A large-scale assay library for targeted protein quantification in renal cell carcinoma tissues
| Authors | |
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| Year of publication | 2021 |
| Type | Conference abstract |
| MU Faculty or unit | |
| Citation | |
| Description | Introduction. Renal cell carcinoma (RCC) represents 2.2 % of cancer incidences, however, prognostic or predictive protein biomarkers specific for RCC are generally not available. To support proteomics research of localized and metastatic RCC, we introduce a new library of targeted mass spectrometry assays for accurate protein quantification in malignant and normal kidney tissue. Methods. Aliquots of 86 initially localized RCC, 75 metastatic RCC and 17 adjacent non-cancerous fresh frozen tissue lysates were trypsin digested, pooled and fractionated using hydrophilic chromatography and analyzed using LC-MS/MS on QExactive HF-X mass spectrometer in data-dependent acquisition mode. The library was generated in Spectronaut software. Two published datasets A-B [1] [2] and two new pilot datasets C-D of localized and metastatic RCC tissues measured in data-independent acquisition (DIA) mode were processed using the new library in Spectronaut. Results. The newly established assay library contains 77,817 peptides representing 7960 protein groups (FDR=1%). Its application resulted in increased numbers of quantified proteins in datasets A (2463 proteins, +4%) and B (4492 protein groups, >2 fold), with a clear separation of tumor and non-tumor tissues in both studies. Analysis of datasets C of metastatic RCC responding vs. non-responding to sunitinib treatment and dataset D of initially localized vs. metastatic RCC tissues led to consistent quantification of 5181 and 5253 protein groups (FDR=1%). Conclusions. Application of our spectral library leads to quantification of substantially increased part of RCC proteome. The new library has potential to contribute to better understanding the RCC development at molecular level, leading to new diagnostic and therapeutic targets. |
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