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Chen Y, Du Z, Zhao H, Fang W, Liu T, Zhang Y, Zhang W, Qin W. SPPUSM: An MS/MS spectra merging strategy for improved low-input and single-cell proteome identification. Anal Chim Acta 2023; 1279:341793. [PMID: 37827637 DOI: 10.1016/j.aca.2023.341793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/26/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023]
Abstract
Single and rare cell analysis provides unique insights into the investigation of biological processes and disease progress by resolving the cellular heterogeneity that is masked by bulk measurements. Although many efforts have been made, the techniques used to measure the proteome in trace amounts of samples or in single cells still lag behind those for DNA and RNA due to the inherent non-amplifiable nature of proteins and the sensitivity limitation of current mass spectrometry. Here, we report an MS/MS spectra merging strategy termed SPPUSM (same precursor-produced unidentified spectra merging) for improved low-input and single-cell proteome data analysis. In this method, all the unidentified MS/MS spectra from multiple test files are first extracted. Then, the corresponding MS/MS spectra produced by the same precursor ion from different files are matched according to their precursor mass and retention time (RT) and are merged into one new spectrum. The newly merged spectra with more fragment ions are next searched against the database to increase the MS/MS spectra identification and proteome coverage. Further improvement can be achieved by increasing the number of test files and spectra to be merged. Up to 18.2% improvement in protein identification was achieved for 1 ng HeLa peptides by SPPUSM. Reliability evaluation by the "entrapment database" strategy using merged spectra from human and E. coli revealed a marginal error rate for the proposed method. For application in single cell proteome (SCP) study, identification enhancement of 28%-61% was achieved for proteins for different SCP data. Furthermore, a lower abundance was found for the SPPUSM-identified peptides, indicating its potential for more sensitive low sample input and SCP studies.
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Affiliation(s)
- Yongle Chen
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing, 102206, PR China
| | - Zhuokun Du
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing, 102206, PR China
| | - Hongxian Zhao
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing, 102206, PR China
| | - Wei Fang
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing, 102206, PR China
| | - Tong Liu
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing, 102206, PR China
| | - Yangjun Zhang
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing, 102206, PR China
| | - Wanjun Zhang
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing, 102206, PR China; College of Chemistry and Materials Science, Hebei University, Baoding, 071002, China
| | - Weijie Qin
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing, 102206, PR China; College of Chemistry and Materials Science, Hebei University, Baoding, 071002, China.
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2
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Sedláčková S, Hubálek M, Vrkoslav V, Blechová M, Kozlík P, Cvačka J. Positive Effect of Acetylation on Proteomic Analysis Based on Liquid Chromatography with Atmospheric Pressure Chemical Ionization and Photoionization Mass Spectrometry. Molecules 2023; 28:molecules28093711. [PMID: 37175121 PMCID: PMC10180487 DOI: 10.3390/molecules28093711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/14/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
A typical bottom-up proteomic workflow comprises sample digestion with trypsin, separation of the hydrolysate using reversed-phase HPLC, and detection of peptides via electrospray ionization (ESI) tandem mass spectrometry. Despite the advantages and wide usage of protein identification and quantification, the procedure has limitations. Some domains or parts of the proteins may remain inadequately described due to inefficient detection of certain peptides. This study presents an alternative approach based on sample acetylation and mass spectrometry with atmospheric pressure chemical ionization (APCI) and atmospheric pressure photoionization (APPI). These ionizations allowed for improved detection of acetylated peptides obtained via chymotrypsin or glutamyl peptidase I (Glu-C) digestion. APCI and APPI spectra of acetylated peptides often provided sequence information already at the full scan level, while fragmentation spectra of protonated molecules and sodium adducts were easy to interpret. As demonstrated for bovine serum albumin, acetylation improved proteomic analysis. Compared to ESI, gas-phase ionizations APCI and APPI made it possible to detect more peptides and provide better sequence coverages in most cases. Importantly, APCI and APPI detected many peptides which passed unnoticed in the ESI source. Therefore, analytical methods based on chymotrypsin or Glu-C digestion, acetylation, and APPI or APCI provide data complementary to classical bottom-up proteomics.
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Affiliation(s)
- Simona Sedláčková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 542/2, 16000 Prague, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12800 Prague, Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 542/2, 16000 Prague, Czech Republic
| | - Vladimír Vrkoslav
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 542/2, 16000 Prague, Czech Republic
| | - Miroslava Blechová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 542/2, 16000 Prague, Czech Republic
| | - Petr Kozlík
- Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12800 Prague, Czech Republic
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 542/2, 16000 Prague, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12800 Prague, Czech Republic
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3
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Huang S, Ji X, Jackson KK, Lubman DM, Ard MB, Bruce TF, Marcus RK. Rapid separation of blood plasma exosomes from low-density lipoproteins via a hydrophobic interaction chromatography method on a polyester capillary-channeled polymer fiber phase. Anal Chim Acta 2021; 1167:338578. [PMID: 34049630 DOI: 10.1016/j.aca.2021.338578] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/12/2021] [Accepted: 04/23/2021] [Indexed: 12/15/2022]
Abstract
Exosomes are membrane-bound, cell-secreted vesicles, with sizes ranging from 30 to 150 nm. Exosomes in blood plasma have become proposed targets as measurable indicators of disease conditions. Current methods for plasma-based exosome isolation are time-consuming, complex, and have high operational costs. One of the most commonly reported shortcomings of current isolation protocols is the co-extraction of lipoproteins (e.g. low-density lipoproteins, LDLs) with the target exosomes. This report describes the use of a rapid, single-operation hydrophobic interaction chromatography (HIC) procedure on a polyester (PET) capillary-channeled polymer (C-CP) fiber column, demonstrating the ability to efficiently purify exosomes. The method has previously been demonstrated for isolation of exosomes from diverse biological matrices, but questions were raised about the potential co-elution of LDLs. In the method described herein, a step-gradient procedure sequentially elutes spiked lipoproteins and blood plasma-originating exosomes in 10 min, with the LDLs excluded from the desired exosome fraction. Mass spectrometry (MS) was used to characterize an impurity in the primary LDL material, identifying the presence of exosomal material. Transmission electron microscopy (TEM) and an enzyme-linked immunosorbent assay (ELISA) were used to identify the various elution components. The method serves both as a rapid means of high purity exosome isolation as well as a screening tool for the purity of LDL samples with respect to extracellular vesicles.
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Affiliation(s)
- Sisi Huang
- Department of Chemistry, Biosystems Research Complex, Clemson University, Clemson, SC, 29634, USA
| | - Xiaohui Ji
- Department of Surgery, Medical Science Research Building I, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kaylan K Jackson
- Department of Chemistry, Biosystems Research Complex, Clemson University, Clemson, SC, 29634, USA
| | - David M Lubman
- Department of Surgery, Medical Science Research Building I, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Mary B Ard
- Georgia Electron Microscopy Core Facility, University of Georgia Athens, GA, 30602, USA
| | - Terri F Bruce
- Department of Bioengineering, Life Sciences Facility, Clemson University, Clemson, SC, 29634, USA
| | - R Kenneth Marcus
- Department of Chemistry, Biosystems Research Complex, Clemson University, Clemson, SC, 29634, USA.
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4
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Huang S, Bruce TF, Ding H, Wei Y, Marcus RK. Rapid isolation of lentivirus particles from cell culture media via a hydrophobic interaction chromatography method on a polyester, capillary-channeled polymer fiber stationary phase. Anal Bioanal Chem 2021; 413:2985-2994. [PMID: 33608753 DOI: 10.1007/s00216-021-03232-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/02/2021] [Accepted: 02/09/2021] [Indexed: 11/26/2022]
Abstract
Lentiviruses are increasingly used as gene delivery vehicles for vaccines and immunotherapies. However, the purification of clinical-grade lentivirus vectors for therapeutic use is still troublesome and limits preclinical and clinical experiments. Current purification methods such as ultracentrifugation and ultrafiltration are time consuming and do not remove all of the impurities such as cellular debris, membrane fragments, and denatured proteins from the lentiviruses. The same challenges exist in terms of their analytical characterization. Presented here is the novel demonstration of the chromatographic isolation of virus particles from culture media based on the hydrophobicity characteristics of the vesicles. A method was developed to isolate lentivirus from media using a hydrophobic interaction chromatography (HIC) method performed on a polyester, capillary-channeled polymer (PET C-CP) stationary phase and a standard liquid chromatography apparatus. The method is an extension of the approach developed in this laboratory for the isolation of extracellular vesicles (EVs). Quantitative polymerase chain reaction (qPCR) was used to verify and quantify lentiviruses in elution fractions. Load and elution mobile phase compositions were optimized to affect high efficiency and throughput. The process has been visualized via scanning electron microscopy (SEM) of the fiber surfaces following media injection, the elution of proteinaceous material, and the elution of lentiviruses. This effort has yielded a rapid (<10 min), low-cost (< $15 per column, providing multiple separations), and efficient method for the isolation/purification of lentivirus particles from cell culture media at the analytical scale.
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Affiliation(s)
- Sisi Huang
- Department of Chemistry, Biosystems Research Complex, Clemson University, Clemson, SC, 29634, USA
| | - Terri F Bruce
- Department of Bioengineering, Life Sciences Facility, Clemson University, Clemson, SC, 29634, USA
| | - Hui Ding
- Department of Biological Sciences, Life Sciences Facility, Clemson University, Clemson, SC, 29634, USA
| | - Yanzhang Wei
- Department of Biological Sciences, Life Sciences Facility, Clemson University, Clemson, SC, 29634, USA
| | - R Kenneth Marcus
- Department of Chemistry, Biosystems Research Complex, Clemson University, Clemson, SC, 29634, USA.
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5
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Zaikin VG, Borisov RS. Options of the Main Derivatization Approaches for Analytical ESI and MALDI Mass Spectrometry. Crit Rev Anal Chem 2021; 52:1287-1342. [PMID: 33557614 DOI: 10.1080/10408347.2021.1873100] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The inclusion of preliminary chemical labeling (derivatization) in the analysis process by such powerful and widespread methods as electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is a popular and widely used methodological approach. This is due to the need to remove some fundamental limitations inherent in these powerful analytic methods. Although a number of special reviews has been published discussing the utilization of derivatization approaches, the purpose of the present critical review is to comprehensively summarize, characterize and evaluate most of the previously developed and practically applied, as well as recently proposed representative derivatization reagents for ESI-MS and MALDI-MS platforms in their mostly sensitive positive ion mode and frequently hyphenated with separation techniques. The review is focused on the use of preliminary chemical labeling to facilitate the detection, identification, structure elucidation, quantification, profiling or MS imaging of compounds within complex matrices. Two main derivatization approaches, namely the introduction of permanent charge-fixed or highly proton affinitive residues into analytes are critically evaluated. In situ charge-generation, charge-switch and charge-transfer derivatizations are considered separately. The potential of using reactive matrices in MALDI-MS and chemical labeling in MS-based omics sciences is given.
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Affiliation(s)
- Vladimir G Zaikin
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
| | - Roman S Borisov
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
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6
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Ji X, Huang S, Zhang J, Bruce TF, Tan Z, Wang D, Zhu J, Marcus RK, Lubman DM. A novel method of high-purity extracellular vesicle enrichment from microliter-scale human serum for proteomic analysis. Electrophoresis 2021; 42:245-256. [PMID: 33169421 PMCID: PMC8018574 DOI: 10.1002/elps.202000223] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 01/02/2023]
Abstract
We have developed a rapid, low-cost, and simple separation strategy to separate extracellular vesicles (EVs) from a small amount of serum (i.e.,<100 μL) with minimal contamination by serum proteins and lipoprotein particles to meet the high purity requirement for EV proteome analysis. EVs were separated by a novel polyester capillary channel polymer (PET C-CP) fiber phase/hydrophobic interaction chromatography (HIC) method which is rapid and can process small size samples. The collected EV fractions were subjected to a post-column cleanup protocol using a centrifugal filter to perform buffer exchange and eliminate potential coeluting non-EV proteins while minimizing EV sample loss. Downstream characterization demonstrated that our current strategy can separate EVs with the anticipated exosome-like particle size distribution and high yield (∼1 × 1011 EV particles per mL of serum) in approximately 15 min. Proteome profiling of the EVs reveals that a group of genuine EV components were identified that have significantly less high-abundance blood proteins and lipoprotein particle contamination in comparison to traditional separation methods. The use of this methodology appears to address the major challenges facing EV separation for proteomics analysis. In addition, the EV post-column cleanup protocol proposed in the current work has the potential to be combined with other separation methods, such as ultracentrifugation (UC), to further purify the separated EV samples.
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Affiliation(s)
- Xiaohui Ji
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, USA
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, P. R. China
| | - Sisi Huang
- Department of Chemistry, Biosystems Research Complex, Clemson University, Clemson, SC, USA
| | - Jie Zhang
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Terri F. Bruce
- Department of Bioengineering, Life Sciences Facility, Clemson University, Clemson, SC, USA
| | - Zhijing Tan
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Donglin Wang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, P. R. China
| | - Jianhui Zhu
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - R. Kenneth Marcus
- Department of Chemistry, Biosystems Research Complex, Clemson University, Clemson, SC, USA
| | - David M. Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, USA
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7
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An M, Wu J, Zhu J, Lubman DM. Comparison of an Optimized Ultracentrifugation Method versus Size-Exclusion Chromatography for Isolation of Exosomes from Human Serum. J Proteome Res 2018; 17:3599-3605. [PMID: 30192545 DOI: 10.1021/acs.jproteome.8b00479] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Exosomes are nanosized vesicles that are abundant in biological fluids. In recent years, exosomes have attracted increasing attention as their cargo may provide promising biomarkers for the early diagnosis of and therapy for many diseases, such as cancer. In addition to ultracentrifugation (UC), many alternative methods including size-exclusion chromatography (SEC) have been developed for isolating exosomes. It has been reported that the SEC method provided improved performance relative to the UC method in isolating exosomes from plasma, where the former contained less residual blood protein contamination. We have compared the SEC method with an optimized UC method in isolating exosomes from human serum. This was based on dilution of the serum to reduce the viscosity and a prolonged cycle of UC, followed by another four cycles. We found that >95% of serum proteins were removed without a significant loss of exosome proteins relative to SEC. We also combined one cycle of UC with SEC and found that this method provided improved results relative to the SEC method, although the serum protein contamination was several times higher than that of our optimized UC method. The TEM showed that the size distribution of exosomes isolated from each of the three methods was similar.
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Affiliation(s)
- Mingrui An
- Department of Surgery , University of Michigan Medical Center , Ann Arbor , Michigan 48109 , United States
| | - Jing Wu
- Department of Surgery , University of Michigan Medical Center , Ann Arbor , Michigan 48109 , United States
| | - Jianhui Zhu
- Department of Surgery , University of Michigan Medical Center , Ann Arbor , Michigan 48109 , United States
| | - David M Lubman
- Department of Surgery , University of Michigan Medical Center , Ann Arbor , Michigan 48109 , United States
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8
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An M, Zhu J, Wu J, Cuneo KC, Lubman DM. Circulating Microvesicles from Pancreatic Cancer Accelerate the Migration and Proliferation of PANC-1 Cells. J Proteome Res 2018; 17:1690-1699. [PMID: 29494150 DOI: 10.1021/acs.jproteome.8b00014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Circulating microvesicles are able to mediate long-distance cell-cell communications. It is essential to understand how microvesicles from pancreatic cancer act on other cells in the body. In this work, serum-derived microvesicles were isolated from 10 patients with locally advanced pancreatic cancer and healthy controls. Using Cell Transwell and WST-1 reagents, we found that microvesicles from pancreatic cancer accelerated migration and proliferation of PANC-1 cells. Meanwhile, the proliferation of these cancer-microvesicle-treated cells (CMTCs) was affected less by 10 μM of gemcitabine relative to healthy microvesicle-treated cells (HMTCs). Next, we optimized the filter-aided sample preparation method to increase the recovery of protein samples and then applied it to the quantification of the proteome of CMTCs and HMTCs. The peptides were labeled and analyzed by liquid chromatography-tandem mass spectrometry. In total, 4102 proteins were identified, where 35 proteins were up-regulated with 27 down-regulated in CMTCs. We verified the quantitative results of three key proteins CD44, PPP2R1A, and TP53 by Western blot. The Ingenuity Pathway Analysis revealed pathways that cancer microvesicles might participate in to promote cell migration and proliferation. These findings may provide novel clues of treatment for tumorigenesis and metastasis.
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Affiliation(s)
- Mingrui An
- Department of Surgery , University of Michigan Medical Center , Ann Arbor , Michigan 48109 , United States
| | - Jianhui Zhu
- Department of Surgery , University of Michigan Medical Center , Ann Arbor , Michigan 48109 , United States
| | - Jing Wu
- Department of Surgery , University of Michigan Medical Center , Ann Arbor , Michigan 48109 , United States
| | - Kyle C Cuneo
- Department of Radiation Oncology , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - David M Lubman
- Department of Surgery , University of Michigan Medical Center , Ann Arbor , Michigan 48109 , United States
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9
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Leitner A. A review of the role of chemical modification methods in contemporary mass spectrometry-based proteomics research. Anal Chim Acta 2018; 1000:2-19. [DOI: 10.1016/j.aca.2017.08.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/11/2017] [Accepted: 08/15/2017] [Indexed: 12/20/2022]
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10
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Setner B, Wierzbicka M, Jerzykiewicz L, Lisowski M, Szewczuk Z. The unexpected racemization and hydrogen–deuterium exchange of the hydrogen at the α-carbon of proline analogs containing the 5-azoniaspiro[4.4]nonyl-group. Org Biomol Chem 2018; 16:825-831. [PMID: 29327743 DOI: 10.1039/c7ob02926h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we present an unexpected racemization and the hydrogen–deuterium exchange (HDX) at the α-C atom of the proline derivative under basic aqueous conditions (1% water solution of triethylamine).
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Affiliation(s)
- B. Setner
- Faculty of Chemistry
- University of Wrocław
- 50-383 Wrocław
- Poland
| | - M. Wierzbicka
- Faculty of Chemistry
- University of Wrocław
- 50-383 Wrocław
- Poland
| | - L. Jerzykiewicz
- Faculty of Chemistry
- University of Wrocław
- 50-383 Wrocław
- Poland
| | - M. Lisowski
- Faculty of Chemistry
- University of Wrocław
- 50-383 Wrocław
- Poland
| | - Z. Szewczuk
- Faculty of Chemistry
- University of Wrocław
- 50-383 Wrocław
- Poland
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11
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Setner B, Rudowska M, Kluczyk A, Stefanowicz P, Szewczuk Z. The 5-azoniaspiro[4.4]nonyl group for improved MS peptide analysis: A novel non-fragmenting ionization tag for mass spectrometric sensitive sequencing of peptides. Anal Chim Acta 2017; 986:71-81. [DOI: 10.1016/j.aca.2017.07.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/10/2017] [Accepted: 07/12/2017] [Indexed: 01/02/2023]
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12
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Horton AP, Robotham SA, Cannon JR, Holden DD, Marcotte EM, Brodbelt JS. Comprehensive de Novo Peptide Sequencing from MS/MS Pairs Generated through Complementary Collision Induced Dissociation and 351 nm Ultraviolet Photodissociation. Anal Chem 2017; 89:3747-3753. [PMID: 28234449 PMCID: PMC5480239 DOI: 10.1021/acs.analchem.7b00130] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We describe a strategy for de novo peptide sequencing based on matched pairs of tandem mass spectra (MS/MS) obtained by collision induced dissociation (CID) and 351 nm ultraviolet photodissociation (UVPD). Each precursor ion is isolated twice with the mass spectrometer switching between CID and UVPD activation modes to obtain a complementary MS/MS pair. To interpret these paired spectra, we modified the UVnovo de novo sequencing software to automatically learn from and interpret fragmentation spectra, provided a representative set of training data. This machine learning procedure, using random forests, synthesizes information from one or multiple complementary spectra, such as the CID/UVPD pairs, into peptide fragmentation site predictions. In doing so, the burden of fragmentation model definition shifts from programmer to machine and opens up the model parameter space for inclusion of nonobvious features and interactions. This spectral synthesis also serves to transform distinct types of spectra into a common representation for subsequent activation-independent processing steps. Then, independent from precursor activation constraints, UVnovo's de novo sequencing procedure generates and scores sequence candidates for each precursor. We demonstrate the combined experimental and computational approach for de novo sequencing using whole cell E. coli lysate. In benchmarks on the CID/UVPD data, UVnovo assigned correct full-length sequences to 83% of the spectral pairs of doubly charged ions with high-confidence database identifications. Considering only top-ranked de novo predictions, 70% of the pairs were deciphered correctly. This de novo sequencing performance exceeds that of PEAKS and PepNovo on the CID spectra and that of UVnovo on CID or UVPD spectra alone. As presented here, the methods for paired CID/UVPD spectral acquisition and interpretation constitute a powerful workflow for high-throughput and accurate de novo peptide sequencing.
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Affiliation(s)
- Andrew P Horton
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas , Austin, Texas 78712, United States
| | - Scott A Robotham
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
| | - Joe R Cannon
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
| | - Dustin D Holden
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
| | - Edward M Marcotte
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
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13
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An M, Lohse I, Tan Z, Zhu J, Wu J, Kurapati H, Morgan MA, Lawrence TS, Cuneo KC, Lubman DM. Quantitative Proteomic Analysis of Serum Exosomes from Patients with Locally Advanced Pancreatic Cancer Undergoing Chemoradiotherapy. J Proteome Res 2017; 16:1763-1772. [PMID: 28240915 DOI: 10.1021/acs.jproteome.7b00024] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Pancreatic cancer is the third leading cause of cancer-related death in the USA. Despite extensive research, minimal improvements in patient outcomes have been achieved. Early identification of treatment response and metastasis would be valuable to determine the appropriate therapeutic course for patients. In this work, we isolated exosomes from the serum of 10 patients with locally advanced pancreatic cancer at serial time points over a course of therapy, and quantitative analysis was performed using the iTRAQ method. We detected approximately 700-800 exosomal proteins per sample, several of which have been implicated in metastasis and treatment resistance. We compared the exosomal proteome of patients at different time points during treatment to healthy controls and identified eight proteins that show global treatment-specific changes. We then tested the effect of patient-derived exosomes on the migration of tumor cells and found that patient-derived exosomes, but not healthy controls, induce cell migration, supporting their role in metastasis. Our data show that exosomes can be reliably extracted from patient serum and analyzed for protein content. The differential loading of exosomes during a course of therapy suggests that exosomes may provide novel insights into the development of treatment resistance and metastasis.
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Affiliation(s)
- Mingrui An
- Department of Surgery, University of Michigan Medical Center , Ann Arbor, Michigan 48109, United States
| | - Ines Lohse
- Department of Radiation Oncology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Zhijing Tan
- Department of Surgery, University of Michigan Medical Center , Ann Arbor, Michigan 48109, United States
| | - Jianhui Zhu
- Department of Surgery, University of Michigan Medical Center , Ann Arbor, Michigan 48109, United States
| | - Jing Wu
- Department of Surgery, University of Michigan Medical Center , Ann Arbor, Michigan 48109, United States
| | - Himabindu Kurapati
- Department of Radiation Oncology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Meredith A Morgan
- Department of Radiation Oncology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Theodore S Lawrence
- Department of Radiation Oncology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Kyle C Cuneo
- Department of Radiation Oncology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - David M Lubman
- Department of Surgery, University of Michigan Medical Center , Ann Arbor, Michigan 48109, United States
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Asakawa D, Osaka I. High-Confidence Sequencing of Phosphopeptides by Electron Transfer Dissociation Mass Spectrometry Using Dinuclear Zinc(II) Complex. Anal Chem 2016; 88:12393-12402. [PMID: 28193068 DOI: 10.1021/acs.analchem.6b03645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Phosphorylation is the most abundant protein modification, and tandem mass spectrometry (MS2) with electron transfer dissociation (ETD) has proven to be a promising method for phosphoproteomic applications owing to its ability to determine phosphorylation sites on proteins. However, low precursor charge states hinder the ability to obtain useful information through peptide sequencing by ETD, and the presence of acidic phosphate groups contributes to a low charge state of peptide ions. In the present report, we used a dinuclear zinc complex, (Zn2L)3+ (L = alkoxide form of 1,3-bis[bis(pyridin-2-ylmethyl)amino]propan-2-ol) for electrospray ionization (ESI), followed by ETD-MS2 analysis. Since (Zn2L)3+ selectively bound to phosphopeptide with addition of a positive charge per phosphate group, the use of (Zn2L)3+ for ESI improved the ionization yield of phosphopeptides in phosphoprotein digest. Additionally, an increase in the charge state of phosphopeptides were observed by addition of (Zn2L)3+, facilitating phosphopeptide sequencing by ETD-MS2. Since the binding between (Zn2L)3+ and the phosphate group was retained during the ETD process, a comparison between the ETD mass spectra obtained using two dinuclear zinc complex derivatives containing different zinc isotopes, namely (64Zn2L)3+ and (68Zn2L)3+, provided information about the number of phosphate groups in each fragment ion, allowing the phosphorylation site to be unambiguously determined. The details of the fragmentation processes of the (Zn2L)3+-phosphopeptide complex were investigated using a density functional theory calculation. As in the case of protonated peptides, ETD induced peptide backbone dissociation in the (Zn2L)3+-phosphopeptide complex proceeded through an aminoketyl radical intermediate.
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Affiliation(s)
- Daiki Asakawa
- National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568 Japan
| | - Issey Osaka
- Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology , 1-1 Asahidai, Nomi, Ishikawa, Japan
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15
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An M, Shen H, Cao J, Pei X, Chang Y, Ma S, Bao J, Zhang X, Bai X, Ma Y. The alteration of H4-K16ac and H3-K27met influences the differentiation of neural stem cells. Anal Biochem 2016; 509:92-99. [PMID: 27396496 DOI: 10.1016/j.ab.2016.07.005] [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: 04/29/2016] [Revised: 06/20/2016] [Accepted: 07/05/2016] [Indexed: 10/21/2022]
Abstract
The neural stem cell therapy provides a promising future for patients with central nerve system damage, thus an insight into its differentiation mechanism is urgently needed. Herein, we aimed to identify various histone modifications and reveal their impact on the differentiation of neural stem cells (NSCs) toward neurons. Firstly, we labeled primary NSCs using the stable isotope labeling with amino acids in cell culture (SILAC) technique. Then we induced these NSCs to differentiate by all-trans retinoic acid (atRA) or SB216763. Next, we identified the alteration of histone modifications in early-differentiated NSCs by mass spectrometry and verified them by Western blot. Interestingly, these modification alterations and phenotype changes were found similar in NSCs induced by the two different drugs. More interestingly, during the differentiation process H3-K27met was significantly up-regulated while H4-K16ac was not altered at the global level but down-regulated in some low-abundance combinatorial codes. We inhibited the methyltransferase of H3-K27 and deacetylase of H4-K16 simultaneously and found the differentiation procedure was obviously delayed. The function of H4-K16ac and H3-K27met in NSCs differentiation would be useful to reveal the differentiation mechanism and valuable for further neural stem cell therapy.
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Affiliation(s)
- Mingrui An
- Department of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States; Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, 48109, United States.
| | - Hongyan Shen
- Key Laboratory of Genomics and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jun Cao
- College of Material Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 310036, China.
| | - Xiucong Pei
- Department of Toxicology, School of Public Health, Shenyang Medical College, Liaoning, 110034, China.
| | - Yanxu Chang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.
| | - Shuaipeng Ma
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Jintao Bao
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Xuefei Zhang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Xue Bai
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Yuanhui Ma
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
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16
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Liu H, Zou X, Li T, Wang X, Yuan W, Chen Y, Han W. Enhanced production of secretory glycoprotein VSTM1-v2 with mouse IgGκ signal peptide in optimized HEK293F transient transfection. J Biosci Bioeng 2015; 121:133-9. [PMID: 26140918 DOI: 10.1016/j.jbiosc.2015.05.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 05/14/2015] [Accepted: 05/25/2015] [Indexed: 01/28/2023]
Abstract
VSTM1-v2 is a secretory glycoprotein identified by our laboratory. Our previous study revealed that VSTM1-v2 could promote differentiation and activation of Th17 cells. To explore the role of VSTM1-v2 in the immune system further, a source of abundant high-quality recombinant protein is warranted. However, high-level expression of bioactive VSTM1-v2 is difficult due to its weak secretion capacity. To obtain sufficient recombinant VSTM1-v2, we developed an improved expression and purification system by replacing the native signal peptide with a mouse IgGκ signal peptide that did not alter the protein cleavage site. We also optimized parameters for a transient gene expression system in HEK293F cells suspended in serum-free media with polyethyleneimine. Finally, 3.6 mg/L recombinant VSTM1-v2 protein with N-glycosylation and no less than 95% purity was obtained through one-step purification with Ni affinity chromatography. The final yield after purification was increased by more than 7-fold compared to the yield from our previously reported HEK293T system (from 0.5 mg/L to 3.6 mg/L). More importantly, VSTM1-v2 protein exhibited excellent bioactivity. In conclusion, the improved system is not only a dependable source of abundant bioactive VSTM1-v2 for functional studies but also demonstrates a highly efficient approach for enhancing the production of proteins in a short time period, especially for secretory proteins with poor yields.
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Affiliation(s)
- Huihui Liu
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology, Ministry of Health, 38 Xueyuan Road, Beijing 100191, China; Peking University Center for Human Disease Genomics, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Xiajuan Zou
- Proteomics Laboratory, Medical and Healthy Analytical Center, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Ting Li
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology, Ministry of Health, 38 Xueyuan Road, Beijing 100191, China; Peking University Center for Human Disease Genomics, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Xiaolin Wang
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology, Ministry of Health, 38 Xueyuan Road, Beijing 100191, China; Peking University Center for Human Disease Genomics, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Wanqiong Yuan
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology, Ministry of Health, 38 Xueyuan Road, Beijing 100191, China; Peking University Center for Human Disease Genomics, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Yingyu Chen
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology, Ministry of Health, 38 Xueyuan Road, Beijing 100191, China; Peking University Center for Human Disease Genomics, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Wenling Han
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology, Ministry of Health, 38 Xueyuan Road, Beijing 100191, China; Peking University Center for Human Disease Genomics, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China.
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17
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Shen H, An M, Zou X, Zhao X, Wang Q, Xing G, Ji J. Evaluation of the accuracy of protein quantification using isotope TMPP-labeled peptides. Proteomics 2015; 15:2903-9. [DOI: 10.1002/pmic.201400495] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 03/12/2015] [Accepted: 04/28/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Hongyan Shen
- State Key Laboratory of Protein and Plant Gene Research; College of Life Sciences; Peking University; Beijing P. R. China
| | - Mingrui An
- State Key Laboratory of Protein and Plant Gene Research; College of Life Sciences; Peking University; Beijing P. R. China
| | - Xiao Zou
- State Key Laboratory of Protein and Plant Gene Research; College of Life Sciences; Peking University; Beijing P. R. China
| | - Xuyang Zhao
- State Key Laboratory of Protein and Plant Gene Research; College of Life Sciences; Peking University; Beijing P. R. China
| | - Qingsong Wang
- State Key Laboratory of Protein and Plant Gene Research; College of Life Sciences; Peking University; Beijing P. R. China
| | - Guowen Xing
- Institute of Organic Chemistry; College of Chemistry; Beijing Normal University; Beijing P. R. China
| | - Jianguo Ji
- State Key Laboratory of Protein and Plant Gene Research; College of Life Sciences; Peking University; Beijing P. R. China
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18
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Setner B, Rudowska M, Klem E, Cebrat M, Szewczuk Z. Peptides derivatized with bicyclic quaternary ammonium ionization tags. Sequencing via tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:995-1001. [PMID: 25303389 DOI: 10.1002/jms.3410] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/28/2014] [Accepted: 06/06/2014] [Indexed: 06/04/2023]
Abstract
Improving the sensitivity of detection and fragmentation of peptides to provide reliable sequencing of peptides is an important goal of mass spectrometric analysis. Peptides derivatized by bicyclic quaternary ammonium ionization tags: 1-azabicyclo[2.2.2]octane (ABCO) or 1,4-diazabicyclo[2.2.2]octane (DABCO), are characterized by an increased detection sensitivity in electrospray ionization mass spectrometry (ESI-MS) and longer retention times on the reverse-phase (RP) chromatography columns. The improvement of the detection limit was observed even for peptides dissolved in 10 mM NaCl. Collision-induced dissociation tandem mass spectrometry of quaternary ammonium salts derivatives of peptides showed dominant a- and b-type ions, allowing facile sequencing of peptides. The bicyclic ionization tags are stable in collision-induced dissociation experiments, and the resulted fragmentation pattern is not significantly influenced by either acidic or basic amino acid residues in the peptide sequence. Obtained results indicate the general usefulness of the bicyclic quaternary ammonium ionization tags for ESI-MS/MS sequencing of peptides.
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Affiliation(s)
- Bartosz Setner
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383, Wrocław, Poland
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19
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Shen H, He Z, Yan H, Xing Z, Chen Y, Xu W, Xu W, Ma M. The fronds tonoplast quantitative proteomic analysis in arsenic hyperaccumulator Pteris vittata L. J Proteomics 2014; 105:46-57. [PMID: 24508335 DOI: 10.1016/j.jprot.2014.01.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 01/22/2014] [Accepted: 01/27/2014] [Indexed: 12/30/2022]
Abstract
UNLABELLED Pteris vittata, the first known arsenic hyperaccumulating plant, can accumulate very high concentration arsenic in its aboveground tissues, while low in roots. Previous studies have suggested that arsenic vacuole compartmentalization may play an important role in the arsenic-hyperaccumulation in P. vittata, but the mechanism(s) of arsenic transport to vacuole are largely unknown. We obtained tonoplast isolated from fronds of P. vittata sporophyte grown under minus and 1mM arsenate for 3weeks by iodixanol step gradient centrifugation method, and then used TMPP protein labeling technology followed by liquid chromatography-a linear ion trap-Orbitrap hybrid mass spectrometer analysis for the quantitative detection of proteins. And we designed and used an "artificial" database for database searching. In total, 56 tonoplast proteins were identified; more than 70% of them were transport proteins. Under arsenate treatment, one TDT transporter protein, a member of the TerC family and a PDR-like protein were upregulated differentially. While V-ATPase subunits c, E, and G, and V-PPase, were downregulated. Additionally, the identified tonoplast proteins in our present study provide an informative basis for arsenic carriers or channels and help to clarify the regulation of tonoplast arsenic transport processes in P. vittata. BIOLOGICAL SIGNIFICANCE Vacuole compartmentalization is crucial to As hyperaccumulator P. vittata, while there is limited known arsenic transport proteins involved in vacuole compartmentalization. In this paper, we obtained tonoplast of P. vittata fronds by iodixanol step gradient centrifugation method and then used TMPP protein labeling proteome technology for the quantitative detection of fronds tonoplast proteins. Our findings are the first challenge to the tonoplast proteins data mining of P. vittata which provide an informative basis for As carriers or channels. The proteomic approach in our study is suited for detecting alterations tonoplast protein and help to clarify the regulation of tonoplast transport processes. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Affiliation(s)
- Hongling Shen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenyan He
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Huili Yan
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zenan Xing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanshan Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenxiu Xu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wenzhong Xu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Mi Ma
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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20
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Robotham SA, Kluwe C, Cannon JR, Ellington A, Brodbelt JS. De novo sequencing of peptides using selective 351 nm ultraviolet photodissociation mass spectrometry. Anal Chem 2013; 85:9832-8. [PMID: 24050806 DOI: 10.1021/ac402309h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Although in silico database search methods remain more popular for shotgun proteomics methods, de novo sequencing offers the ability to identify peptides derived from proteins lacking sequenced genomes and ones with subtle splice variants or truncations. Ultraviolet photodissociation (UVPD) of peptides derivatized by selective attachment of a chromophore at the N-terminus generates a characteristic series of y ions. The UVPD spectra of the chromophore-labeled peptides are simplified and thus amenable to de novo sequencing. This method resulted in an observed sequence coverage of 79% for cytochrome C (eight peptides), 47% for β-lactoglobulin (five peptides), 25% for carbonic anhydrase (six peptides), and 51% for bovine serum albumin (33 peptides). This strategy also allowed differentiation of proteins with high sequence homology as evidenced by de novo sequencing of two variants of green fluorescent protein.
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Affiliation(s)
- Scott A Robotham
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
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