Abstract：
:Isobaric tagging is the method of choice in mass-spectrometry-based proteomics for comparing several conditions at a time. Despite its multiplexing capabilities, some drawbacks appear when multiple experiments are merged for comparison in large sample-size studies due to the presence of missing values, which result from the stochastic nature of the data-dependent acquisition mode. Another indirect cause of data incompleteness might derive from the proteomic-typical data-processing workflow that first identifies proteins in individual experiments and then only quantifies those identified proteins, leaving a large number of unmatched spectra with quantitative information unexploited. Inspired by untargeted metabolomic and label-free proteomic workflows, we developed a quantification-driven bioinformatic pipeline (Quantify then Identify (QtI)) that optimizes the processing of isobaric tandem mass tag (TMT) data from large-scale studies. This pipeline includes innovative features, such as peak filtering with a self-adaptive preprocessing pipeline optimization method, Peptide Match Rescue, and Optimized Post-Translational Modification. QtI outperforms a classical benchmark workflow in terms of quantification and identification rates, significantly reducing missing data while preserving unmatched features for quantitative comparison. The number of unexploited tandem mass spectra was reduced by 77 and 62% for two human cerebrospinal fluid and plasma data sets, respectively.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Corthésy J,Theofilatos K,Mavroudi S,Macron C,Cominetti O,Remlawi M,Ferraro F,Núñez Galindo A,Kussmann M,Likothanassis S,Dayon Ldoi
10.1021/acs.jproteome.8b00110subject
Has Abstractpub_date
2018-06-01 00:00:00pages
2165-2173issue
6eissn
1535-3893issn
1535-3907journal_volume
17pub_type
杂志文章abstract：:Recently, we reported comparative analysis of glycoproteins which express cancer-specific N-glycans on various cancer cells and identified 24 glycoproteins having polylactosamine (polyLacNAc)-type N-glycans that are abundantly present in malignant cells [ Mitsui et al., J. Pharm. Biomed. Anal. 2012 , 70 , 718 - 726 ]....
journal_title：Journal of proteome research
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journal_title：Journal of proteome research
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journal_title：Journal of proteome research
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journal_title：Journal of proteome research
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journal_title：Journal of proteome research
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doi：10.1021/pr050298y
更新日期：2006-02-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章,评审
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00071
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journal_title：Journal of proteome research
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800507x
更新日期：2009-01-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
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更新日期：2012-05-04 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00206
更新日期：2016-08-05 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr201222s
更新日期：2012-05-04 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800304n
更新日期：2009-01-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/acs.jproteome.8b00257
更新日期：2018-08-03 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100224y
更新日期：2010-12-03 00:00:00
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journal_title：Journal of proteome research
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更新日期：2010-04-05 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
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更新日期：2008-11-01 00:00:00
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journal_title：Journal of proteome research
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更新日期：2012-02-03 00:00:00
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journal_title：Journal of proteome research
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journal_title：Journal of proteome research
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更新日期：2005-03-01 00:00:00
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journal_title：Journal of proteome research
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journal_title：Journal of proteome research
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更新日期：2013-12-06 00:00:00
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pub_type： 杂志文章
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