{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T13:45:49Z","timestamp":1792590349398,"version":"4.5.0"},"reference-count":27,"publisher":"MyJove Corporation","issue":"229","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JoVE"],"DOI":"10.3791\/69359","type":"journal-article","created":{"date-parts":[[2026,3,13]],"date-time":"2026-03-13T23:01:30Z","timestamp":1773442890000},"source":"Crossref","is-referenced-by-count":0,"title":["A Comprehensive Workflow for Plasma Proteomics by Mass Spectrometry: A Strategy for Biomarker Discovery in Systemic Human Diseases"],"prefix":"10.3791","author":[{"given":"Vanditha","family":"M","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonu","family":"Das","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evelyn","family":"Maria","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arya","family":"J","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sooraj","family":"Krishna U","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mathew","family":"John","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2098","published-online":{"date-parts":[[2026,3,13]]},"reference":[{"issue":"1","key":"ref1","doi-asserted-by":"crossref","first-page":"3662","DOI":"10.1038\/s41467-020-17033-7","type":"journal-article","article-title":"deep and precise profiling of the plasma proteome with multi-nanoparticle protein corona","volume":"11","author":"Blume","year":"2020","unstructured":"Blume, J. E. et al. Rapid, deep and precise profiling of the plasma proteome with multi-nanoparticle protein corona. Nat Commun. 11 (1), 3662 (2020).","journal-title":"Nat Commun"},{"issue":"2","key":"ref2","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1373\/clinchem.2009.126706","type":"journal-article","article-title":"The clinical plasma proteome: a survey of clinical assays for proteins in plasma and serum","volume":"56","author":"Anderson","year":"2010","unstructured":"Anderson, N. L. The clinical plasma proteome: a survey of clinical assays for proteins in plasma and serum. Clin Chem. 56 (2), 177-185 (2010).","journal-title":"Clin Chem"},{"issue":"6","key":"ref3","doi-asserted-by":"crossref","first-page":"2244","DOI":"10.1016\/j.chest.2021.01.004","type":"journal-article","article-title":"Protein biomarkers for COPD outcomes","volume":"159","author":"Serban","year":"2021","unstructured":"Serban, K. A., Pratte, K. A., Bowler, R. P. Protein biomarkers for COPD outcomes. Chest. 159 (6), 2244-2253 (2021).","journal-title":"Chest"},{"issue":"12","key":"ref4","doi-asserted-by":"crossref","first-page":"4085","DOI":"10.1021\/acs.jproteome.9b00503","type":"journal-article","article-title":"Mass spectrometry-based plasma proteomics: considerations from sample collection to achieving translational data","volume":"18","author":"Ignjatovic","year":"2019","unstructured":"Ignjatovic, V. et al. Mass spectrometry-based plasma proteomics: considerations from sample collection to achieving translational data. J Proteome Res. 18 (12), 4085-4097 (2019).","journal-title":"J Proteome Res"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1038086","DOI":"10.3389\/fimmu.2022.1038086","type":"journal-article","article-title":"Plasma proteomics reveals early, broad release of chemokine, cytokine, TNF, and interferon mediators following trauma with delayed increases in a subset of chemokines and cytokines in patients that remain critically ill","volume":"13","author":"Bonaroti","year":"2022","unstructured":"Bonaroti, J. et al. Plasma proteomics reveals early, broad release of chemokine, cytokine, TNF, and interferon mediators following trauma with delayed increases in a subset of chemokines and cytokines in patients that remain critically ill. Front Immunol. 13, 1038086 (2022).","journal-title":"Front Immunol"},{"issue":"13","key":"ref6","doi-asserted-by":"crossref","first-page":"3226","DOI":"10.1002\/pmic.200500358","type":"journal-article","article-title":"Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database","volume":"5","author":"Omenn","year":"2005","unstructured":"Omenn, G. S. et al. Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics. 5 (13), 3226-3245 (2005).","journal-title":"Proteomics"},{"issue":"10","key":"ref7","doi-asserted-by":"crossref","first-page":"1108","DOI":"10.1158\/2159-8290.CD-13-0219","type":"journal-article","article-title":"Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium","volume":"3","author":"Ellis","year":"2013","unstructured":"Ellis, M. J. et al. Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium. Cancer Discov. 3 (10), 1108-1112 (2013).","journal-title":"Cancer Discov"},{"issue":"11","key":"ref8","doi-asserted-by":"crossref","first-page":"e10427","DOI":"10.15252\/emmm.201910427","type":"journal-article","article-title":"Plasma proteome profiling to detect and avoid sample-related biases in biomarker studies","volume":"11","author":"Geyer","year":"2019","unstructured":"Geyer, P. E. et al. Plasma proteome profiling to detect and avoid sample-related biases in biomarker studies. EMBO Mol Med. 11 (11), e10427 (2019).","journal-title":"EMBO Mol Med"},{"issue":"7","key":"ref9","doi-asserted-by":"crossref","first-page":"6129","DOI":"10.3390\/ijms24076129","type":"journal-article","article-title":"A standardized protocol for assuring the validity of proteomics results from liquid chromatography-high-resolution mass spectrometry","volume":"24","author":"Gawor","year":"2023","unstructured":"Gawor, A., Bulska, E. A standardized protocol for assuring the validity of proteomics results from liquid chromatography-high-resolution mass spectrometry. Int J Mol Sci. 24 (7), 6129 (2023).","journal-title":"Int J Mol Sci"},{"issue":"10","key":"ref10","doi-asserted-by":"crossref","first-page":"4392","DOI":"10.1021\/acs.jproteome.4c00363","type":"journal-article","article-title":"A framework for quality control in quantitative proteomics","volume":"23","author":"Tsantilas","year":"2024","unstructured":"Tsantilas, K. A. et al. A framework for quality control in quantitative proteomics. J Proteome Res. 23 (10), 4392-4408 (2024).","journal-title":"J Proteome Res"},{"issue":"1","key":"ref11","doi-asserted-by":"crossref","first-page":"10261","DOI":"10.1038\/ncomms10261","type":"journal-article","article-title":"Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics","volume":"7","author":"Malmstr\u00f6m","year":"2016","unstructured":"Malmstr\u00f6m, E. et al. Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics. Nat Commun. 7 (1), 10261 (2016).","journal-title":"Nat Commun"},{"issue":"6","key":"ref12","doi-asserted-by":"crossref","DOI":"10.1074\/mcp.O111.016717","type":"journal-article","article-title":"Targeted data extraction of the MS\/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis","volume":"11","author":"Gillet","year":"2012","unstructured":"Gillet, L. C. et al. Targeted data extraction of the MS\/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics. 11 (6), O111-016717 (2012).","journal-title":"Mol Cell Proteomics"},{"issue":"11","key":"ref13","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1074\/mcp.R200007-MCP200","type":"journal-article","article-title":"The human plasma proteome: history, character, and diagnostic prospects","volume":"1","author":"Anderson","year":"2002","unstructured":"Anderson, N. L., Anderson, N. G. The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics. 1 (11), 845-867 (2002).","journal-title":"Mol Cell Proteomics"},{"issue":"1","key":"ref14","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/s12014-024-09459-8","type":"journal-article","article-title":"Exploring the novel duo of Reticulocalbin and Sideroflexin as future biomarker candidates for exacerbated chronic obstructive pulmonary disease","volume":"21","author":"Das","year":"2024","unstructured":"Das, S., Adiody, S., Varghese, J., Vanditha, M., Maria, E., John, M. Exploring the novel duo of Reticulocalbin and Sideroflexin as future biomarker candidates for exacerbated chronic obstructive pulmonary disease. Clin Proteomics. 21 (1), 10 (2024).","journal-title":"Clin Proteomics"},{"issue":"3","key":"ref15","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.1021\/acs.jproteome.4c01054","type":"journal-article","article-title":"Myosin Light Chain 12b and MASP1 as novel biomarker candidates in active juvenile idiopathic arthritis\u2500a combined proteomics\/bioinformatics approach","volume":"24","author":"Mohan","year":"2025","unstructured":"Mohan, V. et al. Myosin Light Chain 12b and MASP1 as novel biomarker candidates in active juvenile idiopathic arthritis\u2500a combined proteomics\/bioinformatics approach. J Proteome Res. 24 (3), 1439-1448 (2025).","journal-title":"J Proteome Res"},{"issue":"1","key":"ref16","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1007\/s00726-010-0628-x","type":"journal-article","article-title":"High-abundance proteins depletion for serum proteomic analysis: concomitant removal of non-targeted proteins","volume":"40","author":"Bellei","year":"2011","unstructured":"Bellei, E. et al. High-abundance proteins depletion for serum proteomic analysis: concomitant removal of non-targeted proteins. Amino Acids. 40 (1), 145-156 (2011).","journal-title":"Amino Acids"},{"issue":"10","key":"ref17","doi-asserted-by":"crossref","first-page":"4982","DOI":"10.1021\/pr100646w","type":"journal-article","article-title":"Depletion of abundant plasma proteins and limitations of plasma proteomics","volume":"9","author":"Tu","year":"2010","unstructured":"Tu, C. et al. Depletion of abundant plasma proteins and limitations of plasma proteomics. J Proteome Res. 9 (10), 4982-4991 (2010).","journal-title":"J Proteome Res"},{"issue":"13","key":"ref18","doi-asserted-by":"crossref","first-page":"3304","DOI":"10.1002\/pmic.200402021","type":"journal-article","article-title":"Differences among techniques for high-abundant protein depletion","volume":"5","author":"Zolotarjova","year":"2005","unstructured":"Zolotarjova, N. et al. Differences among techniques for high-abundant protein depletion. Proteomics. 5 (13), 3304-3313 (2005).","journal-title":"Proteomics"},{"issue":"2","key":"ref19","doi-asserted-by":"crossref","first-page":"1126","DOI":"10.1021\/ac202817q","type":"journal-article","article-title":"Multiplexed cancer biomarker detection using quartz-based photonic crystal surfaces","volume":"84","author":"Huang","year":"2012","unstructured":"Huang, C. S. et al. Multiplexed cancer biomarker detection using quartz-based photonic crystal surfaces. Anal Chem. 84 (2), 1126-1133 (2012).","journal-title":"Anal Chem"},{"issue":"1-2","key":"ref20","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/j.chroma.2007.01.045","type":"journal-article","article-title":"Trends in sample preparation for classical and second-generation proteomics","volume":"1153","author":"Ca\u00f1as","year":"2007","unstructured":"Ca\u00f1as, B. et al. Trends in sample preparation for classical and second-generation proteomics. J Chromatogr A. 1153 (1-2), 235-258 (2007).","journal-title":"J Chromatogr A"},{"issue":"25","key":"ref21","doi-asserted-by":"crossref","first-page":"9040","DOI":"10.1021\/acs.analchem.2c01118","type":"journal-article","article-title":"Benefits of ion mobility separation in GC-APCI-HRMS screening: from the construction of a CCS library to the application to real-world samples","volume":"94","author":"Izquierdo-Sandoval","year":"2022","unstructured":"Izquierdo-Sandoval, D. et al. Benefits of ion mobility separation in GC-APCI-HRMS screening: from the construction of a CCS library to the application to real-world samples. Anal Chem. 94 (25), 9040-9047 (2022).","journal-title":"Anal Chem"},{"issue":"1","key":"ref22","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1186\/s13195-021-00907-3","type":"journal-article","article-title":"Meta-analysis of cerebrospinal fluid neuron-specific enolase levels in Alzheimer's disease, Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy","volume":"13","author":"Katayama","year":"2021","unstructured":"Katayama, T., Sawada, J., Takahashi, K., Yahara, O., Hasebe, N. Meta-analysis of cerebrospinal fluid neuron-specific enolase levels in Alzheimer's disease, Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy. Alzheimers Res Ther. 13 (1), 163 (2021).","journal-title":"Alzheimers Res Ther"},{"issue":"1","key":"ref23","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/s12014-024-09497-2","type":"journal-article","article-title":"Frontiers in plasma proteome profiling platforms: innovations and applications","volume":"21","author":"Soni","year":"2024","unstructured":"Soni, R. K. Frontiers in plasma proteome profiling platforms: innovations and applications. Clin Proteomics. 21 (1), 43 (2024).","journal-title":"Clin Proteomics"},{"issue":"5","key":"ref24","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1016\/j.nbt.2011.11.016","type":"journal-article","article-title":"Advances in human proteomics at high scale with the SOMAscan proteomics platform","volume":"29","author":"Gold","year":"2012","unstructured":"Gold, L., Walker, J. J., Wilcox, S. K., Williams, S. Advances in human proteomics at high scale with the SOMAscan proteomics platform. New Biotechnol. 29 (5), 543-549 (2012).","journal-title":"New Biotechnol"},{"issue":"4","key":"ref25","doi-asserted-by":"crossref","first-page":"e95192","DOI":"10.1371\/journal.pone.0095192","type":"journal-article","article-title":"Homogenous 96-plex PEA immunoassay exhibiting high sensitivity, specificity, and excellent scalability","volume":"9","author":"Assarsson","year":"2014","unstructured":"Assarsson, E. et al. Homogenous 96-plex PEA immunoassay exhibiting high sensitivity, specificity, and excellent scalability. PLoS One. 9 (4), e95192 (2014).","journal-title":"PLoS One"},{"issue":"10","key":"ref26","first-page":"100947","type":"journal-article","article-title":"Advances, obstacles, and opportunities for machine learning in proteomics","volume":"3","author":"Desaire","year":"2022","unstructured":"Desaire, H., Go, E. P., Hua, D. Advances, obstacles, and opportunities for machine learning in proteomics. Cell Rep Phys Sci. 3 (10), 100947 (2022).","journal-title":"Cell Rep Phys Sci"},{"key":"ref27","first-page":"26","type":"journal-article","article-title":"Integrative machine learning approaches for multi-omics data analysis in cancer research","volume":"1","author":"Shoaib","year":"2024","unstructured":"Shoaib, A. S., Nishat, N., Raasetti, M., Arif, I. Integrative machine learning approaches for multi-omics data analysis in cancer research. Int J Health Med. 1, 26 (2024).","journal-title":"Int J Health Med"}],"container-title":["Journal of Visualized Experiments"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/app.jove.com\/t\/69359\/a-comprehensive-workflow-for-plasma-proteomics-mass-spectrometry","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T13:16:21Z","timestamp":1792588581000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.jove.com\/t\/69359\/a-comprehensive-workflow-for-plasma-proteomics-mass-spectrometry"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,13]]},"references-count":27,"journal-issue":{"issue":"229","published-online":{"date-parts":[[2026]]}},"URL":"https:\/\/doi.org\/10.3791\/69359","relation":{},"ISSN":["1940-087X"],"issn-type":[{"value":"1940-087X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,13]]}}}