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Limitation of predictive 2‐ D liquid chromatography in reducing the database search space in shotgun proteomics: In silico studies
Author(s) -
Moskovets Eugene,
Goloborodko Anton A.,
Gorshkov Alexander V.,
Gorshkov Mikhail V.
Publication year - 2012
Publication title -
journal of separation science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.72
H-Index - 102
eISSN - 1615-9314
pISSN - 1615-9306
DOI - 10.1002/jssc.201100798
Subject(s) - chemistry , chromatography , shotgun proteomics , peptide , mass spectrometry , resolution (logic) , phase (matter) , analytical chemistry (journal) , proteomics , computer science , biochemistry , artificial intelligence , gene , organic chemistry
A two‐dimensional (2‐ D ) liquid chromatography ( LC ) separation of complex peptide mixtures that combines a normal phase utilizing hydrophilic interactions and a reversed phase offers reportedly the highest level of 2‐ D LC orthogonality by providing an even spread of peptides across multiple LC fractions. Matching experimental peptide retention times to those predicted by empirical models describing chromatographic separation in each LC dimension leads to a significant reduction in a database search space. In this work, we calculated the retention times of tryptic peptides separated in the C 18 reversed phase at different separation conditions (pH 2 and pH 10) and in TSK gel Amide‐80 normal phase. We show that retention times calculated for different 2‐ D LC separation schemes utilizing these phases start to correlate once the mass range of peptides under analysis becomes progressively narrow. This effect is explained by high degree of correlation between retention coefficients in the considered phases.