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To perform quantitative proteomics of FFPE samples, paraffin has to be removed and formalin-induced crosslinks have to be reversed prior to proteolytic digestion. A central component of almost all deparaffinization protocols is xylene, a toxic and highly flammable solvent that has been reported to negatively affect protein extraction and quantitative proteome analysis. Here, we present a \u2018green\u2019 xylene-free protocol for accelerated sample preparation of FFPE tissues based on paraffin-removal with hot water. Combined with tissue homogenization using disposable micropestles and a modified protein aggregation capture (PAC) digestion protocol, our workflow enables streamlined and reproducible quantitative proteomic profiling of FFPE tissue. Label-free quantitation of FFPE cores from human ductal breast carcinoma in situ (DCIS) xenografts with a volume of only 0.79 mm3 showed a high correlation between replicates (r2 = 0.992) with a median %CV of 16.9%. Importantly, this small volume is already compatible with tissue micro array (TMA) cores and core needle biopsies, while our results and its ease-of-use indicate that further downsizing is feasible. Finally, our FFPE workflow does not require costly equipment and can be established in every standard clinical laboratory.<\/jats:p>","DOI":"10.3390\/ijms23084443","type":"journal-article","created":{"date-parts":[[2022,4,18]],"date-time":"2022-04-18T22:04:02Z","timestamp":1650319442000},"page":"4443","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["A Non-Hazardous Deparaffinization Protocol Enables Quantitative Proteomics of Core Needle Biopsy-Sized Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Specimens"],"prefix":"10.3390","volume":"23","author":[{"given":"Georgia","family":"Mitsa","sequence":"first","affiliation":[{"name":"Division of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada"},{"name":"Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qianyu","family":"Guo","sequence":"additional","affiliation":[{"name":"Division of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada"},{"name":"Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC H4A 3T2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christophe","family":"Goncalves","sequence":"additional","affiliation":[{"name":"Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC H4A 3T2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2618-8326","authenticated-orcid":false,"given":"Samuel E. J.","family":"Preston","sequence":"additional","affiliation":[{"name":"Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC H4A 3T2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1545-5617","authenticated-orcid":false,"given":"Vincent","family":"Lacasse","sequence":"additional","affiliation":[{"name":"Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada"},{"name":"Research Pathology Core Facility, Department of Pathology, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adriana","family":"Aguilar-Mahecha","sequence":"additional","affiliation":[{"name":"Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC H4A 3T2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naciba","family":"Benlimame","sequence":"additional","affiliation":[{"name":"Research Pathology Core Facility, Department of Pathology, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Basik","sequence":"additional","affiliation":[{"name":"Division of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada"},{"name":"Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC H4A 3T2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3020-1420","authenticated-orcid":false,"given":"Alan","family":"Spatz","sequence":"additional","affiliation":[{"name":"Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC H4A 3T2, Canada"},{"name":"Research Pathology Core Facility, Department of Pathology, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerald","family":"Batist","sequence":"additional","affiliation":[{"name":"Division of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada"},{"name":"Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC H4A 3T2, Canada"},{"name":"Exactis Innovation, 5450 Cote-des-Neiges, Suite 522, Montreal, QC H3T 1Y6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"Jr.","given":"Wilson H.","family":"Miller","sequence":"additional","affiliation":[{"name":"Division of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada"},{"name":"Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC H4A 3T2, Canada"},{"name":"Rossy Cancer Network, McGill University, Montreal, QC H3H 1E8, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonia V.","family":"del Rincon","sequence":"additional","affiliation":[{"name":"Division of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada"},{"name":"Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC H4A 3T2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ren\u00e9 P.","family":"Zahedi","sequence":"additional","affiliation":[{"name":"Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2394-6512","authenticated-orcid":false,"given":"Christoph H.","family":"Borchers","sequence":"additional","affiliation":[{"name":"Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada"},{"name":"Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC H4A 3T2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,4,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1080\/10520295.2018.1446101","article-title":"Factors that drive the increasing use of FFPE tissue in basic and translational cancer research","volume":"93","author":"Gaffney","year":"2018","journal-title":"Biotech. Histochem."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s12014-018-9188-y","article-title":"Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization","volume":"15","author":"Foll","year":"2018","journal-title":"Clin. Proteom."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1007\/s00726-013-1494-0","article-title":"Analysis of the formalin-fixed paraffin-embedded tissue proteome: Pitfalls, challenges, and future prospectives","volume":"45","author":"Maes","year":"2013","journal-title":"Amino Acids"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"2686","DOI":"10.1039\/c3mb70177h","article-title":"Proteomic analysis of formalin-fixed paraffin-embedded colorectal cancer tissue using tandem mass tag protein labeling","volume":"9","author":"Maes","year":"2013","journal-title":"Mol. Biosyst."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1136\/jcp.2010.086835","article-title":"The use of formalin fixed wax embedded tissue for proteomic analysis","volume":"64","author":"Ralton","year":"2011","journal-title":"J. Clin. Pathol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1186\/s12967-019-1864-9","article-title":"Are innovation and new technologies in precision medicine paving a new era in patients centric care?","volume":"17","author":"Seyhan","year":"2019","journal-title":"J. Transl. Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"e1900029","DOI":"10.1002\/pmic.201900029","article-title":"Targeted and Untargeted Proteomics Approaches in Biomarker Development","volume":"20","author":"Sobsey","year":"2019","journal-title":"Proteomics"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1007\/978-1-4939-7765-9_16","article-title":"Proteomic Profiling for Colorectal Cancer Biomarker Discovery","volume":"1765","year":"2018","journal-title":"Methods Mol. Biol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1016\/j.ygyno.2020.02.017","article-title":"Chemoradiotherapy response prediction model by proteomic expressional profiling in patients with locally advanced cervical cancer","volume":"157","author":"Choi","year":"2020","journal-title":"Gynecol. Oncol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1186\/s12967-020-02273-4","article-title":"Identification and clinical impact of potentially actionable somatic oncogenic mutations in solid tumor samples","volume":"18","author":"Toomey","year":"2020","journal-title":"J. Transl. Med."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1177\/002215540505300114","article-title":"Raman spectroscopic evaluation of efficacy of current paraffin wax section dewaxing agents","volume":"53","author":"Hunter","year":"2005","journal-title":"J. Histochem. Cytochem."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.4103\/0973-029X.64299","article-title":"Xylene: An overview of its health hazards and preventive measures","volume":"14","author":"Kandyala","year":"2010","journal-title":"J. Oral Maxillofac. Pathol."},{"key":"ref_13","unstructured":"European Chemical Agency (2021, August 11). Xylene (Last Updated: 16 April 2020). Available online: https:\/\/echa.europa.eu\/brief-profile\/-\/briefprofile\/100.014.124."},{"key":"ref_14","first-page":"307","article-title":"An optimized xylene-free protein extraction method adapted to formalin-fixed paraffin embedded tissue sections for western blot analysis","volume":"32","author":"Mansour","year":"2017","journal-title":"Histol. Histopathol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1002\/pmic.201100550","article-title":"Toward deciphering proteomes of formalin-fixed paraffin-embedded (FFPE) tissues","volume":"12","author":"Magdeldin","year":"2012","journal-title":"Proteomics"},{"key":"ref_16","unstructured":"Anastas, P.T., and Warner, J.C. (1998). Green Chemistry: Theory and Practice, Oxford University Press."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1646","DOI":"10.1158\/0008-5472.CAN-18-1602","article-title":"MNK1\/NODAL Signaling Promotes Invasive Progression of Breast Ductal Carcinoma In Situ","volume":"79","author":"Guo","year":"2019","journal-title":"Cancer Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.ab.2016.05.015","article-title":"Deparaffinization of formalin-fixed paraffin-embedded tissue blocks using hot water instead of xylene","volume":"507","author":"Kalantari","year":"2016","journal-title":"Anal. Biochem."},{"key":"ref_19","unstructured":"(2021, August 11). The Human Protein Atlas. Available online: https:\/\/www.proteinatlas.org\/."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"4106","DOI":"10.1038\/s41598-020-60456-x","article-title":"Functionally Enigmatic Genes in Cancer: Using TCGA Data to Map the Limitations of Annotations","volume":"10","author":"Maertens","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1028","DOI":"10.1016\/j.molcel.2019.01.002","article-title":"Reciprocal roles of Tom7 and OMA1 during mitochondrial import and activation of PINK1","volume":"73","author":"Sekine","year":"2019","journal-title":"Mol. Cell"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1093\/toxsci\/kfn268","article-title":"Bile Acid Sulfation: A Pathway of Bile Acid Elimination and Detoxification","volume":"108","author":"Alnouti","year":"2009","journal-title":"Toxicol. Sci."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Zhong, K., Chen, K., Han, L., and Li, B. (2014). MicroRNA-30b\/c inhibits non-small cell lung cancer cell proliferation by targeting Rab18. BMC Cancer, 14.","DOI":"10.1186\/1471-2407-14-703"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/S0378-1119(02)01098-3","article-title":"Genomic structure of the human BCCIP gene and its expression in cancer","volume":"302","author":"Meng","year":"2003","journal-title":"Gene"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Fujikawa, T., Miyata, S.-I., and Iwanami, T. (2013). Convenient detection of the citrus greening (huanglongbing) bacterium \u2018Candidatus Liberibacter asiaticus\u2019 by direct PCR from the midrib extract. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0057011"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.forsciint.2016.02.011","article-title":"Quantitative and qualitative study of STR DNA from ethanol and formalin fixed tissues","volume":"262","author":"Alqaydi","year":"2016","journal-title":"Forensic Sci. Int."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1561","DOI":"10.1292\/jvms.12-0213","article-title":"Improved RNA extraction method using the BioMasher and BioMasher power-plus","volume":"74","author":"Yamamoto","year":"2012","journal-title":"J. Vet. Med. Sci."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1016\/j.jviromet.2008.01.018","article-title":"An advantageous method utilizing new homogenizing device BioMasher and a sensitive ELISA to detect bovine spongiform encephalopathy accurately in brain tissue","volume":"149","author":"Yamamoto","year":"2008","journal-title":"J. Virol. Methods"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2568","DOI":"10.1002\/pmic.201400454","article-title":"Unrestricted modification search reveals lysine methylation as major modification induced by tissue formalin fixation and paraffin embedding","volume":"15","author":"Zhang","year":"2015","journal-title":"Proteomics"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1988","DOI":"10.1074\/mcp.M800518-MCP200","article-title":"Equivalence of Protein Inventories Obtained from Formalin-fixed Paraffin-embedded and Frozen Tissue in Multidimensional Liquid Chromatography-Tandem Mass Spectrometry Shotgun Proteomic Analysis","volume":"8","author":"Sprung","year":"2009","journal-title":"Mol. Cell. Proteom."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1002\/path.5420","article-title":"A streamlined mass spectrometry\u2013based proteomics workflow for large-scale FFPE tissue analysis","volume":"251","author":"Coscia","year":"2020","journal-title":"J. Pathol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1021\/bc050340f","article-title":"Identification of Formaldehyde-Induced Modifications in Proteins:\u2009 Reactions with Insulin","volume":"17","author":"Metz","year":"2006","journal-title":"Bioconjugate Chem."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1369\/jhc.5B6851.2006","article-title":"Protein extraction from formalin-fixed, paraffin-embedded tissue sections: Quality evaluation by mass spectrometry","volume":"54","author":"Shi","year":"2006","journal-title":"J. Histochem. Cytochem."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"5422","DOI":"10.1021\/pr100656u","article-title":"A quantitative study of the effects of chaotropic agents, surfactants, and solvents on the digestion efficiency of human plasma proteins by trypsin","volume":"9","author":"Proc","year":"2010","journal-title":"J. Proteome Res."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"3321","DOI":"10.1002\/jssc.201400569","article-title":"Improvement of a sample preparation method assisted by sodium deoxycholate for mass-spectrometry-based shotgun membrane proteomics","volume":"37","author":"Lin","year":"2014","journal-title":"J. Sep. Sci."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1885","DOI":"10.1021\/pr4010019","article-title":"Enhanced FASP (eFASP) to increase proteome coverage and sample recovery for quantitative proteomic experiments","volume":"13","author":"Erde","year":"2014","journal-title":"J. Proteome Res."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1038\/nmeth.1322","article-title":"Universal sample preparation method for proteome analysis","volume":"6","author":"Wisniewski","year":"2009","journal-title":"Nat. Methods"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1742","DOI":"10.1002\/pmic.200401063","article-title":"Sample preparation and digestion for proteomic analyses using spin filters","volume":"5","author":"Manza","year":"2005","journal-title":"Proteomics"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1074\/mcp.TIR118.001270","article-title":"Protein aggregation capture on microparticles enables multi-purpose proteomics sample preparation","volume":"18","author":"Batth","year":"2019","journal-title":"Mol. Cell. Proteom."},{"key":"ref_40","unstructured":"Wilson, J., Mayyappan, V., Narducci, D.N., Neely, B., Laugharn, J., and Pappin, D. (2021, August 11). Universal Sample Processing of Multiple Sample Types for Reproducible Proteomic Sample Preparation. HUPO, Available online: https:\/\/cdn.shopify.com\/s\/files\/1\/0271\/1964\/8832\/files\/HUPO-ProtiFi-Covaris-poster-final.pdf."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"e9111","DOI":"10.15252\/msb.20199111","article-title":"Automated sample preparation with SP3 for low-input clinical proteomics","volume":"16","author":"Kalxdorf","year":"2020","journal-title":"Mol. Syst. Biol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1074\/mcp.RA117.000189","article-title":"Spatial tissue proteomics quantifies inter- and intra-tumor heterogeneity in hepatocellular carcinoma","volume":"17","author":"Buczak","year":"2018","journal-title":"Mol. Cell. Proteom."},{"key":"ref_43","unstructured":"Schweizer, L., Coscia, F., M\u00fcller, J., Doll, S., Wierer, M., and Mann, M. (2021, August 11). AFA-sonication Followed by Modified Protein Aggregation Capture (APAC) Enables Direct, Reproducible and Non-toxic Sample Preparation of FFPE Tissue for Mass Spectrometrybased Proteomics. Covaris Appl. Note-M020141, Available online: https:\/\/d24ci5y4j5ezt1.cloudfront.net\/wp\/wp-content\/uploads\/2020\/06\/M020141.pdf."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/s41596-018-0082-x","article-title":"Single-pot, solid-phase-enhanced sample preparation for proteomics experiments","volume":"14","author":"Hughes","year":"2019","journal-title":"Nat. Protoc."},{"key":"ref_45","unstructured":"Stoychev, S., Govender, I., Naicker, P., Gerber, I., Jordaan, J., Pauw, M., Tabb, D., Arribas Diez, I., Norregaard Jensen, O., and Baath, T. (2021, August 11). Development of a fully automated high throughput magnetic workflow for phosphoproteome profiling. HUPO, Available online: https:\/\/resynbio.com\/wp-content\/uploads\/2020\/01\/HUPO_2019_Poster_SS_Phos_coupled_clean-up.pdf."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"10296","DOI":"10.1021\/ac5025842","article-title":"Reproducible automated phosphopeptide enrichment using magnetic TiO2 and Ti-IMAC","volume":"86","author":"Tape","year":"2014","journal-title":"Anal. Chem."},{"key":"ref_47","unstructured":"Mart\u00ednez-Val, A., Bekker-Jensen, D.B., Steigerwald, S., Stoychev, S., Gerber, I., Jordaan, J., Bache, N., and Olsen, J.V. (2021, August 11). Fast and reproducible phosphoproteomics using MagReSyn Amine and Ti-IMAC HP magnetic beads and the Evosep One. Tech. Note, Available online: https:\/\/www.evosep.com\/wp-content\/uploads\/2020\/03\/Phospho-app-note-Evosep-Resyn-A5layout-v5-lores.pdf."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"e9021","DOI":"10.15252\/msb.20199021","article-title":"R2-P2 rapid-robotic phosphoproteomics enables multidimensional cell signaling studies","volume":"15","author":"Leutert","year":"2019","journal-title":"Mol. Syst. Biol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"12648","DOI":"10.1038\/s41598-018-31154-6","article-title":"Instant Clue: A Software Suite for Interactive Data Visualization and Analysis","volume":"8","author":"Nolte","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_50","unstructured":"(2022, February 23). The Human Proteome Atlas. Available online: https:\/\/www.proteinatlas.org."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1021\/acs.jproteome.9b00686","article-title":"HYPERsol: High-Quality Data from Archival FFPE Tissue for Clinical Proteomics","volume":"19","author":"Marchione","year":"2020","journal-title":"J. Proteome Res."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"4060","DOI":"10.1021\/acs.jproteome.7b00433","article-title":"Evaluation of FASP, SP3, and iST Protocols for Proteomic Sample Preparation in the Low Microgram Range","volume":"16","author":"Sielaff","year":"2017","journal-title":"J. Proteome Res."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.aca.2019.08.032","article-title":"Filter Aided Sample Preparation\u2014A tutorial","volume":"1090","year":"2019","journal-title":"Anal. Chim. Acta"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"98","DOI":"10.3390\/microarrays4020098","article-title":"Reverse Phase Protein Arrays-Quantitative Assessment of Multiple Biomarkers in Biopsies for Clinical Use","volume":"4","author":"Boellner","year":"2015","journal-title":"Microarrays"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"826","DOI":"10.1074\/mcp.TIR117.000302","article-title":"Simple, scalable, and ultrasensitive tip-based identification of protease substrates","volume":"17","author":"Shema","year":"2018","journal-title":"Mol. Cell. Proteom."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"941","DOI":"10.1002\/pmic.201200452","article-title":"Protein carbamylation: In vivo modification or in vitro artefact?","volume":"13","author":"Kollipara","year":"2013","journal-title":"Proteomics"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1186\/1559-0275-11-28","article-title":"Critical comparison of sample preparation strategies for shotgun proteomic analysis of formalin-fixed, paraffin-embedded samples: Insights from liver tissue","volume":"11","author":"Tanca","year":"2014","journal-title":"Clin. Proteom."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1038\/nbt.2839","article-title":"ProteomeXchange provides globally coordinated proteomics data submission and dissemination","volume":"32","author":"Vizcaino","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"10816","DOI":"10.1021\/acs.analchem.1c00975","article-title":"Precise quantitation of PTEN by immuno-MRM: A tool to resolve the breast cancer biomarker controversy","volume":"93","author":"Ibrahim","year":"2021","journal-title":"Anal. 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