Proteomics

Dataset Information

0

Comparison of LFQ and IPTL for protein identification and relative quantification


ABSTRACT: 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. To enable tryptic digestion of IPTL samples, a novel labeling for IPTL was developed which combines metabolic labeling (Arg-0/Lys-0 and Arg-d4/Lys-d4, respectively) with crosswise N-terminal dimethylation (d4 and d0, respectively). The comparison of IPTL with LFQ revealed significantly more protein identifications for LFQ above homology ion scores but not above identity ion score. However, the quantification accuracy was superior for LFQ despite the many quantification points obtained with IPTL. A reason for this outcome is probably because of the significantly higher signal intensities in MS1 compared to MS2.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): T Cell, Cell Culture

SUBMITTER: Bernd Thiede  

LAB HEAD: Bernd Thiede

PROVIDER: PXD026942 | Pride | 2022-02-17

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
CJ_190611_IPTL_1.raw Raw
CJ_190611_IPTL_2.raw Raw
CJ_190611_IPTL_3.raw Raw
CJ_190611_IPTL_4.raw Raw
CJ_190611_IPTL_5.raw Raw
Items per page:
1 - 5 of 20
altmetric image

Publications

Comparison of LFQ and IPTL for Protein Identification and Relative Quantification.

Johannsen Christina C   Koehler Christian J CJ   Thiede Bernd B  

Molecules (Basel, Switzerland) 20210902 17


(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 m  ...[more]

Similar Datasets

2018-03-13 | PXD007145 | Pride
2015-04-16 | E-GEOD-66519 | biostudies-arrayexpress
2010-06-20 | E-GEOD-15502 | biostudies-arrayexpress
2015-04-16 | E-GEOD-66518 | biostudies-arrayexpress
2023-08-30 | PXD038632 | Pride
2011-01-01 | E-GEOD-25141 | biostudies-arrayexpress
2024-06-19 | PXD041260 | Pride
2021-05-11 | PXD021661 | Pride
2022-04-07 | PXD031114 | Pride
2015-04-16 | E-GEOD-66517 | biostudies-arrayexpress