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For: Lenčo J, Khalikova MA, Švec F. Dissolving Peptides in 0.1% Formic Acid Brings Risk of Artificial Formylation. J Proteome Res 2020;19:993-999. [DOI: 10.1021/acs.jproteome.9b00823] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Number Cited by Other Article(s)
1
Jadeja S, Karsakov AA, Sklenářová H, Lenčo J. Evaluating C18 stationary phases with a positively charged surface for proteomic LC-MS applications using mobile phase acidified with reduced formic acid concentration. J Chromatogr A 2024;1730:465142. [PMID: 39002507 DOI: 10.1016/j.chroma.2024.465142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/15/2024]
2
Correia I, Oliveira C, Reis A, Guimarães AR, Aveiro S, Domingues P, Bezerra AR, Vitorino R, Moura G, Santos MAS. A proteogenomic pipeline for the analysis of protein biosynthesis errors in the human pathogen Candida albicans. Mol Cell Proteomics 2024:100818. [PMID: 39047911 DOI: 10.1016/j.mcpro.2024.100818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/20/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]  Open
3
Goulden T, Bodachivskyi I, Padula MP, Williams DBG. Concentrated ionic liquids for proteomics: Caveat emptor! Int J Biol Macromol 2023;253:127438. [PMID: 37839603 DOI: 10.1016/j.ijbiomac.2023.127438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/03/2023] [Accepted: 10/12/2023] [Indexed: 10/17/2023]
4
Jadeja S, Kupcik R, Fabrik I, Sklenářová H, Lenčo J. A stationary phase with a positively charged surface allows for minimizing formic acid concentration in the mobile phase, enhancing electrospray ionization in LC-MS proteomic experiments. Analyst 2023;148:5980-5990. [PMID: 37870390 DOI: 10.1039/d3an01508d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
5
Neale Q, Prefontaine A, Battellino T, Mizero B, Yeung D, Spicer V, Budisa N, Perreault H, Zahedi RP, Krokhin OV. Compendium of Chromatographic Behavior of Post-translationally and Chemically Modified Peptides in Bottom-Up Proteomic Experiments. Anal Chem 2023;95:14634-14642. [PMID: 37739932 DOI: 10.1021/acs.analchem.3c02412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
6
Naplekov D, Jadeja S, Fučíková AM, Švec F, Sklenářová H, Lenčo J. Easy, Robust, and Repeatable Online Acid Cleavage of Proteins in Mobile Phase for Fast Quantitative LC-MS Bottom-Up Protein Analysis─Application for Ricin Detection. Anal Chem 2023;95:12339-12348. [PMID: 37565982 PMCID: PMC10448442 DOI: 10.1021/acs.analchem.3c01772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023]
7
Zenin V, Tsedilin A, Yurkova M, Siniavin A, Fedorov A. Thermostable chaperone-based polypeptide biosynthesis: Enfuvirtide model product quality and protocol-related impurities. PLoS One 2023;18:e0286752. [PMID: 37289764 PMCID: PMC10249821 DOI: 10.1371/journal.pone.0286752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 05/23/2023] [Indexed: 06/10/2023]  Open
8
Nickerson JL, Baghalabadi V, Rajendran SRCK, Jakubec PJ, Said H, McMillen TS, Dang Z, Doucette AA. Recent advances in top-down proteome sample processing ahead of MS analysis. MASS SPECTROMETRY REVIEWS 2023;42:457-495. [PMID: 34047392 DOI: 10.1002/mas.21706] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/21/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
9
Lenčo J, Jadeja S, Naplekov DK, Krokhin OV, Khalikova MA, Chocholouš P, Urban J, Broeckhoven K, Nováková L, Švec F. Reversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial. J Proteome Res 2022;21:2846-2892. [PMID: 36355445 DOI: 10.1021/acs.jproteome.2c00407] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
10
Recombinant Spider Silk Fiber with High Dimensional Stability in Water and Its NMR Characterization. MOLECULES (BASEL, SWITZERLAND) 2022;27:molecules27238479. [PMID: 36500566 PMCID: PMC9739919 DOI: 10.3390/molecules27238479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
11
Asakura T, Matsuda H, Naito A, Abe Y. Formylation of Recombinant Spider Silk in Formic Acid and Wet Spinning Studied Using Nuclear Magnetic Resonance and Infrared Spectroscopies. ACS Biomater Sci Eng 2022;8:2390-2402. [PMID: 35532754 DOI: 10.1021/acsbiomaterials.2c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
12
A systematic evaluation of yeast sample preparation protocols for spectral identifications, proteome coverage and post-isolation modifications. J Proteomics 2022;261:104576. [DOI: 10.1016/j.jprot.2022.104576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 11/20/2022]
13
Zhi Y, Jia L, Shen J, Li J, Chen Z, Zhu B, Hao Z, Xu Y, Sun S. Formylation: an undesirable modification on glycopeptides and glycans during storage in formic acid solution. Anal Bioanal Chem 2022;414:3311-3317. [PMID: 35229171 DOI: 10.1007/s00216-022-03989-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 11/30/2022]
14
Presence of β-Turn Structure in Recombinant Spider Silk Dissolved in Formic Acid Revealed with NMR. MOLECULES (BASEL, SWITZERLAND) 2022;27:molecules27020511. [PMID: 35056828 PMCID: PMC8778467 DOI: 10.3390/molecules27020511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 11/23/2022]
15
De Clerck L, Willems S, Daled S, Van Puyvelde B, Verhelst S, Corveleyn L, Deforce D, Dhaenens M. An experimental design to extract more information from MS-based histone studies. Mol Omics 2021;17:929-938. [PMID: 34522942 DOI: 10.1039/d1mo00201e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
16
Kaulich PT, Winkels K, Kaulich TB, Treitz C, Cassidy L, Tholey A. MSTopDiff: A Tool for the Visualization of Mass Shifts in Deconvoluted Top-Down Proteomics Data for the Database-Independent Detection of Protein Modifications. J Proteome Res 2021;21:20-29. [PMID: 34818005 DOI: 10.1021/acs.jproteome.1c00766] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
17
Kulyyassov A, Fresnais M, Longuespée R. Targeted liquid chromatography-tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives. Proteomics 2021;21:e2100153. [PMID: 34591362 DOI: 10.1002/pmic.202100153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/25/2022]
18
Hayes AJ, Lewis JM, Davies MR, Scott NE. Burkholderia PglL enzymes are Serine preferring oligosaccharyltransferases which target conserved proteins across the Burkholderia genus. Commun Biol 2021;4:1045. [PMID: 34493791 PMCID: PMC8423747 DOI: 10.1038/s42003-021-02588-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/23/2021] [Indexed: 12/14/2022]  Open
19
Evaluation of strategies for overcoming trifluoroacetic acid ionization suppression resulted in single-column intact level, middle-up, and bottom-up reversed-phase LC-MS analyses of antibody biopharmaceuticals. Talanta 2021;233:122512. [PMID: 34215127 DOI: 10.1016/j.talanta.2021.122512] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 11/22/2022]
20
Daled S, Willems S, Van Puyvelde B, Corveleyn L, Verhelst S, De Clerck L, Deforce D, Dhaenens M. Histone Sample Preparation for Bottom-Up Mass Spectrometry: A Roadmap to Informed Decisions. Proteomes 2021;9:17. [PMID: 33919160 PMCID: PMC8167631 DOI: 10.3390/proteomes9020017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/08/2021] [Accepted: 04/19/2021] [Indexed: 11/16/2022]  Open
21
Folz JS, Patterson JA, Hanson AD, Fiehn O. Quantification of N6-formylated lysine in bacterial protein digests using liquid chromatography/tandem mass spectrometry despite spontaneous formation and matrix effects. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021;35:e9019. [PMID: 33617101 DOI: 10.1002/rcm.9019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/04/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
22
Geiszler DJ, Kong AT, Avtonomov DM, Yu F, Leprevost FDV, Nesvizhskii AI. PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results. Mol Cell Proteomics 2020;20:100018. [PMID: 33568339 PMCID: PMC7950090 DOI: 10.1074/mcp.tir120.002216] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/13/2020] [Accepted: 12/01/2020] [Indexed: 01/17/2023]  Open
23
Ahmad Izaham AR, Ang CS, Nie S, Bird LE, Williamson NA, Scott NE. What Are We Missing by Using Hydrophilic Enrichment? Improving Bacterial Glycoproteome Coverage Using Total Proteome and FAIMS Analyses. J Proteome Res 2020;20:599-612. [PMID: 33125241 DOI: 10.1021/acs.jproteome.0c00565] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
24
Lenčo J, Šemlej T, Khalikova MA, Fabrik I, Švec F. Sense and Nonsense of Elevated Column Temperature in Proteomic Bottom-up LC-MS Analyses. J Proteome Res 2020;20:420-432. [PMID: 33085896 DOI: 10.1021/acs.jproteome.0c00479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
25
Ahmad Izaham AR, Scott NE. Open Database Searching Enables the Identification and Comparison of Bacterial Glycoproteomes without Defining Glycan Compositions Prior to Searching. Mol Cell Proteomics 2020. [PMID: 32576591 DOI: 10.1101/2020.04.21.052845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]  Open
26
Ahmad Izaham AR, Scott NE. Open Database Searching Enables the Identification and Comparison of Bacterial Glycoproteomes without Defining Glycan Compositions Prior to Searching. Mol Cell Proteomics 2020;19:1561-1574. [PMID: 32576591 PMCID: PMC8143609 DOI: 10.1074/mcp.tir120.002100] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/27/2020] [Indexed: 12/23/2022]  Open
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