A mouse SWATH-MS reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts

Abstract

2 SWATH-mass spectrometry (MS) enables accurate and reproducible proteomic profiling in 3 multiple model organisms including the mouse. Here we present a comprehensive mouse 4 reference spectral library (MouseRefSWATH) that permits quantification of up to 10,597 5 proteins (62.2% of the mouse proteome) by SWATH-MS. We exploit MouseRefSWATH to 6 develop an analytical pipeline for species-specific deconvolution of proteomic alterations in 7 human tumour xenografts (XenoSWATH). This method overcomes the challenge of high 8 sequence similarity between mouse and human proteins, facilitating the study of host 9 microenvironment-tumour interactions from 'bulk tumour' measurements. We apply the 10 XenoSWATH pipeline to characterise an intraductal xenograft model of breast ductal 11 carcinoma in-situ and uncover complex regulation of cell migration pathways that are not 12 restricted to tumour cells but also operate in the mouse stroma upon progression to invasive 13 disease. MouseRefSWATH and XenoSWATH opens new opportunities for in-depth and 14 reproducible proteomic assessment to address wide-ranging biological questions involving 15 this important model organism. 16 17 18 19Key to the success of SWATH-MS is the use of retention-time calibrated spectral libraries to 20 identify and quantify peptides from the complex fragment ion mass spectra encoded within 21 digital proteome maps [13]. While most published SWATH-MS studies have utilised study-22

Data-independent acquisition mass spectrometry (DIA-MS) for proteomic applications in oncology

“…As a result of the extensive number of DDA-MS experiments required to generate study-specific spectral libraries, there are also cost and time implications to consider which may decrease the attractiveness of DIA-MS. More recently, the generation of comprehensive spectral libraries as a community resource have been employed as an alternative solution. To date, comprehensive reference libraries have been generated for number of organisms including human, 24 mouse, 25,26 zebrafish, 27 fruit fly, 28 yeast, 29 and various bacteria. [30][31][32] Most of these libraries are publicly available in repositories such as SWATHAtlas.org for community use.…”