Geyer PE, Holdt LM, Teupser D, Mann M. Revisiting biomarker discovery by plasma proteomics. Mol Syst Biol. 2017;13:942.

Article  Google Scholar 

Borrebaeck CA. Precision diagnostics: moving towards protein biomarker signatures of clinical utility in cancer. Nat Rev Cancer. 2017;17:199–204.

Article  Google Scholar 

Bretthauer M. Colorectal cancer screening. J Intern Med. 2011;270:87–98.

Article  Google Scholar 

Lin JS, Perdue LA, Henrikson NB, Bean SI, Blasi PR. Screening for colorectal cancer: updated evidence report and systematic review for the us preventive services task force. JAMA. 2021;325:1978–98.

Article  Google Scholar 

Werner S, Krause F, Rolny V, Strobl M, Morgenstern D, Datz C, Chen H, Brenner H. Evaluation of a 5-marker blood test for colorectal cancer early detection in a colorectal cancer screening setting. Clinical Cancer Res. 2016;22:1725–33.

Article  Google Scholar 

Chen H, Zucknick M, Werner S, Knebel P, Brenner H. Head-to-head comparison and evaluation of 92 plasma protein biomarkers for early detection of colorectal cancer in a true screening setting. Clinical Cancer Res. 2015;21:3318–26.

Article  Google Scholar 

Bhardwaj M, Weigl K, Tikk K, Benner A, Schrotz-King P, Brenner H. Multiplex screening of 275 plasma protein biomarkers to identify a signature for early detection of colorectal cancer. Mol Oncol. 2020;14:8–21.

Article  Google Scholar 

Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics. 2002;1:845–67.

Article  Google Scholar 

Mortezai N, Harder S, Schnabel C, Moors E, Gauly M, Schlüter H, Wagener C, Buck F. Tandem affinity depletion: a combination of affinity fractionation and immunoaffinity depletion allows the detection of low-abundance components in the complex proteomes of body fluids. J Proteome Res. 2010;9:6126–34.

Article  Google Scholar 

Bellei E, Bergamini S, Monari E, Fantoni LI, Cuoghi A, Ozben T, Tomasi A. High-abundance proteins depletion for serum proteomic analysis: concomitant removal of non-targeted proteins. Amino Acids. 2011;40:145–56.

Article  Google Scholar 

Kulak NA, Pichler G, Paron I, Nagaraj N, Mann M. Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells. Nat Methods. 2014;11:319–24.

Article  Google Scholar 

Geyer PE, Kulak NA, Pichler G, Holdt LM, Teupser D, Mann M. Plasma proteome profiling to assess human health and disease. Cell Syst. 2016;2:185–95.

Article  Google Scholar 

Niu L, Geyer PE, Wewer Albrechtsen NJ, Gluud LL, Santos A, Doll S, Treit PV, Holst JJ, Knop FK, Vilsbøll T, et al. Plasma proteome profiling discovers novel proteins associated with non-alcoholic fatty liver disease. Mol Syst Biol. 2019;15:e8793.

Article  Google Scholar 

Geyer PE, Arend FM, Doll S, Louiset ML, Virreira Winter S, Müller-Reif JB, Torun FM, Weigand M, Eichhorn P, Bruegel M, et al. High-resolution serum proteome trajectories in COVID-19 reveal patient-specific seroconversion. EMBO Mol Med. 2021;13:e14167.

Article  Google Scholar 

Xue L, Lin L, Zhou W, Chen W, Tang J, Sun X, Huang P, Tian R. Mixed-mode ion exchange-based integrated proteomics technology for fast and deep plasma proteome profiling. J Chromatogr A. 2018;1564:76–84.

Article  Google Scholar 

Gao W, Zhang Q, Su Y, Huang P, Lu X, Gong Q, Chen W, Xu R, Tian R. Multiomic analysis of a dried single-drop plasma sample using an integrated mass spectrometry approach. Analyst. 2020;145:6441–6.

Article  Google Scholar 

Lin L, Zheng J, Yu Q, Chen W, Xing J, Chen C, Tian R. High throughput and accurate serum proteome profiling by integrated sample preparation technology and single-run data independent mass spectrometry analysis. J Proteomics. 2018;174:9–16.

Article  Google Scholar 

Naldrett MJ, Zeidler R, Wilson KE, Kocourek A. Concentration and desalting of peptide and protein samples with a newly developed C18 membrane in a microspin column format. J Biomol Tech. 2005;16:423–8.

Google Scholar 

Bian Y, Zheng R, Bayer FP, Wong C, Chang YC, Meng C, Zolg DP, Reinecke M, Zecha J, Wiechmann S, et al. Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC-MS/MS. Nat Commun. 2020;11:157.

Article  Google Scholar 

Eng JK, McCormack AL, Yates JR. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom. 1994;5:976–89.

Article  Google Scholar 

Käll L, Canterbury JD, Weston J, Noble WS, MacCoss MJ. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods. 2007;4:923–5.

Article  Google Scholar 

Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol. 2008;26:1367–72.

Article  Google Scholar 

Wilson SR, Vehus T, Berg HS, Lundanes E. Nano-LC in proteomics: recent advances and approaches. Bioanalysis. 2015;7:1799–815.

Article  Google Scholar 

Anderson NL. The clinical plasma proteome: a survey of clinical assays for proteins in plasma and serum. Clin Chem. 2010;56:177–85.

Article  Google Scholar 

Hoshino A, Kim HS, Bojmar L, Gyan KE, Cioffi M, Hernandez J, Zambirinis CP, Rodrigues G, Molina H, Heissel S, et al. Extracellular vesicle and particle biomarkers define multiple human cancers. Cell. 2020;182:1044-61.e18.

Article  Google Scholar 

Deutsch EW, Omenn GS, Sun Z, Maes M, Pernemalm M, Palaniappan KK, Letunica N, Vandenbrouck Y, Brun V, Tao SC, et al. Advances and utility of the human plasma proteome. J Proteome Res. 2021;20:5241–63.

Article  Google Scholar 

Braga-Lagache S, Buchs N, Iacovache MI, Zuber B, Jackson CB, Heller M. Robust label-free, quantitative profiling of circulating plasma microparticle (MP) associated proteins. Molecul Cell Proteomics. 2016;15:3640–52.

Article  Google Scholar 

Blume JE, Manning WC, Troiano G, Hornburg D, Figa M, Hesterberg L, Platt TL, Zhao X, Cuaresma RA, Everley PA, et al. Rapid, deep and precise profiling of the plasma proteome with multi-nanoparticle protein corona. Nat Commun. 2020;11:3662.

Article  Google Scholar 

Santos-Lozano A, Valenzuela PL, Llavero F, Lista S, Carrera-Bastos P, Hampel H, Pareja-Galeano H, Gálvez BG, López JA, Vázquez J, et al. Successful aging: insights from proteome analyses of healthy centenarians. Aging. 2020;12:3502–15.

Article  Google Scholar 

Ye S, Ma L, Zhang R, Liu F, Jiang P, Xu J, Cao H, Du X, Lin F, Cheng L, et al. Plasma proteomic and autoantibody profiles reveal the proteomic characteristics involved in longevity families in Bama. China Clinical proteomics. 2019;16:22.

Article  Google Scholar 

Wang Z, Zhang R, Liu F, Jiang P, Xu J, Cao H, Du X, Ma L, Lin F, Cheng L, et al. TMT-based quantitative proteomic analysis reveals proteomic changes involved in longevity. Proteomics Clin Appl. 2019;13:e1800024.

Article  Google Scholar 

Xu R, Gong CX, Duan CM, Huang JC, Yang GQ, Yuan JJ, Zhang Q, Xiong XY, Yang QW. Age-dependent changes in the plasma proteome of healthy adults. J Nutr Health Aging. 2020;24:846–56.

Article  Google Scholar 

Tanaka T, Basisty N, Fantoni G, Candia J, Moore AZ, Biancotto A, Schilling B, Bandinelli S, Ferrucci L. Plasma proteomic biomarker signature of age predicts health and life span. Elife. 2020. https://doi.org/10.7554/eLife.61073.

Article  Google Scholar 

Surinova S, Choi M, Tao S, Schüffler PJ, Chang CY, Clough T, Vysloužil K, Khoylou M, Srovnal J, Liu Y, et al. Prediction of colorectal cancer diagnosis based on circulating plasma proteins. EMBO Mol Med. 2015;7:1166–78.

Article  Google Scholar