PXD026942

PXD026942 is an original dataset announced via ProteomeXchange.

Title	Comparison of LFQ and IPTL for protein identification and relative quantification
Description	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.
HostingRepository	PRIDE
AnnounceDate	2022-02-17
AnnouncementXML	Submission_2022-02-17_04:54:12.535.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Bernd Thiede
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-06-27 15:30:20	ID requested
⏵ 1	2022-02-17 04:54:14	announced

Johannsen C, Koehler CJ, Thiede B, Comparison of LFQ and IPTL for Protein Identification and Relative Quantification. Molecules, 26(17):(2021) [pubmed]

submitter keyword: IPTL, LFQ, quantitative proteomics, SILAC, TMT

Bernd Thiede
contact affiliation	Department of Biosciences, University of Oslo, Norway
contact email	bernd.thiede@ibv.uio.no
lab head
Bernd Thiede
contact affiliation	University of Oslo
contact email	bernd.thiede@ibv.uio.no
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD026942
     1. Label: PRIDE project
     2. Name: Comparison of LFQ and IPTL for protein identification and relative quantification