SuperQuantNode

SuperQuant performs complementary fragment-ion-based identification and precursor-level quantification of multiple coisolated peptides in high mass accuracy shotgun proteomics data processed in Thermo Proteome Discoverer 2.x.

Key Features:

• Complementary fragment-ion analysis: Leverages complementary fragment ions from tandem mass spectra to identify and quantify multiple coisolated peptides.
• MS(1)-level quantification: Performs quantification at the MS(1) (precursor ion) level for high mass accuracy datasets.
• Compatibility with shotgun proteomics: Applicable to any shotgun proteomics dataset acquired with high mass accuracy.
• Tested sample design: Validated on dimethyl-labeled HeLa lysate samples with heavy:medium:light channel ratios of 10:4:1.
• Fragmentation and isolation settings: Evaluated using collision-induced dissociation within isolation windows of 1–4 Th.
• Resolution conditions: Performance assessed on data acquired at both high-resolution and low-resolution settings.
• Improved identification: Identifies up to 70% more peptide-spectrum matches (PSMs), 40% more peptides, and 20% more proteins compared to ion trap-based approaches using low mass accuracy MS(2) spectra (at FDR 0.01).
• Improved quantification: Quantifies up to 10% more PSMs, 15% more peptides, and 10% more proteins from the same raw data compared to the ion trap-based approach.
• Accuracy and precision: Maintains high accuracy in quantification while preserving replicate coefficients of variation consistent with precursor ion–based quantification methods.
• Data provenance: Supporting raw data deposited to ProteomeXchange under identifier PXD001907.
• Integration: Implemented as a processing node for Thermo Proteome Discoverer 2.x.

Scientific Applications:

• Shotgun quantitative proteomics: Identification and precursor-level quantification of peptides and proteins in high mass accuracy datasets.
• Multiplexed dimethyl labeling experiments: Quantification across heavy, medium, and light channels (10:4:1) in labeled HeLa lysate samples.
• Method comparison and benchmarking: Comparative evaluation against ion trap-based low mass accuracy MS(2) workflows for identification and quantification performance.
• High-accuracy quantitative studies: Enabling protein-level quantification with controlled identification FDR (0.01).

Methodology:

Uses complementary fragment ions from tandem mass spectra to identify and quantify coisolated peptides at the MS(1) level within Thermo Proteome Discoverer 2.x, with identifications evaluated at an FDR of 0.01.