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Shi J, Meng S, Wan L, Zhang Z, Jiang S, Zhu H, Dai E, Chang L, Gao H, Wan K, Zhang L, Zhao X, Liu H, Lyu Z, Zhang Y, Xu P. Deep N-terminomics of Mycobacterium tuberculosis H37Rv extensively correct annotated encoding genes. Genomics 2021; 114:292-304. [PMID: 34915127 DOI: 10.1016/j.ygeno.2021.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/28/2021] [Accepted: 12/09/2021] [Indexed: 11/24/2022]
Abstract
Mycobacterium tuberculosis (MTB) is a severe causing agent of tuberculosis (TB). Although H37Rv, the type strain of M. tuberculosis was sequenced in 1998, annotation errors of encoding genes have been frequently reported in hundreds of papers. This phenomenon is particularly severe at the 5' end of the genes. Here, we applied a TMPP [(N-Succinimidyloxycarbonylmethyl) tris (2,4,6-trimethoxyphenyl) phosphonium bromide] labeling combined with StageTip separating strategy on M. tuberculosis H37Rv to characterize the N-terminal start sites of its annotated encoding genes. Totally, 1047 proteins were identified with 2058 TMPP labeled N-terminal peptides from all the 2625 mass spectrometer (MS) sequenced proteins. Comparative genomics analysis allowed the re-annotation of 43 proteins' N-termini in H37Rv and 762 proteins in Mycobacteriaceae. All revised N-termini start sites were distributed in 5'-UTR of annotated genes due to over-annotation of previous N-terminal initiation codon, especially the ATG. In addition, we identified and verified a novel gene Rv1078A in +3 frame different from the annotated gene Rv1078 in +2 frame. Altogether, our findings contribute to the better understanding of N-terminal of H37Rv and other species from Mycobacteriaceae that can assist future studies on biological study.
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Li X, Franz T, Atanassov I, Colby T. Step-by-Step Sample Preparation of Proteins for Mass Spectrometric Analysis. Methods Mol Biol 2021; 2261:13-23. [PMID: 33420981 DOI: 10.1007/978-1-0716-1186-9_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Nowadays identification and quantification of proteins from biological samples by mass spectrometry are widely used. For the identification of proteins, there are two scenarios. Proteins are either pre-fractionated in some way, e.g., by gel electrophoresis or chromatography, or analyzed as complex mixture (shotgun). Because of technological developments of mass spectrometry, the identification of several thousand proteins from complex biological matrix becomes possible. However, in many cases, it is still useful to separate proteins first in a gel. For quantifying proteins, label-free, isotopic labeling, and data-independent acquisition (DIA) library are widely used. Not only mass spectrometry technology made progress. This is also true for the sample preparation. Protocols and techniques developed recently not only make the analysis of starting material in the low microgram range possible but also simplify the whole procedure. Here, we will describe some detailed protocols of preparing samples for mass spectrometry-based protein identification and protein quantification, as in-gel digestion, in-solution digestion, peptide cleaning, and TMT labeling. This will allow also inexperienced beginners to get good results.
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Affiliation(s)
- Xinping Li
- Max-Planck-Institute for Biology of Ageing, Cologne, Germany.
| | | | - Ilian Atanassov
- Max-Planck-Institute for Biology of Ageing, Cologne, Germany
| | - Thomas Colby
- Max-Planck-Institute for Biology of Ageing, Cologne, Germany
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Zhang J, Hu J, Wang S, Lin X, Liang H, Li S, Yu C, Dong X, Ji C. Developing and Validating a UPLC-MS Method with a StageTip-Based Extraction for the Biogenic Amines Analysis in Fish. J Food Sci 2019; 84:1138-1144. [PMID: 30990887 DOI: 10.1111/1750-3841.14597] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/15/2019] [Accepted: 03/01/2019] [Indexed: 11/28/2022]
Abstract
To effectively extract biogenic amines (BAs) from complex food matrices is an important issue. In this study, a stop-and-go-extraction tip (StageTip)-based method for simultaneous enrichment of six BAs including histamine, tyramine, putrescine, cadaverine, tryptamine, and β-phenylethylamine in fish samples was developed and optimized. This StageTip-based BAs extraction method required short extraction time, small sample size, and minimal consumption of organic solvents. In addition, an ultrahigh-performance liquid chromatography coupled with triple quadrupole mass spectrometer was used to identify and quantify BAs without derivatization. Target recovery efficiencies of BAs from spiked fish samples ranged from 84% to 110%. Linear regression models were established to determine BAs in the range of 0.4 to 3.0 mg/L (R2 > 0.995). Good repeatability was obtained with relative standard deviation of peak areas (1.17 to 5.61%) and retention time (0.09 to 0.20%). High sensitivity was achieved for the detection of six BAs (0.064 to 1.00 ng/L for the limit of detection, 0.10 to 5 ng/L for the limit of quantification). The proposed method had an obvious advantage in the analysis of BAs in complex food matrices such as fish tissues since it could reflect the subtle distribution of BAs from one fish fillet. PRACTICAL APPLICATION: A StageTip-based BAs enrichment combined with UPLC-MS analysis method was developed and optimized, which was low-cost, environmentally friendly, and with good analytical performances. As such, it has the potential to become a powerful tool for the analysis of BAs in different complex food matrices.
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Affiliation(s)
- Jingbo Zhang
- School of Food Science and Technology, Dalian Polytechnic Univ., Natl. Engineering Research Center of Seafood, 1 Qinggongyuan, Ganjingzi District, Dalian, 116034, PR China
| | - Jing Hu
- School of Food Science and Technology, Dalian Polytechnic Univ., Natl. Engineering Research Center of Seafood, 1 Qinggongyuan, Ganjingzi District, Dalian, 116034, PR China
| | - Shuai Wang
- School of Food Science and Technology, Dalian Polytechnic Univ., Natl. Engineering Research Center of Seafood, 1 Qinggongyuan, Ganjingzi District, Dalian, 116034, PR China
| | - Xinping Lin
- School of Food Science and Technology, Dalian Polytechnic Univ., Natl. Engineering Research Center of Seafood, 1 Qinggongyuan, Ganjingzi District, Dalian, 116034, PR China
| | - Huipeng Liang
- School of Food Science and Technology, Dalian Polytechnic Univ., Natl. Engineering Research Center of Seafood, 1 Qinggongyuan, Ganjingzi District, Dalian, 116034, PR China
| | - Shengjie Li
- School of Food Science and Technology, Dalian Polytechnic Univ., Natl. Engineering Research Center of Seafood, 1 Qinggongyuan, Ganjingzi District, Dalian, 116034, PR China
| | - Chenxu Yu
- Dept. of Agricultural and Biosystems Engineering, Iowa State Univ., Ames, IA, 50011, U.S.A
| | - Xiuping Dong
- School of Food Science and Technology, Dalian, Polytechnic Univ., National Engineering Research Center of Seafood, 1 Qinggongyuan, Ganjingzi District, Dalian, 116034, PR China
| | - Chaofan Ji
- School of Food Science and Technology, Dalian, Polytechnic Univ., National Engineering Research Center of Seafood, 1 Qinggongyuan, Ganjingzi District, Dalian, 116034, PR China
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Bache N, Geyer PE, Bekker-Jensen DB, Hoerning O, Falkenby L, Treit PV, Doll S, Paron I, Müller JB, Meier F, Olsen JV, Vorm O, Mann M. A Novel LC System Embeds Analytes in Pre-formed Gradients for Rapid, Ultra-robust Proteomics. Mol Cell Proteomics 2018; 17:2284-2296. [PMID: 30104208 PMCID: PMC6210218 DOI: 10.1074/mcp.tir118.000853] [Citation(s) in RCA: 188] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/13/2018] [Indexed: 12/03/2022] Open
Abstract
Because of low throughput and limited robustness, nano-scale liquid chromatography has been a bottleneck for advancing proteomics in biomedical research. Here, we developed and evaluated two new LC concepts—“pre-formed gradients” and “offset gradients for peptide re-focusing”—that are both implemented in the Evosep One instrument. We evaluated robustness with more than 2000 HeLa runs, demonstrated absence of cross-contamination with crude plasma samples, high proteome coverage by fractionated HeLa and routinely measuring more than 5000 proteins/sample in just 21 minutes. To further integrate mass spectrometry (MS)-based proteomics into biomedical research and especially into clinical settings, high throughput and robustness are essential requirements. They are largely met in high-flow rate chromatographic systems for small molecules but these are not sufficiently sensitive for proteomics applications. Here we describe a new concept that delivers on these requirements while maintaining the sensitivity of current nano-flow LC systems. Low-pressure pumps elute the sample from a disposable trap column, simultaneously forming a chromatographic gradient that is stored in a long storage loop. An auxiliary gradient creates an offset, ensuring the re-focusing of the peptides before the separation on the analytical column by a single high-pressure pump. This simplified design enables robust operation over thousands of sample injections. Furthermore, the steps between injections are performed in parallel, reducing overhead time to a few minutes and allowing analysis of more than 200 samples per day. From fractionated HeLa cell lysates, deep proteomes covering more than 130,000 sequence unique peptides and close to 10,000 proteins were rapidly acquired. Using this data as a library, we demonstrate quantitation of 5200 proteins in only 21 min. Thus, the new system - termed Evosep One - analyzes samples in an extremely robust and high throughput manner, without sacrificing in depth proteomics coverage.
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Affiliation(s)
| | - Philipp E Geyer
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,¶Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dorte B Bekker-Jensen
- ¶Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Peter V Treit
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sophia Doll
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Igor Paron
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Johannes B Müller
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Meier
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jesper V Olsen
- ¶Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Vorm
- From the ‡Evosep Biosystems, Odense, Denmark
| | - Matthias Mann
- §Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; .,¶Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Abstract
A true and accurate bottom-up global proteomic measurement will only be achieved when all proteins in a sample can be digested efficiently and at least some peptides recovered on which to base an estimate of abundance. Integral membrane proteins make up around one-third of the proteome and require specialized protocols if they are to be successfully solubilized for efficient digestion by the enzymes used in bottom-up proteomics. The protocol described relies upon solubilization using the detergents sodium deoxycholate and lauryl sarcosine with heating to 95 °C. A subset of peptides is purified by reverse-phase solid-phase extraction and fractionated by strong-cation exchange prior to nano-liquid chromatography with data-dependent tandem mass spectrometry. For quantitative proteomics experiments a protocol is described for stable-isotope coding of peptides using dimethylation of primary amines allowing for three-way sample multiplexing.
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Affiliation(s)
- Joseph Capri
- Department of Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Julian P Whitelegge
- The Pasarow Mass Spectrometry Laboratory, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Box 42, 760 Westwood Plaza, Los Angeles, CA, 90095, USA.
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Hernandez-Valladares M, Aasebø E, Selheim F, Berven FS, Bruserud Ø. Selecting Sample Preparation Workflows for Mass Spectrometry-Based Proteomic and Phosphoproteomic Analysis of Patient Samples with Acute Myeloid Leukemia. Proteomes 2016; 4:proteomes4030024. [PMID: 28248234 PMCID: PMC5217354 DOI: 10.3390/proteomes4030024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/09/2016] [Accepted: 08/12/2016] [Indexed: 12/31/2022] Open
Abstract
Global mass spectrometry (MS)-based proteomic and phosphoproteomic studies of acute myeloid leukemia (AML) biomarkers represent a powerful strategy to identify and confirm proteins and their phosphorylated modifications that could be applied in diagnosis and prognosis, as a support for individual treatment regimens and selection of patients for bone marrow transplant. MS-based studies require optimal and reproducible workflows that allow a satisfactory coverage of the proteome and its modifications. Preparation of samples for global MS analysis is a crucial step and it usually requires method testing, tuning and optimization. Different proteomic workflows that have been used to prepare AML patient samples for global MS analysis usually include a standard protein in-solution digestion procedure with a urea-based lysis buffer. The enrichment of phosphopeptides from AML patient samples has previously been carried out either with immobilized metal affinity chromatography (IMAC) or metal oxide affinity chromatography (MOAC). We have recently tested several methods of sample preparation for MS analysis of the AML proteome and phosphoproteome and introduced filter-aided sample preparation (FASP) as a superior methodology for the sensitive and reproducible generation of peptides from patient samples. FASP-prepared peptides can be further fractionated or IMAC-enriched for proteome or phosphoproteome analyses. Herein, we will review both in-solution and FASP-based sample preparation workflows and encourage the use of the latter for the highest protein and phosphorylation coverage and reproducibility.
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Affiliation(s)
- Maria Hernandez-Valladares
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
| | - Elise Aasebø
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
| | - Frode Selheim
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
| | - Frode S Berven
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
| | - Øystein Bruserud
- Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
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