Comparison of lfq and iptl for protein identification and relative quantification
| Autor: | Bernd Thiede, Christina Johannsen, Christian J. Koehler |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
Proteomics
quantitative proteomics Absolute quantification Quantitative proteomics Pharmaceutical Science Organic chemistry Peptide LFQ Mass spectrometry SILAC Article Analytical Chemistry Isotopic labeling QD241-441 Stable isotope labeling by amino acids in cell culture Drug Discovery Humans Physical and Theoretical Chemistry IPTL Cells Cultured chemistry.chemical_classification Chromatography Chemistry Proteins Isobaric labeling Chemistry (miscellaneous) Isotope Labeling TMT Molecular Medicine Protein identification Peptides |
| Zdroj: | Molecules Molecules, Vol 26, Iss 5330, p 5330 (2021) Volume 26 Issue 17 |
| ISSN: | 1420-3049 |
| Popis: | (1) Background: Mass spectrometry-based quantitative proteome profiling is most commonly performed by label-free quantification (LFQ), stable isotopic labeling with amino acids in cell culture (SILAC), and reporter ion-based isobaric labeling methods (TMT and iTRAQ). Isobaric peptide termini labeling (IPTL) was described as an alternative to these methods and is based on crosswise labeling of both peptide termini and MS2 quantification. High quantification accuracy was assumed for IPTL because multiple quantification points are obtained per identified MS2 spectrum. A direct comparison of IPTL with other quantification methods has not been performed yet because IPTL commonly requires digestion with endoproteinase Lys-C. (2) Methods: To enable tryptic digestion of IPTL samples, a novel labeling for IPTL was developed that combines metabolic labeling (Arg-0/Lys-0 and Arg-d4/Lys-d4, respectively) with crosswise N-terminal dimethylation (d4 and d0, respectively). (3) Results: The comparison of IPTL with LFQ revealed significantly more protein identifications for LFQ above homology ion scores but not above identity ion scores. (4) Conclusions: The quantification accuracy was superior for LFQ despite the many quantification points obtained with IPTL. |
| Databáze: | OpenAIRE |
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