Harrison Specht

How to design 1000-plex mass tags using the differential mass defect

This paper explores designing high-plex mass tags using differential mass defect to enable large-scale multiplexing in proteomics.

Proteome asymmetry in mouse and human embryos before fate specification

The paper shows proteomic asymmetry in mouse and human embryos that influences lineage segregation.

JMod: Joint modeling of mass spectra for empowering multiplexed DIA proteomics

JMod improves sequence identification and quantification in multiplexed DIA proteomics by jointly modeling overlapping mass spectra, enabling higher throughput with maintained accuracy.

timePlex: Increasing mass spectrometry throughput using time-encoded sample multiplexing

timePlex increases LC-MS throughput by multiplexing samples in the time domain, achieving combinatorial scaling and enabling high-throughput proteomics.

PSMtags improve peptide sequencing and throughput in sensitive proteomics

PSMtags enhance peptide detection and sequence identification in proteomics, enabling 9-plexDIA and significantly increasing sample throughput.

Increasing the throughput of sensitive proteomics by plexDIA

Multiplexing nonisobaric isotopologous mass tags (mTRAQ) with data-independent acquisition and DIA-NN increases sensitive proteomics throughput 3-fold while cutting missing data below 3% in bulk and single cells.

TAILS identifies candidate substrates and biomarkers of ADAMTS7, a therapeutic protease target in coronary artery disease

The paper identifies ADAMTS7 substrates and cleavage sites using TAILS, revealing potential biomarkers for coronary artery disease.

Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity

This paper develops SCoPE2, a single-cell proteomic method, to analyze macrophage heterogeneity and finds a continuous proteome gradient in macrophages without polarizing cytokines.

Optimizing accuracy and depth of protein quantification in experiments using isobaric carriers

This paper characterizes trade-offs in using isobaric carriers for proteomic analysis and provides strategies to optimize their use in different applications.

DO-MS: Data-Driven Optimization of Mass Spectrometry Methods

DO-MS identifies and optimizes bottlenecks in LC-MS/MS methods by interactively visualizing and analyzing data from all analysis levels, improving ion delivery efficiency by 370% in one case.

Automated sample preparation for high-throughput single-cell proteomics

Minimal ProteOmic sample Preparation (mPOP) eliminates cleanup losses in single-cell mass spectrometry proteomics, enabling automated SCoPE-MS profiling that separates mammalian cells by cell type and cell-division-cycle phase.