Orthogonal proteomic platforms and their implications for the stable classification of high-grade serous ovarian cancer subtypes

Abstract

<jats:title>Summary</jats:title><jats:p>The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) has established a two-dimensional liquid chromatography-tandem mass spectrometry (2DLC-MS/MS) workflow using isobaric tagging to compare protein abundance across samples. The workflow has been used for large-scale clinical proteomic studies with deep proteomic coverage within and outside of CPTAC. SWATH-MS, an instance of data-independent acquisition (DIA) proteomic methods, was recently developed as an alternate proteomic approach. In this study, we analyzed remaining aliquots of peptides using SWATH-MS from the original retrospective TCGA samples generated for the CPTAC ovarian cancer proteogenomic study (Zhang et al., 2016). The SWATH-MS results indicated that both methods confidently identified differentially expressed proteins in enriched pathways associated with the robust Mesenchymal subtype of high-grade serous ovarian cancer (HGSOC) and the homologous recombination deficient tumors also present in the original study. The results demonstrated that SWATH/DIA-MS presents a promising complementary or orthogonal alternative to the CPTAC harmonized proteomic method, with the advantages of simpler, faster, and cheaper workflows, as well as lower sample consumption. However, the SWATH/DIA-MS workflow resulted in shallower proteome coverage. Overall, we concluded that both analytical methods are suitable to characterize clinical samples such as in the high-grade serous ovarian cancer study, providing proteomic workflow alternatives for cancer researchers depending on the specific goals and context of the studies.</jats:p>

Proteomic signatures of 16 major types of human cancer reveal universal and cancer-type-specific proteins for the identification of potential therapeutic targets

“…Recently, data-independent acquisition (DIA) of mass spectrometry (MS), also called Sequential Window Acquisition of all THeoretical fragment ion spectra (SWATH), has emerged as an alternative technology for proteomic analysis of biological samples to minimize the data-dependent acquisition (DDA)-based analytic limitations, for instance, the stochastic nature of precursor ion selection and low sampling efficiency [15][16][17][18][19]. DIA is an unbiased methodology that allows peptide precursor ions divided into several consecutive windows during fragmentation resulting in a comprehensive fragmentation map of all detectable precursors for accurate quantification of the given sample.…”

Accelerated Protein Biomarker Discovery from FFPE tissue samples using Single-shot, Short Gradient Microflow SWATH MS

“…Overall, these challenges convincingly support the need for the proteomic measurement of large sample cohorts at moderate cost, limited batch effects and high degree of reproducibility. At present state-of-the art, large scale clinical proteomic studies consist of 100 to 200 clinical samples (9-11) and there are indication, e.g the lack of stability of discovered marker panels that suggest that this number of samples is at the lower end of the required size range(12). Further, these studies were for the most part carried out by highly specialized groups or consortia using highly optimized analytical platforms.…”

A Simple Optimization Workflow to Enable Precise and Accurate Imputation of Missing Values in Proteomic Datasets

“…al. 21 , and as also performed by others on the same publicly available dataset 22 . To this library, we added an internally generated data set produced by, cation-exchange chromatography (SCX) fractionation of the trypsin digested pooled tumor protein lysates (described above) resulting in 6 fractions.…”