MassIVEapplication/xmlftp://massive-ftp.ucsd.edu/v03/MSV000086411/primaryOK2000000Prof Mark S. Bakerhttps://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=2735badb90d14d00bf0d3e9272d0a397mark.baker@mq.edu.auMassIVE153MS:1002864 - No post-translational-modifications are included in the identified peptides of this datasetProteomicsTripleTOF 6600Homo Sapiens (ncbitaxon:9606)Macquarie UniversityCredible detection and quantification of low abundance proteins from human blood plasma is a major challenge in precision medicine biomarker discovery when using mass spectrometry (MS). In this proof-of-concept study, we employed a mixture of selected recombinant proteins in DDA libraries to subsequently identify (not quantify) cancer-associated low abundance plasma proteins using SWATH/DIA. The exemplar DDA recombinant protein spectral library (rPSL) was derived from tryptic digestion of 36 recombinant human proteins that had been previously implicated as possible cancer biomarkers from both our own and other studies. The rPSL was then used to identify proteins from nondepleted colorectal cancer (CRC) EDTA plasmas by SWATH-MS. Most (32/36) of the proteins used in the rPSL were reliably identified from CRC plasma samples, including 8 proteins (i.e., BTC, CXCL10, IL1B, IL6, ITGB6, TGFα, TNF, TP53) not previously detected using high-stringency protein inference MS according to PeptideAtlas. The rPSL SWATH-MS protocol was compared to DDA-MS using MARS-depleted and postdigestion peptide fractionated plasmas (here referred to as a human plasma DDA library). Of the 32 proteins identified using rPSL SWATH, only 12 could be identified using DDA-MS. The 20 additional proteins exclusively identified using the rPSL SWATH approach were almost exclusively lower abundance (i.e., <10 ng/mL) proteins. To mitigate justified FDR concerns, and to replicate a more typical library creation approach, the DDA rPSL library was merged with a human plasma DDA library and SWATH identification repeated using such a merged library. The majority (33/36) of the low abundance plasma proteins added from the rPSL were still able to be identified using such a merged library when high-stringency HPP Guidelines v3.0 protein inference criteria were applied to our data set. The MS data set has been deposited to ProteomeXchange Consortium via the PRIDE partner repository (PXD022361).Use of a Recombinant Biomarker Protein DDA Library Increases DIA Coverage of Low Abundance Plasma Proteins.Ahn Seong Beom SB, Kamath Karthik S KS, Mohamedali Abidali A, Noor Zainab Z, Wu Jemma X JX, Pascovici Dana D, Adhikari Subash S, Cheruku Harish R HR, Guillemin Gilles J GJ, McKay Matthew J MJ, Nice Edouard C EC, Baker Mark S MSPlasma, Fresh, Fresh Frozen Plasmas, Fresh Frozen, Blood Plasma, me75, Frozen Plasma, human being, cou, Man (Taxonomy), Fresh Frozen Plasma, Protein., Blood, Modern, Proteins, portion of plasma, Gene, Tl3, Tl2, Plasmas, D17Mit170, T1, human, Human, Protein Gene Products, Frozen Plasmas, Gene Proteins, Lr, Homo sapiens, Modern Man, Blood Plasmas, Protein, Bra, Gene Products, Low, Library, Man, plasma, humansPlasma, Fresh, Fresh Frozen Plasmas, Fresh Frozen, Blood Plasma, me75, Frozen Plasma, human being, cou, Man (Taxonomy), Fresh Frozen Plasma, 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Differentiation Inducing Protein, CG1768, Peptide, Xp53, tnfsf2, natural protein, Protein, MLPLI, Dias, Disodium Ethylene, DDA, B-Cell Differentiation Factor-2, Plasma, large bowel cancer, Mass Spectrum, Cancer Biomarkers, IFN-beta 2, Serum Marker, Tumor Metabolite Marker, Chelaton 3, Dihydrate, hereditary pyropoikilocytosis, portion of plasma, Disodium, Surrogate Marker, Protein Gene Products, DmelCG9429, Deimos, Hybridoma, Modulator of antigen receptor signaling, Modern Man, Egr, P Health, Peptid, Chromium, Tnfsf1a0PXD022361falseRecombinant SWATH library for identification of low abundant human plasma proteinsRecombinant SWATH library for identification of low abundant human plasma proteinsWed Nov 04 21:18:00 GMT 2020MSV00008641133752330