Jimenez CR, Verheul HM. Mass spectrometry-based proteomics: from cancer biology to protein biomarkers, drug targets, and clinical applications. Am Soc Clin Oncol Educational Book. 2014;34(1):e504–10.

Article  Google Scholar 

Sevimoglu T, Arga KY. The role of protein interaction networks in systems biomedicine. Comput Struct Biotechnol J. 2014;11(18):22–7.

Article  PubMed Central  PubMed  Google Scholar 

Gonzalez MW, Kann MG. Chap. 4: Protein interactions and disease PLoS computational biology, 2012. 8(12): p. e1002819.

Khodadadi E, et al. Proteomic applications in antimicrobial resistance and clinical microbiology studies. Infect Drug Resist. 2020;13:1785.

Article  CAS  PubMed Central  PubMed  Google Scholar 

Iwamoto N, Shimada T. Recent advances in mass spectrometry-based approaches for proteomics and biologics: great contribution for developing therapeutic antibodies. Volume 185. Pharmacology & Therapeutics; 2018. pp. 147–54.

Clarke NJ, Zhang Y, Reitz RE. A novel mass spectrometry–based assay for the accurate measurement of thyroglobulin from patient samples containing antithyroglobulin autoantibodies. J Investig Med. 2012;60(8):1157–63.

Article  CAS  PubMed  Google Scholar 

Rostaing L, et al. Falsely elevated whole-blood tacrolimus concentrations in a kidney‐transplant patient: potential hazards. Transpl Int. 2010;23(2):227–30.

Article  PubMed  Google Scholar 

Hanash S. Disease proteomics. Nature. 2003;422(6928):226–32.

Article  CAS  PubMed  Google Scholar 

Oliveira BM, et al. Is clinical proteomics heading towards to “bench to bedside. Transl Proteom. 2013;1(1):53–6.

Google Scholar 

Mischak H. How to get proteomics to the clinic? Issues in clinical proteomics, exemplified by CE-MS. PROTEOMICS–Clinical Appl. 2012;6(9–10):437–42.

Article  CAS  Google Scholar 

Mischak H, et al. Implementation of proteomic biomarkers: making it work. Eur J Clin Invest. 2012;42(9):1027–36.

Article  CAS  PubMed Central  PubMed  Google Scholar 

Baker ES, et al. Mass spectrometry for translational proteomics: progress and clinical implications. Genome Med. 2012;4(8):1–11.

Article  Google Scholar 

Boja ES, Rodriguez H. The path to clinical proteomics research: integration of proteomics, genomics, clinical laboratory and regulatory science. Korean J Lab Med. 2011;31(2):61–71.

CAS  PubMed Central  PubMed  Google Scholar 

Maes E, et al. Proteomics in cancer research: are we ready for clinical practice? Crit Rev Oncol/Hematol. 2015;96(3):437–48.

Article  PubMed  Google Scholar 

Findeisen P, Neumaier M. Mass spectrometry-based clinical proteomics profiling: current status and future directions. Expert Rev Proteomics. 2009;6(5):457–9.

Article  CAS  PubMed  Google Scholar 

Lill JR, et al. Proteomics in the pharmaceutical and biotechnology industry: a look to the next decade. Expert Rev Proteomics. 2021;18(7):503–26.

Article  CAS  PubMed  Google Scholar 

Parker CE, Borchers CH. Mass spectrometry based biomarker discovery, verification, and validation–quality assurance and control of protein biomarker assays. Mol Oncol. 2014;8(4):840–58.

Article  CAS  PubMed Central  PubMed  Google Scholar 

Srinivas PR, et al. Proteomics for cancer biomarker discovery. Clin Chem. 2002;48(8):1160–9.

CAS  PubMed  Google Scholar 

Olsson B, et al. CSF and blood biomarkers for the diagnosis of Alzheimer’s disease: a systematic review and meta-analysis. Lancet Neurol. 2016;15(7):673–84.

Article  CAS  PubMed  Google Scholar 

Jang HN et al. Mass Spectrometry-Based Proteomic Discovery of prognostic biomarkers in adrenal cortical carcinoma. Cancers (Basel), 2021. 13(15).

Gam L-H. Breast cancer and protein biomarkers. World J experimental Med. 2012;2(5):86.

Article  Google Scholar 

Hamdan MH. Cancer biomarkers: analytical techniques for discovery. John Wiley & Sons; 2007.

Amiri-Dashatan N, et al. Proteomics applications in health: biomarker and drug discovery and food industry. Iran J Pharm research: IJPR. 2018;17(4):1523.

CAS  PubMed Central  PubMed  Google Scholar 

Yang WS, et al. Proteomic approach reveals FKBP4 and S100A9 as potential prediction markers of therapeutic response to neoadjuvant chemotherapy in patients with breast cancer. J Proteome Res. 2012;11(2):1078–88.

Article  CAS  PubMed  Google Scholar 

Zhang D, Putti TC. Over-expression of ERp29 attenuates doxorubicin-induced cell apoptosis through up-regulation of Hsp27 in breast cancer cells. Exp Cell Res. 2010;316(20):3522–31.

Article  CAS  PubMed  Google Scholar 

Banerjee S. Empowering clinical diagnostics with mass spectrometry. ACS omega. 2020;5(5):2041–8.

Article  CAS  PubMed Central  PubMed  Google Scholar 

Blattmann P, Aebersold R. The Advent of Mass Spectrometry-Based Proteomics in Systems Biology Research 2016.

Macklin A, Khan S, Kislinger T. Recent advances in mass spectrometry based clinical proteomics: applications to cancer research. Clin Proteom. 2020;17(1):17.

Article  CAS  Google Scholar 

Lange V, et al. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol. 2008;4(1):222.

Article  PubMed Central  PubMed  Google Scholar 

Wu W, Dai R-T, Bendixen E. Comparing SRM and SWATH methods for quantitation of bovine muscle proteomes. J Agric Food Chem. 2019;67(5):1608–18.

Article  CAS  PubMed  Google Scholar 

Mermelekas G, Vlahou A, Zoidakis J. SRM/MRM targeted proteomics as a tool for biomarker validation and absolute quantification in human urine. Expert Rev Mol Diagn. 2015;15(11):1441–54.

Article  CAS  PubMed  Google Scholar 

Jones JJ, et al. A plasma-based protein marker panel for Colorectal Cancer Detection identified by Multiplex targeted Mass Spectrometry. Clin Colorectal Cancer. 2016;15(2):186–194e13.

Article  PubMed Central  PubMed  Google Scholar 

Kontostathi G, et al. Applications of multiple reaction monitoring targeted proteomics assays in human plasma. Expert Rev Mol Diagn. 2019;19(6):499–515.

Article  CAS  PubMed  Google Scholar 

Boys EL, et al. Clinical applications of mass spectrometry-based proteomics in cancer: where are we? Proteomics. 2023;23(7–8):e2200238.

Article  PubMed  Google Scholar 

Ludwig C, et al. Data-independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial. Mol Syst Biol. 2018;14(8):e8126.

Article  PubMed Central  PubMed  Google Scholar 

Tully B, et al. Addressing the challenges of high-throughput cancer tissue proteomics for clinical application: proCan. Proteomics. 2019;19(21–22):1900109.

Article  CAS  Google Scholar 

Poulos RC, et al. Strategies to enable large-scale proteomics for reproducible research. Nat Commun. 2020;11(1):1–13.

Article  Google Scholar 

Gillet LC, et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Volume 11. Molecular & Cellular Proteomics; 2012. 6.

Collins BC, et al. Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry. Nat Commun. 2017;8(1):1–12.

Article  Google Scholar 

Reubsaet L, Sweredoski MJ, Moradian A. Data-independent acquisition for the Orbitrap Q Exactive HF: a tutorial. J Proteome Res. 2018;18(3):803–13.

Article  Google Scholar 

Chang RY, et al. SWATH analysis of the synaptic proteome in Alzheimer’s disease. Neurochem Int. 2015;87:1–12.

Article  CAS  PubMed  Google Scholar 

Kim YJ, et al. Targeted data-independent acquisition for mass spectrometric detection of RAS mutations in formalin-fixed, paraffin-embedded tumor biopsies. J Proteom. 2018;189:91–6.

Article  CAS  Google Scholar 

Anjo SI, Santa C, Manadas B. SWATH-MS as a tool for biomarker discovery: from basic research to clinical applications. Proteomics. 2017;17:3–4.

Article  Google Scholar 

de Wit M, et al. Proteomics in colorectal cancer translational research: biomarker discovery for clinical applications. Clin Biochem. 2013;46(6):466–79.

Article  PubMed  Google Scholar 

Patterson SD, Aebersold RH. Proteomics: the first decade and beyond. Nat Genet. 2003;33(3):311–23.

Article  CAS  PubMed  Google Scholar 

Fung AW, et al. Emerging role of clinical mass spectrometry in pathology. J Clin Pathol. 2020;73(2):61–9.

Article  CAS  PubMed  Google Scholar