword(s):  
Mass Spectrometry ◽  
Multivariate Analysis ◽  
Large Scale ◽  
Complex Composition ◽  
Unified Protocol ◽  
Chromatography Mass Spectrometry ◽  
Marker Substances ◽  
Selection Testing ◽  
Untargeted Profiling

A viral development of statistical data processing, computing capabilities, chromatography-mass spectrometry, and omics technologies (technologies based on the achievements of genomics, transcriptomics, proteomics, metabolomics) in recent decades has not led to formation of a unified protocol for untargeted profiling. Systematic errors reduce the reproducibility and reliability of the obtained results, and at the same time hinder consolidation and analysis of data gained in large-scale multi-day experiments. We propose an algorithm for conducting omics profiling to identify potential markers in the samples of complex composition and present the case study of urine samples obtained from different clinical groups of patients. Profiling was carried out by the method of liquid chromatography mass spectrometry. The markers were selected using methods of multivariate analysis including machine learning and feature selection. Testing of the approach was performed using an independent dataset by clustering and projection on principal components.

scholarly journals Qualitative and semi-quantitative assessment of anthocyanins in Tibetan hulless barley from different geographical locations by UPLC-QTOF-MS and their antioxidant capacities

2021 ◽  
Vol 19 (1) ◽  
pp. 1-8
Author(s):  
Tangwei Zhang ◽  
Jialin Ma ◽  
Xuelian Wu ◽  
Zhihua Hao ◽  
Ci Dun ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Antioxidant Activity ◽  
Quantitative Assessment ◽  
Ultra Performance Liquid Chromatography ◽  
Total Anthocyanin ◽  
Hulless Barley ◽  
Flight Mass Spectrometry ◽  
Antioxidant Capacities ◽  
Tibetan Hulless Barley ◽  
Geographical Locations

Abstract Tibetan hulless barley (“qingke” in Chinese) is a valuable food in Tibet. Purple qingke (PQK) and black qingke (BQK), two special pigmented types of hulless barley, have traditionally been widely cultivated and consumed in Tibet for thousands of years. The composition and contents of anthocyanins of two cultivars are unknown. This study aimed to explore the composition and contents of anthocyanins of two cultivars and their antioxidant capacities. Six anthocyanins were identified by ultra-performance liquid chromatography-quadrupole-time of flight mass spectrometry from barley, most of the anthocyanins were acylated by malonyl group. The total anthocyanin contents ranged from 141 to 2,304 μg/g in PQK and from 248.7 to 2902.9 μg/g in BQK. Furthermore, qingke has strong antioxidant activity against DPPH, ABTS˙+, and FRAP. Qingke may be useful for treating or preventing diseases caused by the overproduction of radicals.

scholarly journals Automated 16-Plex Plasma Proteomics with Real-Time Search and Ion Mobility Mass Spectrometry Enables Large-Scale Profiling in Naked Mole-Rats and Mice

2021 ◽  
Vol 20 (2) ◽  
pp. 1280-1295
Author(s):  
Aleksandr Gaun ◽  
Kaitlyn N. Lewis Hardell ◽  
Niclas Olsson ◽  
Jonathon J. O’Brien ◽  
Sudha Gollapudi ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Real Time ◽  
Ion Mobility ◽  
Large Scale ◽  
Ion Mobility Mass Spectrometry ◽  
Plasma Proteomics ◽  
Rats And Mice
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