Dataset Information

IsobaricQuant enables cross-platform quantification, visualization, and filtering of isobarically-labeled peptides

ABSTRACT: In mass spectrometry (MS)-based quantitative proteomics, labeling with isobaric mass tags such as iTRAQ and TMT can substantially improve sample throughput and reduce peptide missing values. Nonetheless, the quantification of labeled peptides tends to suffer from reduced quantitative accuracy due to the co-isolation of co-eluting precursors of similar mass-to-charge. Acquisition approaches such as MS3 level quantification or ion mobility separation address this problem, yet are difficult to audit and limited to expensive instrumentation. Here we introduce IsobaricQuant, an open-source software tool for the quantification, visualization, and filtering of peptides labeled with isobaric mass tags, with specific focus on precursor interference. IsobaricQuant is compatible with MS2- and MS3 level acquisition strategies, has a viewer that allows assessing interference, and provides several scores to aid the filtering of scans with compression. We demonstrate that IsobaricQuant quantifications are accurate by comparing it with commonly used software. We further show that its QC scores can successfully filter scans with reduced quantitative accuracy at MS2- and MS3 level, removing inaccurate peptide quantifications and decreasing protein CVs. Finally, we apply IsobaricQuant to a PISA dataset and show that QC scores improve the sensitivity of the identification of protein targets of a kinase inhibitor. IsobaricQuant is available at https://github.com/Villen-Lab/isobaricquant.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human) Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Alexander Hogrebe

LAB HEAD: Judit Villen

PROVIDER: PXD034534 | Pride | 2022-07-11

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	HYpro16_Comet.zip	Other
	HYpro16_FragPipe.zip	Other
	HYpro16_IsobaricQuant.zip	Other
	HYpro16_MaxQuant.zip	Other
	HYpro16_benchmark_analysis_unpack_in_data_folder.zip	Other

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Publications

TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples.

Li Jiaming J Van Vranken Jonathan G JG Pontano Vaites Laura L Schweppe Devin K DK Huttlin Edward L EL Etienne Chris C Nandhikonda Premchendar P Viner Rosa R Robitaille Aaron M AM Thompson Andrew H AH Kuhn Karsten K Pike Ian I Bomgarden Ryan D RD Rogers John C JC Gygi Steven P SP Paulo Joao A JA

Nature methods 20200316 4

Isobaric labeling empowers proteome-wide expression measurements simultaneously across multiple samples. Here an expanded set of 16 isobaric reagents based on an isobutyl-proline immonium ion reporter structure (TMTpro) is presented. These reagents have similar characteristics to existing tandem mass tag reagents but with increased fragmentation efficiency and signal. In a proteome-scale example dataset, we compared eight common cell lines with and without Torin1 treatment with three replicates, ...[more]

PMID: 32203386

Publication: 1/3

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