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For: Collins BC, Hunter CL, Liu Y, Schilling B, Rosenberger G, Bader SL, Chan DW, Gibson BW, Gingras AC, Held JM, Hirayama-Kurogi M, Hou G, Krisp C, Larsen B, Lin L, Liu S, Molloy MP, Moritz RL, Ohtsuki S, Schlapbach R, Selevsek N, Thomas SN, Tzeng SC, Zhang H, Aebersold R. Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry. Nat Commun 2017;8:291. [PMID: 28827567 PMCID: PMC5566333 DOI: 10.1038/s41467-017-00249-5] [Citation(s) in RCA: 367] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/12/2017] [Indexed: 01/15/2023]  Open
Number Cited by Other Article(s)
301
Omics in CF – Where are we now? J Cyst Fibros 2019;18:443-444. [DOI: 10.1016/j.jcf.2019.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
302
Mehnert M, Li W, Wu C, Salovska B, Liu Y. Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1. Proteomics 2019;19:e1800438. [PMID: 30901150 DOI: 10.1002/pmic.201800438] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/24/2019] [Indexed: 12/21/2022]
303
Sun Z, Chang HM, Wang A, Song J, Zhang X, Guo J, Leung PCK, Lian F. Identification of potential metabolic biomarkers of polycystic ovary syndrome in follicular fluid by SWATH mass spectrometry. Reprod Biol Endocrinol 2019;17:45. [PMID: 31186025 PMCID: PMC6560878 DOI: 10.1186/s12958-019-0490-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/04/2019] [Indexed: 01/29/2023]  Open
304
Kadokami K, Ueno D. Comprehensive Target Analysis for 484 Organic Micropollutants in Environmental Waters by the Combination of Tandem Solid-Phase Extraction and Quadrupole Time-of-Flight Mass Spectrometry with Sequential Window Acquisition of All Theoretical Fragment-Ion Spectra Acquisition. Anal Chem 2019;91:7749-7755. [PMID: 31132244 DOI: 10.1021/acs.analchem.9b01141] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
305
Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins. Nat Commun 2019;10:2524. [PMID: 31175306 PMCID: PMC6555818 DOI: 10.1038/s41467-019-10513-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/16/2019] [Indexed: 01/18/2023]  Open
306
He Y, Mohamedali A, Huang C, Baker MS, Nice EC. Oncoproteomics: Current status and future opportunities. Clin Chim Acta 2019;495:611-624. [PMID: 31176645 DOI: 10.1016/j.cca.2019.06.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/05/2019] [Accepted: 06/05/2019] [Indexed: 02/07/2023]
307
Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews P, Bernfur K, Borchers C, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis T, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez C, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kukačka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Ferreira AGC, Ninnis R, Novák P, O’Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A. First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study. Anal Chem 2019;91:6953-6961. [PMID: 31045356 PMCID: PMC6625963 DOI: 10.1021/acs.analchem.9b00658] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
308
Carne NA, Bell S, Brown AP, Määttä A, Flagler MJ, Benham AM. Reductive Stress Selectively Disrupts Collagen Homeostasis and Modifies Growth Factor-independent Signaling Through the MAPK/Akt Pathway in Human Dermal Fibroblasts. Mol Cell Proteomics 2019;18:1123-1137. [PMID: 30890563 PMCID: PMC6553930 DOI: 10.1074/mcp.ra118.001140] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 03/15/2019] [Indexed: 01/03/2023]  Open
309
Giudice G, Petsalaki E. Proteomics and phosphoproteomics in precision medicine: applications and challenges. Brief Bioinform 2019;20:767-777. [PMID: 29077858 PMCID: PMC6585152 DOI: 10.1093/bib/bbx141] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 09/21/2017] [Indexed: 12/11/2022]  Open
310
Wang G, Meyer JG, Cai W, Softic S, Li ME, Verdin E, Newgard C, Schilling B, Kahn CR. Regulation of UCP1 and Mitochondrial Metabolism in Brown Adipose Tissue by Reversible Succinylation. Mol Cell 2019;74:844-857.e7. [PMID: 31000437 PMCID: PMC6525068 DOI: 10.1016/j.molcel.2019.03.021] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 02/06/2019] [Accepted: 03/20/2019] [Indexed: 11/23/2022]
311
A new class of protein biomarkers based on subcellular distribution: application to a mouse liver cancer model. Sci Rep 2019;9:6913. [PMID: 31061415 PMCID: PMC6502816 DOI: 10.1038/s41598-019-43091-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/15/2019] [Indexed: 12/18/2022]  Open
312
Vincent RM, Wright BW, Jaschke PR. Measuring Amber Initiator tRNA Orthogonality in a Genomically Recoded Organism. ACS Synth Biol 2019;8:675-685. [PMID: 30856316 DOI: 10.1021/acssynbio.9b00021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
313
DeLaney K, Li L. Data Independent Acquisition Mass Spectrometry Method for Improved Neuropeptidomic Coverage in Crustacean Neural Tissue Extracts. Anal Chem 2019;91:5150-5158. [PMID: 30888792 PMCID: PMC6481171 DOI: 10.1021/acs.analchem.8b05734] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
314
Masuda T, Hoshiyama T, Uemura T, Hirayama-Kurogi M, Ogata S, Furukawa A, Couraud PO, Furihata T, Ito S, Ohtsuki S. Large-Scale Quantitative Comparison of Plasma Transmembrane Proteins between Two Human Blood–Brain Barrier Model Cell Lines, hCMEC/D3 and HBMEC/ciβ. Mol Pharm 2019;16:2162-2171. [DOI: 10.1021/acs.molpharmaceut.9b00114] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
315
Global Lysine Acetylation in Escherichia coli Results from Growth Conditions That Favor Acetate Fermentation. J Bacteriol 2019;201:JB.00768-18. [PMID: 30782634 DOI: 10.1128/jb.00768-18] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 02/11/2019] [Indexed: 01/17/2023]  Open
316
Grabowski P, Hesse S, Hollizeck S, Rohlfs M, Behrends U, Sherkat R, Tamary H, Ünal E, Somech R, Patıroğlu T, Canzar S, van der Werff Ten Bosch J, Klein C, Rappsilber J. Proteome Analysis of Human Neutrophil Granulocytes From Patients With Monogenic Disease Using Data-independent Acquisition. Mol Cell Proteomics 2019;18:760-772. [PMID: 30630937 PMCID: PMC6442368 DOI: 10.1074/mcp.ra118.001141] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/14/2018] [Indexed: 11/06/2022]  Open
317
Label-free absolute protein quantification with data-independent acquisition. J Proteomics 2019;200:51-59. [PMID: 30880166 DOI: 10.1016/j.jprot.2019.03.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/19/2019] [Accepted: 03/06/2019] [Indexed: 02/05/2023]
318
Tong Y, Ku X, Wu C, Liu J, Yang C, Tang W, Yan W, Tang J. Data-independent acquisition-based quantitative proteomic analysis reveals differences in host immune response of peripheral blood mononuclear cells to sepsis. Scand J Immunol 2019;89:e12748. [PMID: 30667541 DOI: 10.1111/sji.12748] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 12/24/2018] [Accepted: 01/08/2019] [Indexed: 01/19/2023]
319
Chen Y, Vu J, Thompson MG, Sharpless WA, Chan LJG, Gin JW, Keasling JD, Adams PD, Petzold CJ. A rapid methods development workflow for high-throughput quantitative proteomic applications. PLoS One 2019;14:e0211582. [PMID: 30763335 PMCID: PMC6375547 DOI: 10.1371/journal.pone.0211582] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/16/2019] [Indexed: 12/13/2022]  Open
320
Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins. Sci Data 2019;6:190011. [PMID: 30747917 PMCID: PMC6371892 DOI: 10.1038/sdata.2019.11] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/17/2018] [Indexed: 12/12/2022]  Open
321
Murphy S, Dowling P, Zweyer M, Swandulla D, Ohlendieck K. Proteomic profiling of giant skeletal muscle proteins. Expert Rev Proteomics 2019;16:241-256. [DOI: 10.1080/14789450.2019.1575205] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
322
Wu W, Dai RT, Bendixen E. Comparing SRM and SWATH Methods for Quantitation of Bovine Muscle Proteomes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019;67:1608-1618. [PMID: 30624930 DOI: 10.1021/acs.jafc.8b05459] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
323
Rice SJ, Liu X, Zhang J, Belani CP. Absolute Quantification of All Identified Plasma Proteins from SWATH Data for Biomarker Discovery. Proteomics 2019;19:e1800135. [DOI: 10.1002/pmic.201800135] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 09/27/2018] [Indexed: 02/05/2023]
324
Heusel M, Bludau I, Rosenberger G, Hafen R, Frank M, Banaei-Esfahani A, van Drogen A, Collins BC, Gstaiger M, Aebersold R. Complex-centric proteome profiling by SEC-SWATH-MS. Mol Syst Biol 2019;15:e8438. [PMID: 30642884 PMCID: PMC6346213 DOI: 10.15252/msb.20188438] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]  Open
325
Anania VG, Yu K, Pingitore F, Li Q, Rose CM, Liu P, Sandoval W, Herman AE, Lill JR, Mathews WR. Discovery and Qualification of Candidate Urinary Biomarkers of Disease Activity in Lupus Nephritis. J Proteome Res 2019;18:1264-1277. [PMID: 30525646 DOI: 10.1021/acs.jproteome.8b00874] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
326
Orlando E, Aebersold R. On the contribution of mass spectrometry-based platforms to the field of personalized oncology. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
327
O'Neill JR. An Overview of Mass Spectrometry-Based Methods for Functional Proteomics. Methods Mol Biol 2019;1871:179-196. [PMID: 30276741 DOI: 10.1007/978-1-4939-8814-3_13] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
328
Fulton KM, Baltat I, Twine SM. Immunoproteomics Methods and Techniques. Methods Mol Biol 2019;2024:25-58. [PMID: 31364041 DOI: 10.1007/978-1-4939-9597-4_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
329
Muntel J, Gandhi T, Verbeke L, Bernhardt OM, Treiber T, Bruderer R, Reiter L. Surpassing 10 000 identified and quantified proteins in a single run by optimizing current LC-MS instrumentation and data analysis strategy. Mol Omics 2019;15:348-360. [DOI: 10.1039/c9mo00082h] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
330
Yang Y, Zeng B, Sun Z, Esfahani AM, Hou J, Jiao ND, Liu L, Chen L, Basson MD, Dong L, Yang R, Xi N. Optimization of Protein-Protein Interaction Measurements for Drug Discovery Using AFM Force Spectroscopy. IEEE TRANSACTIONS ON NANOTECHNOLOGY 2019;18:509-517. [PMID: 32051682 PMCID: PMC7015265 DOI: 10.1109/tnano.2019.2915507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
331
Temporal dynamics of liver mitochondrial protein acetylation and succinylation and metabolites due to high fat diet and/or excess glucose or fructose. PLoS One 2018;13:e0208973. [PMID: 30586434 PMCID: PMC6306174 DOI: 10.1371/journal.pone.0208973] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 11/28/2018] [Indexed: 12/11/2022]  Open
332
Reubsaet L, Sweredoski MJ, Moradian A. Data-Independent Acquisition for the Orbitrap Q Exactive HF: A Tutorial. J Proteome Res 2018;18:803-813. [DOI: 10.1021/acs.jproteome.8b00845] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
333
Kim YJ, Sweet SMM, Egertson JD, Sedgewick AJ, Woo S, Liao WL, Merrihew GE, Searle BC, Vaske C, Heaton R, MacCoss MJ, Hembrough T. Data-Independent Acquisition Mass Spectrometry To Quantify Protein Levels in FFPE Tumor Biopsies for Molecular Diagnostics. J Proteome Res 2018;18:426-435. [PMID: 30481034 DOI: 10.1021/acs.jproteome.8b00699] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
334
Lucas N, Robinson AB, Marcker Espersen M, Mahboob S, Xavier D, Xue J, Balleine RL, deFazio A, Hains PG, Robinson PJ. Accelerated Barocycler Lysis and Extraction Sample Preparation for Clinical Proteomics by Mass Spectrometry. J Proteome Res 2018;18:399-405. [DOI: 10.1021/acs.jproteome.8b00684] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
335
Cominetti O, Núñez Galindo A, Corthésy J, Valsesia A, Irincheeva I, Kussmann M, Saris WHM, Astrup A, McPherson R, Harper ME, Dent R, Hager J, Dayon L. Obesity shows preserved plasma proteome in large independent clinical cohorts. Sci Rep 2018;8:16981. [PMID: 30451909 PMCID: PMC6242904 DOI: 10.1038/s41598-018-35321-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/02/2018] [Indexed: 12/21/2022]  Open
336
Mandad S, Rahman RU, Centeno TP, Vidal RO, Wildhagen H, Rammner B, Keihani S, Opazo F, Urban I, Ischebeck T, Kirli K, Benito E, Fischer A, Yousefi RY, Dennerlein S, Rehling P, Feussner I, Urlaub H, Bonn S, Rizzoli SO, Fornasiero EF. The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain. Sci Rep 2018;8:16913. [PMID: 30443017 PMCID: PMC6237891 DOI: 10.1038/s41598-018-35277-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 11/02/2018] [Indexed: 12/14/2022]  Open
337
Limonier F, Willems S, Waeterloos G, Sneyers M, Dhaenens M, Deforce D. Estimating the Reliability of Low-Abundant Signals and Limited Replicate Measurements through MS2 Peak Area in SWATH. Proteomics 2018;18:e1800186. [PMID: 30387297 DOI: 10.1002/pmic.201800186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 09/25/2018] [Indexed: 12/26/2022]
338
Snyder DT, Szalwinski LJ, Wells JM, Cooks RG. Logical MS/MS scans: a new set of operations for tandem mass spectrometry. Analyst 2018;143:5438-5452. [PMID: 30311922 DOI: 10.1039/c8an01661e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
339
Lau E, Paik DT, Wu JC. Systems-Wide Approaches in Induced Pluripotent Stem Cell Models. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2018;14:395-419. [PMID: 30379619 DOI: 10.1146/annurev-pathmechdis-012418-013046] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
340
Krasny L, Bland P, Kogata N, Wai P, Howard BA, Natrajan RC, Huang PH. SWATH mass spectrometry as a tool for quantitative profiling of the matrisome. J Proteomics 2018;189:11-22. [PMID: 29501709 PMCID: PMC6215756 DOI: 10.1016/j.jprot.2018.02.026] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 02/16/2018] [Accepted: 02/19/2018] [Indexed: 12/16/2022]
341
Braccia C, Tomati V, Caci E, Pedemonte N, Armirotti A. SWATH label-free proteomics for cystic fibrosis research. J Cyst Fibros 2018;18:501-506. [PMID: 30348611 DOI: 10.1016/j.jcf.2018.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/05/2018] [Accepted: 10/09/2018] [Indexed: 01/05/2023]
342
Chutipongtanate S, Greis KD. Multiplex Biomarker Screening Assay for Urinary Extracellular Vesicles Study: A Targeted Label-Free Proteomic Approach. Sci Rep 2018;8:15039. [PMID: 30301925 PMCID: PMC6177456 DOI: 10.1038/s41598-018-33280-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 09/26/2018] [Indexed: 12/18/2022]  Open
343
Kruse R, Højlund K. Proteomic study of skeletal muscle in obesity and type 2 diabetes: progress and potential. Expert Rev Proteomics 2018;15:817-828. [PMID: 30251560 DOI: 10.1080/14789450.2018.1528147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
344
Swiatly A, Plewa S, Matysiak J, Kokot ZJ. Mass spectrometry-based proteomics techniques and their application in ovarian cancer research. J Ovarian Res 2018;11:88. [PMID: 30270814 PMCID: PMC6166298 DOI: 10.1186/s13048-018-0460-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 09/20/2018] [Indexed: 12/26/2022]  Open
345
Banerjee SL, Dionne U, Lambert JP, Bisson N. Targeted proteomics analyses of phosphorylation-dependent signalling networks. J Proteomics 2018;189:39-47. [DOI: 10.1016/j.jprot.2018.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/19/2018] [Accepted: 02/01/2018] [Indexed: 01/18/2023]
346
Lin H, He QY, Shi L, Sleeman M, Baker MS, Nice EC. Proteomics and the microbiome: pitfalls and potential. Expert Rev Proteomics 2018;16:501-511. [PMID: 30223687 DOI: 10.1080/14789450.2018.1523724] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
347
Ludwig C, Gillet L, Rosenberger G, Amon S, Collins BC, Aebersold R. Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial. Mol Syst Biol 2018;14:e8126. [PMID: 30104418 PMCID: PMC6088389 DOI: 10.15252/msb.20178126] [Citation(s) in RCA: 625] [Impact Index Per Article: 104.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 05/11/2018] [Accepted: 05/15/2018] [Indexed: 01/16/2023]  Open
348
Haynes SE, Majmudar JD, Martin BR. DIA-SIFT: A Precursor and Product Ion Filter for Accurate Stable Isotope Data-Independent Acquisition Proteomics. Anal Chem 2018;90:8722-8726. [PMID: 29989796 DOI: 10.1021/acs.analchem.8b01618] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
349
Hakobyan A, Liesack W, Glatter T. Crude-MS Strategy for in-Depth Proteome Analysis of the Methane-Oxidizing Methylocystis sp. strain SC2. J Proteome Res 2018;17:3086-3103. [DOI: 10.1021/acs.jproteome.8b00216] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
350
Piekos SC, Chen L, Wang P, Shi J, Yaqoob S, Zhu HJ, Ma X, Zhong XB. Consequences of Phenytoin Exposure on Hepatic Cytochrome P450 Expression during Postnatal Liver Maturation in Mice. Drug Metab Dispos 2018;46:1241-1250. [PMID: 29884652 DOI: 10.1124/dmd.118.080861] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/01/2018] [Indexed: 12/15/2022]  Open
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