Proteomics

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A causal model of ion interference enables assessment and correction of ratio compression in multiplex proteomics

ABSTRACT: We thoroughly characterize isobaric labeling (TMT)-associated reporter ion interference at the MS2 level using a defined two-proteome experimental system with known ground truth. We discover remarkably poor agreement between the apparent precursor purity in the isolation window and the actual level of observed reporter ion interference in MS2-scans - a discrepancy that we find resolved by considering co-fragmentation of peptide ions hidden within the spectral “noise” of the MS1 isolation window. On this basis, we establish a comprehensive regression modeling strategy for predicting accurate, feature-wise estimates of reporter ion interference. Finally, we demonstrate the utility of accurate ion purity estimates for accurate fold change estimation and unbiased PTM site-to-protein normalization.

INSTRUMENT(S): Orbitrap Eclipse, Q Exactive HF-X

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

TISSUE(S): T Cell

SUBMITTER: Moritz Madern  

LAB HEAD: Markus Hartl

PROVIDER: PXD040449 | Pride | 2023-12-19

REPOSITORIES: Pride

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20200909_QExHFX1_RSLC1_Madern_Hartl_UW_MFPL_master_exp_p1_acet.raw Raw
20200909_QExHFX1_RSLC1_Madern_Hartl_UW_MFPL_master_exp_p1_phospho.raw Raw
20200909_QExHFX1_RSLC1_Madern_Hartl_UW_MFPL_master_exp_p2_acet.raw Raw
20200909_QExHFX1_RSLC1_Madern_Hartl_UW_MFPL_master_exp_p2_phospho.raw Raw
20200909_QExHFX1_RSLC1_Madern_Hartl_UW_MFPL_master_exp_p3_acet.raw Raw
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Publications

A Causal Model of Ion Interference Enables Assessment and Correction of Ratio Compression in Multiplex Proteomics.

Madern Moritz M   Reiter Wolfgang W   Stanek Florian F   Hartl Natascha N   Mechtler Karl K   Hartl Markus M  

Molecular & cellular proteomics : MCP 20231212 1

Multiplex proteomics using isobaric labeling tags has emerged as a powerful tool for the simultaneous relative quantification of peptides and proteins across multiple experimental conditions. However, the quantitative accuracy of the approach is largely compromised by ion interference, a phenomenon that causes fold changes to appear compressed. The degree of compression is generally unknown, and the contributing factors are poorly understood. In this study, we thoroughly characterized ion interf  ...[more]

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