PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics - catching the (un)usual suspects.

Variant peptides resulting from single nucleotide polymorphisms (SNPs) can lead to aberrant protein functions and have translational potential for disease diagnosis and personalized therapy. Variant peptides detected by proteogenomics are fraught with high number of false positives, but there is no uniform and comprehensive approach to assess variant quality across analysis pipelines. Despite class-specific FDR along with ad-hoc filters, the problem is far from solved.

A High Throughput Lipidomics Method Using Multiple Reaction Monitoring.

Lipid compositions of cells, tissues, and bio-fluids are complex, with varying concentrations and structural diversity making their identification challenging. Newer methods for comprehensive analysis of lipids are thus necessary. Herein, we propose a targeted-mass spectrometry based lipidomics screening method using a combination of variable retention time window and relative dwell time weightage.

False discovery rate: the Achilles' heel of proteogenomics.

Proteogenomics refers to the integrated analysis of the genome and proteome that leverages mass-spectrometry (MS)-based proteomics data to improve genome annotations, understand gene expression control through proteoforms and find sequence variants to develop novel insights for disease classification and therapeutic strategies. However, proteogenomic studies often suffer from reduced sensitivity and specificity due to inflated database size. To control the error rates, proteogenomics depends on the target-decoy search strategy, the de-facto method for false discovery rate (FDR) estimation in proteomics.

Sputum Protein Biomarkers in Airway Diseases: A Pilot Study.

Background: Chronic mucous hypersecretion (CMH or chronic bronchitis) per se or when associated with chronic inflammatory airway diseases such as asthma or chronic obstructive pulmonary disease (COPD) has several adverse clinical consequences. The sputum fluid phase has several candidate proteins including mucins which have the potential of being therapeutic targets, but has not yet been explored in-depth. This study aimed at exploring the profile of sputum proteins in various airway diseases.