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Retention Time Prediction for TMT-Labeled Peptides in Proteomic LC-MS Experiments.
Mizero, Benilde; Villacrés, Carina; Spicer, Victor; Viner, Rosa; Saba, Julian; Patel, Bhavinkumar; Snovida, Sergei; Jensen, Penny; Huhmer, Andreas; Krokhin, Oleg V.
Afiliação
  • Mizero B; Department of Chemistry, University of Manitoba, Winnipeg R3T 2N2, Canada.
  • Villacrés C; Manitoba Centre for Proteomics and Systems Biology, Winnipeg R3E 3P4, Canada.
  • Spicer V; Manitoba Centre for Proteomics and Systems Biology, Winnipeg R3E 3P4, Canada.
  • Viner R; Thermo Fisher Scientific, San Jose, California 95134, United States.
  • Saba J; Thermo Fisher Scientific, San Jose, California 95134, United States.
  • Patel B; Thermo Fisher Scientific, Rockford, Illinois 61101, United States.
  • Snovida S; Thermo Fisher Scientific, Rockford, Illinois 61101, United States.
  • Jensen P; Thermo Fisher Scientific, Rockford, Illinois 61101, United States.
  • Huhmer A; Thermo Fisher Scientific, San Jose, California 95134, United States.
  • Krokhin OV; Department of Chemistry, University of Manitoba, Winnipeg R3T 2N2, Canada.
J Proteome Res ; 21(5): 1218-1228, 2022 05 06.
Article em En | MEDLINE | ID: mdl-35363494
We present the first detailed study of chromatographic behavior of peptides labeled with tandem mass tags (TMT and TMTpro) in 2D LC for proteomic applications. Carefully designed experimental procedures have permitted generating data sets of over 100,000 nonlabeled and TMT-labeled peptide pairs for the low pH RP in the second separation dimension and data sets of over 10,000 peptide pairs for high-pH RP, HILIC (amide and silica), and SCX separations in the first separation dimension. The average increase in peptide RPLC (0.1% formic acid) retention upon TMT labeling was found to be 3.3% acetonitrile (linear water/acetonitrile gradients), spanning a range of -4 to 10.3%. In addition to the bulk peptide properties such as length, hydrophobicity, and the number of labeled residues, we found several sequence-dependent features mostly associated with differences in N-terminal chemistry. The behavior of TMTpro-labeled peptides was found to be very similar except for a slightly higher hydrophobicity: an average retention shift of 3.7% acetonitrile. The respective versions of the sequence-specific retention calculator (SSRCalc) model have been developed to accommodate both TMT chemistries, showing identical prediction accuracy (R2 ∼ 0.98) for labeled and nonlabeled peptides. Higher retention for TMT-labeled peptides was observed for high-pH RP and HILIC separations, while SCX selectivity remained virtually unchanged.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Proteômica / Espectrometria de Massas em Tandem Tipo de estudo: Prognostic_studies / Risk_factors_studies Idioma: En Revista: J Proteome Res Assunto da revista: BIOQUIMICA Ano de publicação: 2022 Tipo de documento: Article País de afiliação: Canadá

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Proteômica / Espectrometria de Massas em Tandem Tipo de estudo: Prognostic_studies / Risk_factors_studies Idioma: En Revista: J Proteome Res Assunto da revista: BIOQUIMICA Ano de publicação: 2022 Tipo de documento: Article País de afiliação: Canadá