Robert J. Chalkley

Optimization of Search and Acquisition Strategies for DSSO Crosslinking Mass Spectrometry using Protein Prospector and Touchstone.

The paper evaluates DSSO crosslinking strategies using Protein Prospector and Touchstone, finding that DSSO's advantage comes from backbone fragmentation, not diagnostic ions, and that MS3 is better for proteome-scale samples.

Extracellular matrix proteolysis maintains synapse plasticity during brain development

The paper shows ECM proteolysis, specifically via MMP14 and brevican, maintains dynamic synapse plasticity during brain development in zebrafish and human iPSC-derived cultures.

Assessing Heterogeneity in the N-Telopeptides of Type I Collagen by Mass Spectrometry

The paper develops a method to identify N-terminal cross-linked peptides from collagen I in Achilles tendon using mass spectrometry, revealing differences in cross-links in bovine pulmonary hypertension.

ADAR1 Restricts Poliovirus Infection through dual disruption of translation initiation and protein coding

The paper identifies ADAR1 as a host factor that restricts poliovirus infection by editing viral RNA to disrupt translation initiation and introduce a coding error.

A community audit of error control in crosslinking mass spectrometry

The paper audits error control in twelve crosslinking mass spectrometry pipelines using ground-truth designs, finding some pipelines exceed false discovery rates by up to 29-fold.

Comparative Analysis of Glycoproteomic Software Using a Tailored Glycan Database

This paper compares five glycoproteomic software tools using a tailored glycan database, finding that Protein Prospector has the highest agreement with known glycosites.

A two-step probing method to compare lysine accessibility across macromolecular complex conformations

The paper introduces a two-step chemical probing method using tandem mass-spectrometry to assess lysine reactivity in macromolecular complexes, showing it reflects structural models of ribosomes and spliceosomes.

Proteomics Standards Initiative Extended FASTA Format (PEFF)

The paper introduces PEFF, a new format for proteomics data that enhances FASTA with metadata for sequence variants and PTMs, enabling better analysis in proteogenomics and top-down proteomics.