Cell Proteins & Exosome Analysis

A project performed for a therapeutic company involved the study of the impact of differential therapeutic treatments on mouse muscle, combining both proteome and phospho-proteome profiling.

With a 60-minute LC-MS DIA profiling approach, the ProteiQ team identified, on average, over 4.7k proteins in each unenriched sample and 9.8k phosphopeptides after enrichment with 5.9% and 7.5% missing values respectively.

Proteome analysis of nasopharyngeal swabs resulted in  > 4.2k identifications for the study using 60 minutes of LC-MS DIA analysis with a non-linear gradient.

Challenging sampling conditions, impacted technical variability, and the number of missing values per sample lead to > 20% in both cases. ProteiQ addressed all of the challenges in statistical analysis by factoring in batch effects, sampling effects, and the increase in missing identifications.

A project in which liver tissue cells were analysed with/without palmitoylated protein enrichment focused on the validation of selective pathway inhibition after treatment.

> 6.3k proteins were identified with 60 minutes of LC-MS DIA analysis – with a missing value of ~ 1% for non-enriched samples before treatment. The number of identifications varied from 0.2k to 2.4k after treatment and enrichment.

HeLa cells are a common quality reference used in LC-MS proteomics, yet they are also representative of an average number of identifications in wide ranges of other cell types, e.g., MEF, A549, HEPP.
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With the current ProteiQ pipeline, around 4k proteins can be identified in 60 minutes of LC-MS DIA analysis; this value can go as high as 6–7k with increased analysis time or with the utilization of ion mobility.