FRACPRED‐2D‐PRM: A Fraction Prediction Algorithm‐Assisted 2D Liquid Chromatography‐Based Parallel Reaction Monitoring‐Mass Spectrometry Approach for Measuring Low‐Abundance Proteins in Human Plasma

Multidimensional fractionation‐based enrichment methods improve the sensitivity of proteomic analysis for low‐abundance proteins. However, a major limitation of conventional multidimensional proteomics is the extensive labor and instrument time required for analyzing many fractions obtained from the...

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Veröffentlicht in:Proteomics (Weinheim) Jg. 20; H. 24; S. e2000175 - n/a
Hauptverfasser: Shi, Jian, Xiao, Jingcheng, Li, Jiapeng, Wang, Xinwen, Her, Lucy, Sorensen, Matthew J., Zhu, Hao‐Jie
Format: Journal Article
Sprache:Englisch
Veröffentlicht: Germany Wiley Subscription Services, Inc 01.12.2020
Schlagworte:
2D‐LC
Aldolase
Algorithms
Biological properties
Biological samples
Blood plasma
Carboxylesterase
fraction prediction algorithm
Fractionation
Liquid chromatography
low‐abundance proteins
Mass spectrometry
Mass spectroscopy
Monitoring
Multidimensional methods
Peptides
pH effects
Plasma
Predictions
PRM
Proteins
Proteomics
Scientific imaging
Sensitivity analysis
Separation
Spectroscopy
fraction prediction algorithm
2D-LC
PRM
plasma
low-abundance proteins
ISSN:1615-9853, 1615-9861, 1615-9861
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Zusammenfassung:Multidimensional fractionation‐based enrichment methods improve the sensitivity of proteomic analysis for low‐abundance proteins. However, a major limitation of conventional multidimensional proteomics is the extensive labor and instrument time required for analyzing many fractions obtained from the first dimension separation. Here, a fraction prediction algorithm‐assisted 2D LC‐based parallel reaction monitoring‐mass spectrometry (FRACPRED‐2D‐PRM) approach for measuring low‐abundance proteins in human plasma is presented. Plasma digests are separated by the first dimension high‐pH RP‐LC with data‐dependent acquisition (DDA). The FRACPRED algorithm is then usedto predict the retention times of undetectable target peptides according to those of other abundant plasma peptides during the first dimension separation. Fractions predicted to contain target peptides are analyzed by the second dimension low‐pH nano RP‐LC PRM. The accuracy and robustness of fraction prediction with the FRACPRED algorithm are demonstrated by measuring two low‐abundance proteins, aldolase B and carboxylesterase 1, in human plasma. The FRACPRED‐2D‐PRM proteomics approach demonstrates markedly improved efficiency and sensitivity over conventional 2D‐LC proteomics assays. It is expected that this approach will be widely used in the study of low‐abundance proteins in plasma and other complex biological samples.
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ISSN:1615-9853
1615-9861
1615-9861
DOI:10.1002/pmic.202000175