A Strategy for Precise and Large Scale Identification of Core Fucosylated Glycoproteins

Jia, Wei; Lu, Zhenwu; Fu, Yan; Wang, Haipeng; Wang, Le-Heng; Chi, Hao; Yuan, Zuo‐Fei; Zheng, Zhao-Bin; Song, Lu; Han, Huanhuan; Liang, Yimin; Wang, Jinglan; Cai, Yun; Zhang, Yukui; Deng, Yulin; Ying, Wantao; He, Shan; Qian, Xiaohong

doi:10.1074/mcp.m800504-mcp200

Cited by 82 publications

(112 citation statements)

References 29 publications

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“…The results of mass spectral analysis of blood from different physiological states and the searching conditions used may be reported in an .xml format to facilitate the parsing of the data (Craig, Cortens, & Beavis, 2004;Craig et al, 2006;Zhang, Wu, & Li, 2006b;Mann et al, 2008). Searching for glycoproteins and other emerging post-translational modifications will be a significant challenge (Joenvaara et al, 2008;Jia et al, 2009). Ultimately, a database of all correlations and annotations found using each method from large populations of LC-ESI-MS/MS experiments will be required (Pruess et al, 2003;Zhu et al, 2006;Zhang, Wu, & Li, 2006b).…”

Section: H Blood Protein Peptide and Ion Databasementioning

confidence: 99%

Mass spectrometry of peptides and proteins from human blood

Zhu

Bowden

Zhang

et al. 2010

Mass Spectrometry Reviews

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It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.

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Section: H Blood Protein Peptide and Ion Databasementioning

confidence: 99%

Mass spectrometry of peptides and proteins from human blood

Zhu

Bowden

Zhang

et al. 2010

Mass Spectrometry Reviews

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“…The extraction of fucosylated glycoproteins was performed as described with modifications [13]. Briefly, albumin/IgG-depleted samples (400 μl) were supplemented with 1.6 ml of lectin adsorption buffer (GALAB, Germany) and incubated at 4°C for 16 h with AAL in a spin column (Bio-Spin; Bio-Rad).…”

Section: Fucosylated Glycoprotein Enrichment By Aal Lectin Columnmentioning

confidence: 99%

Fucosylated glycoproteomic approach to identify a complement component 9 associated with squamous cell lung cancer (SQLC)

Narayanasamy

Ahn

Sung

et al. 2011

Journal of Proteomics

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“…To this end, it takes only several minutes for DeltAMT to analyze one LC-MS/MS run and report discoveries, based on which experimental protocols can be improved. In fact, we have successfully performed such data analysis and protocol improvement in experiments for core fucosylated glycoprotein identification using a preliminary version of the algorithm (62,63). The analysis results of DeltAMT are also potentially beneficial for quantitation analysis of proteins.…”

Section: Results For the Maxquant Hela Proteome Data Setmentioning

confidence: 99%

DeltAMT: A Statistical Algorithm for Fast Detection of Protein Modifications From LC-MS/MS Data

Xiu

Jia

et al. 2011

Molecular & Cellular Proteomics

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Identification of proteins and their modifications via liquid chromatography-tandem mass spectrometry is an important task for the field of proteomics. However, because of the complexity of tandem mass spectra, the majority of the spectra cannot be identified. The presence of unanticipated protein modifications is among the major reasons for the low spectral identification rate. The conventional database search approach to protein identification has inherent difficulties in comprehensive detection of protein modifications. In recent years, increasing efforts have been devoted to developing unrestrictive approaches to modification identification, but they often suffer from their lack of speed. This paper presents a statistical algorithm named DeltAMT (Delta Accurate Mass and Time) for fast detection of abundant protein modifications from tandem mass spectra with high-accuracy precursor masses. The algorithm is based on the fact that the modified and unmodified versions of a peptide are usually present simultaneously in a sample and their spectra are correlated with each other in precursor masses and retention times. By representing each pair of spectra as a delta mass and time vector, bivariate Gaussian mixture models are used to detect modification-related spectral pairs. Unlike previous approaches to unrestrictive modification identification that mainly rely upon the fragment information and the mass dimension in liquid chromatography-tandem mass spectrometry, the proposed algorithm makes the most of precursor information. Thus, it is highly efficient while being accurate and sensitive. On two published data sets, the algorithm effectively detected various modifications and other interesting events, yielding deep insights into the data. Based on these discoveries, the spectral identification rates were significantly increased and many modified peptides were identified. Molecular & Cellular Proteomics 10: 10.1074/ mcp.M110.000455, 1-15, 2011.Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) 1 is currently the predominant technology used to identify proteins and their modifications (1-3). The most successful approach for interpreting tandem mass spectra involves searching the database of known protein sequences (4 -9). Other approaches include the databaseindependent de novo peptide sequencing (10 -13) and the hybrid sequence tag-based approach (14 -16). However, in a typical shotgun proteomics experiment, only ϳ10 -30% of the tandem mass spectra can be successfully identified, and the remaining majority is discarded (17). Many factors contribute to the complexity of protein digests and the low identification rate of tandem mass spectra (18). Understanding the origin and identity of the unidentified spectra is of great importance in expanding our knowledge about biological systems and sample processing protocols. Nesvizhskii et al. (19) have shown that by properly mining the unidentified spectra, insights can be gained that are of interest to biologists, such as identification of post-transl...

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A Strategy for Precise and Large Scale Identification of Core Fucosylated Glycoproteins

Cited by 82 publications

References 29 publications

Mass spectrometry of peptides and proteins from human blood

Mass spectrometry of peptides and proteins from human blood

Fucosylated glycoproteomic approach to identify a complement component 9 associated with squamous cell lung cancer (SQLC)

DeltAMT: A Statistical Algorithm for Fast Detection of Protein Modifications From LC-MS/MS Data

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