1
|
James Sanford E, Bustamante Smolka M. A field guide to the proteomics of post-translational modifications in DNA repair. Proteomics 2022; 22:e2200064. [PMID: 35695711 PMCID: PMC9950963 DOI: 10.1002/pmic.202200064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 12/15/2022]
Abstract
All cells incur DNA damage from exogenous and endogenous sources and possess pathways to detect and repair DNA damage. Post-translational modifications (PTMs), in the past 20 years, have risen to ineluctable importance in the study of the regulation of DNA repair mechanisms. For example, DNA damage response kinases are critical in both the initial sensing of DNA damage as well as in orchestrating downstream activities of DNA repair factors. Mass spectrometry-based proteomics revolutionized the study of the role of PTMs in the DNA damage response and has canonized PTMs as central modulators of nearly all aspects of DNA damage signaling and repair. This review provides a biologist-friendly guide for the mass spectrometry analysis of PTMs in the context of DNA repair and DNA damage responses. We reflect on the current state of proteomics for exploring new mechanisms of PTM-based regulation and outline a roadmap for designing PTM mapping experiments that focus on the DNA repair and DNA damage responses.
Collapse
Key Words
- LC-MS/MS, technology, bottom-up proteomics, technology, signal transduction, cell biology
- phosphoproteomics, technology, post-translational modification analysis, technology, post-translational modifications, cell biology, mass spectrometry
Collapse
Affiliation(s)
- Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853,Corresponding author:
| |
Collapse
|
2
|
Hollerbach AL, Giberson CM, Lee JY, Huntley AP, Smith RD, Ibrahim YM. Improving Signal to Noise Ratios in Ion Mobility Spectrometry and Structures for Lossless Ion Manipulations (SLIM) using a High Dynamic Range Analog-to-Digital Converter. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2698-2706. [PMID: 34590845 PMCID: PMC8742676 DOI: 10.1021/jasms.1c00226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Signal digitization is a commonly overlooked part of ion mobility-mass spectrometry (IMS-MS) workflows, yet it greatly affects signal-to-noise ratio and MS resolution measurements. Here, we report on the integration of a 2 GS/s, 14-bit ADC with structures for lossless ion manipulations (SLIM-IMS-MS) and compare the performance to a commonly used 8-bit ADC. The 14-bit ADC provided a reduction in the digitized noise by a factor of ∼6, owing largely to the use of smaller bit sizes. The low baseline allowed threshold voltage levels to be set very close to the MCP baseline voltage, allowing for as much signal to be acquired as possible without overloading or excessive digitization of MCP baseline noise. Analyses of Agilent tuning mixture ions and a mixture of heavy labeled phosphopeptides showed that the 14-bit ADC provided a ∼1.5-2× signal-to-noise (S/N) increase for high intensity ions, such as the Agilent tuning mixture ions and the 2+ and 3+ charge states of many phosphopeptide constituents. However, signal enhancements were as much as 10-fold for low intensity ions, and the 14-bit ADC enabled discernible signal intensities otherwise lost using an 8-bit digitizer. Additionally, the 14-bit ADC required ∼14-fold fewer mass spectra to be averaged to produce a mass spectrum with a similar S/N as the 8-bit ADC, demonstrating ∼10× higher measurement throughput. The high resolution, low baseline, and fast speed of the new 14-bit ADC enables high performance digitization of MS, IMS-MS, and SLIM-IMS-MS spectra and provides a much better picture of analyte profiles in complex mixtures.
Collapse
Affiliation(s)
- Adam L Hollerbach
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Cameron M Giberson
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Joon-Yong Lee
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Adam P Huntley
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| |
Collapse
|
3
|
Ivanov MV, Bubis JA, Gorshkov V, Abdrakhimov DA, Kjeldsen F, Gorshkov MV. Boosting MS1-only Proteomics with Machine Learning Allows 2000 Protein Identifications in Single-Shot Human Proteome Analysis Using 5 min HPLC Gradient. J Proteome Res 2021; 20:1864-1873. [PMID: 33720732 DOI: 10.1021/acs.jproteome.0c00863] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Proteome-wide analyses rely on tandem mass spectrometry and the extensive separation of proteolytic mixtures. This imposes considerable instrumental time consumption, which is one of the main obstacles in the broader acceptance of proteomics in biomedical and clinical research. Recently, we presented a fast proteomic method termed DirectMS1 based on ultrashort LC gradients as well as MS1-only mass spectra acquisition and data processing. The method allows significant reduction of the proteome-wide analysis time to a few minutes at the depth of quantitative proteome coverage of 1000 proteins at 1% false discovery rate (FDR). In this work, to further increase the capabilities of the DirectMS1 method, we explored the opportunities presented by the recent progress in the machine-learning area and applied the LightGBM decision tree boosting algorithm to the scoring of peptide feature matches when processing MS1 spectra. Furthermore, we integrated the peptide feature identification algorithm of DirectMS1 with the recently introduced peptide retention time prediction utility, DeepLC. Additional approaches to improve the performance of the DirectMS1 method are discussed and demonstrated, such as using FAIMS for gas-phase ion separation. As a result of all improvements to DirectMS1, we succeeded in identifying more than 2000 proteins at 1% FDR from the HeLa cell line in a 5 min gradient LC-FAIMS/MS1 analysis. The data sets generated and analyzed during the current study have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD023977.
Collapse
Affiliation(s)
- Mark V Ivanov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
| | - Julia A Bubis
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
| | - Vladimir Gorshkov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Daniil A Abdrakhimov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia.,Moscow Institute of Physics and Technology, Institutsky lane 9, Dolgoprudny, Moscow Region 141700, Russia
| | - Frank Kjeldsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
| |
Collapse
|
4
|
Kim SW, Kwon S, Kim YK. Graphene Oxide Derivatives and Their Nanohybrid Structures for Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Analysis of Small Molecules. NANOMATERIALS 2021; 11:nano11020288. [PMID: 33499396 PMCID: PMC7910985 DOI: 10.3390/nano11020288] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/12/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) has been considered as one of the most powerful analytical tools for mass spectrometry (MS) analysis of large molecular weight compounds such as proteins, nucleic acids, and synthetic polymers thanks to its high sensitivity, high resolution, and compatibility with high-throughput analysis. Despite these advantages, MALDI cannot be applied to MS analysis of small molecular weight compounds (<500 Da) because of the matrix interference in low mass region. Therefore, numerous efforts have been devoted to solving this issue by using metal, semiconductor, and carbon nanomaterials for MALDI time-of-flight MS (MALDI-TOF-MS) analysis instead of organic matrices. Among those nanomaterials, graphene oxide (GO) is of particular interest considering its unique and highly tunable chemical structures composed of the segregated sp2 carbon domains surrounded by sp3 carbon matrix. Chemical modification of GO can precisely tune its physicochemical properties, and it can be readily incorporated with other functional nanomaterials. In this review, the advances of GO derivatives and their nanohybrid structures as alternatives to organic matrices are summarized to demonstrate their potential and practical aspect for MALDI-TOF-MS analysis of small molecules.
Collapse
Affiliation(s)
- Seung-Woo Kim
- Department of Chemistry, Dongguk University-Seoul, 30 Pildong-ro, Jung-gu, Seoul 04620, Korea;
| | - Sunbum Kwon
- Department of Chemistry, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Korea
- Correspondence: (S.-W.K.); (Y.-K.K.); Tel.: +82-2-820-5201 (S.-W.K.); +82-2-2260-3214 (Y.-K.K.)
| | - Young-Kwan Kim
- Department of Chemistry, Dongguk University-Seoul, 30 Pildong-ro, Jung-gu, Seoul 04620, Korea;
- Correspondence: (S.-W.K.); (Y.-K.K.); Tel.: +82-2-820-5201 (S.-W.K.); +82-2-2260-3214 (Y.-K.K.)
| |
Collapse
|
5
|
Corbett JR, Robinson DE, Patrie SM. Robustness and Ruggedness of Isoelectric Focusing and Superficially Porous Liquid Chromatography with Fourier Transform Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:346-354. [PMID: 33274937 PMCID: PMC10476448 DOI: 10.1021/jasms.0c00355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
An investigation of a multidimensional proteomics workflow composed of off-gel isoelectric focusing (IEF) and superficially porous liquid chromatography (SPLC) with Fourier transform mass spectrometry (FTMS) was completed in order to assess various figures of merit associated with intact protein measurements. Triplicate analysis performed at both high and low FTMS resolutions on the E. coli proteome resulted in ∼900 redundant proteoforms from 3 to 95 kDa. Normalization of the chromatographic axis to identified proteoforms enabled reproducible physicochemical property measurements between proteome replicates with inter-replicate variances of ±3 ppm mass error for proteoforms <30 kDa, ±1.1 Da for proteins >30 kDa, ±12 s retention time error, and ±0.21 pI units. The results for E. coli and standard proteins revealed a correlation between pI precision and proteoform abundance with species detected in multiple IEF fractions exhibiting pI precisions less than the theoretical resolution of the off-gel system (±0.05 vs ±0.17, respectively). Evaluation of differentially modified proteoforms of standard proteins revealed that high sample loads (100s μgrams) change the IEF pH gradient profile, leading to sample broadening that facilitates resolution of charged post-translational modifications (e.g., phosphorylation, sialylation). Despite the impact of sample load on IEF resolution, results on standard proteins measured directly or after being spiked into E. coli demonstrated that the reproducibility of the workflow permitted recombination of the MS signal across IEF fractions in a manner supporting the evaluation of three label-free quantitation metrics for intact protein studies (proteoforms, proteoform ratios, and protein) over 102-103 sample amount with low femtomole detection limits.
Collapse
Affiliation(s)
- John R Corbett
- Department of Pathology, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
- Department of Bioengineering, UT Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Dana E Robinson
- Department of Pathology, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Steven M Patrie
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Pathology, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| |
Collapse
|
6
|
Kuhring M, Doellinger J, Nitsche A, Muth T, Renard BY. TaxIt: An Iterative Computational Pipeline for Untargeted Strain-Level Identification Using MS/MS Spectra from Pathogenic Single-Organism Samples. J Proteome Res 2020; 19:2501-2510. [PMID: 32362126 DOI: 10.1021/acs.jproteome.9b00714] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Untargeted accurate strain-level classification of a priori unidentified organisms using tandem mass spectrometry is a challenging task. Reference databases often lack taxonomic depth, limiting peptide assignments to the species level. However, the extension with detailed strain information increases runtime and decreases statistical power. In addition, larger databases contain a higher number of similar proteomes. We present TaxIt, an iterative workflow to address the increasing search space required for MS/MS-based strain-level classification of samples with unknown taxonomic origin. TaxIt first applies reference sequence data for initial identification of species candidates, followed by automated acquisition of relevant strain sequences for low level classification. Furthermore, proteome similarities resulting in ambiguous taxonomic assignments are addressed with an abundance weighting strategy to increase the confidence in candidate taxa. For benchmarking the performance of our method, we apply our iterative workflow on several samples of bacterial and viral origin. In comparison to noniterative approaches using unique peptides or advanced abundance correction, TaxIt identifies microbial strains correctly in all examples presented (with one tie), thereby demonstrating the potential for untargeted and deeper taxonomic classification. TaxIt makes extensive use of public, unrestricted, and continuously growing sequence resources such as the NCBI databases and is available under open-source BSD license at https://gitlab.com/rki_bioinformatics/TaxIt.
Collapse
Affiliation(s)
- Mathias Kuhring
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353 Berlin, Germany.,Core Unit Bioinformatics, Berlin Institute of Health (BIH), 10178 Berlin, Germany.,Berlin Institute of Health Metabolomics Platform, Berlin Institute of Health (BIH), 10178 Berlin, Germany.,Max Delbrück Center (MDC) for Molecular Medicine, 13125 Berlin, Germany
| | - Joerg Doellinger
- Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS 6), Robert Koch Institute, 13353 Berlin, Germany.,Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, 13353 Berlin, Germany
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, 13353 Berlin, Germany
| | - Thilo Muth
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353 Berlin, Germany.,eScience Division (S.3), Federal Institute for Materials Research and Testing, 12489 Berlin, Germany
| | - Bernhard Y Renard
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353 Berlin, Germany.,Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, 14482 Potsdam, Germany
| |
Collapse
|
7
|
Ivanov MV, Bubis JA, Gorshkov V, Tarasova IA, Levitsky LI, Lobas AA, Solovyeva EM, Pridatchenko ML, Kjeldsen F, Gorshkov MV. DirectMS1: MS/MS-Free Identification of 1000 Proteins of Cellular Proteomes in 5 Minutes. Anal Chem 2020; 92:4326-4333. [DOI: 10.1021/acs.analchem.9b05095] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Mark V. Ivanov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Julia A. Bubis
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Vladimir Gorshkov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Irina A. Tarasova
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Lev I. Levitsky
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Anna A. Lobas
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Elizaveta M. Solovyeva
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Marina L. Pridatchenko
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Frank Kjeldsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Mikhail V. Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology (State University), 141700 Dolgoprudny, Russia
| |
Collapse
|
8
|
Timp W, Timp G. Beyond mass spectrometry, the next step in proteomics. SCIENCE ADVANCES 2020; 6:eaax8978. [PMID: 31950079 PMCID: PMC6954058 DOI: 10.1126/sciadv.aax8978] [Citation(s) in RCA: 167] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 11/19/2019] [Indexed: 05/08/2023]
Abstract
Proteins can be the root cause of a disease, and they can be used to cure it. The need to identify these critical actors was recognized early (1951) by Sanger; the first biopolymer sequenced was a peptide, insulin. With the advent of scalable, single-molecule DNA sequencing, genomics and transcriptomics have since propelled medicine through improved sensitivity and lower costs, but proteomics has lagged behind. Currently, proteomics relies mainly on mass spectrometry (MS), but instead of truly sequencing, it classifies a protein and typically requires about a billion copies of a protein to do it. Here, we offer a survey that illuminates a few alternatives with the brightest prospects for identifying whole proteins and displacing MS for sequencing them. These alternatives all boast sensitivity superior to MS and promise to be scalable and seem to be adaptable to bioinformatics tools for calling the sequence of amino acids that constitute a protein.
Collapse
Affiliation(s)
- Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Gregory Timp
- Departments of Electrical Engineering and Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| |
Collapse
|
9
|
Fu L, Sun X, Gao Y, Chen R. Tannic Acid: a Novel Calibrator for Facile and Accurate Mass Measurement of Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1545-1549. [PMID: 31214925 DOI: 10.1007/s13361-019-02211-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/06/2019] [Accepted: 02/24/2019] [Indexed: 06/09/2023]
Abstract
Accurate mass calibration is beneficial to the identification of the unknown compounds quickly and accurately. The ESI mass spectrum of tannic acid (TA) tends to a normal distribution of the cluster ion peaks in m/z range from 371.0368 to 1739.1169. Based on the interesting result, we reported the use of TA, a natural plant polyphenol, as a novel calibrator for electrospray ionization mass spectrometry (ESI MS), which has the following three advantages, including (1) easy preparation, (2) the calibration range of m/z 200~2000, and (3) the calibration error is around 3.00 ppm in positive ion mode, which is less than the use of sodium formate (SF) and Prod #88323 calibrators. This TA calibrator has great potential for the wide applications in biological, chemical, and pharmacal analysis.
Collapse
Affiliation(s)
- Ling Fu
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, 650500, China
| | - Xiaochun Sun
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, 650500, China
| | - Yumei Gao
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, 650500, China
| | - Rui Chen
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, 650500, China.
| |
Collapse
|
10
|
Wang L, Wang Y, Jiang S, Ye M, Su P, Xiong B. Microfluidic nitrogen-assisted nanoelectrospray emitter: A monolithic interface for accurate mass measurements based on a single nozzle. J Chromatogr A 2016; 1470:1-8. [DOI: 10.1016/j.chroma.2016.09.065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 09/25/2016] [Accepted: 09/27/2016] [Indexed: 01/07/2023]
|
11
|
Park SG, Anderson GA, Navare AT, Bruce JE. Parallel Spectral Acquisition with an Ion Cyclotron Resonance Cell Array. Anal Chem 2016; 88:1162-8. [PMID: 26669509 PMCID: PMC4848028 DOI: 10.1021/acs.analchem.5b02987] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mass measurement accuracy is a critical analytical figure-of-merit in most areas of mass spectrometry application. However, the time required for acquisition of high-resolution, high mass accuracy data limits many applications and is an aspect under continual pressure for development. Current efforts target implementation of higher electrostatic and magnetic fields because ion oscillatory frequencies increase linearly with field strength. As such, the time required for spectral acquisition of a given resolving power and mass accuracy decreases linearly with increasing fields. Mass spectrometer developments to include multiple high-resolution detectors that can be operated in parallel could further decrease the acquisition time by a factor of n, the number of detectors. Efforts described here resulted in development of an instrument with a set of Fourier transform ion cyclotron resonance (ICR) cells as detectors that constitute the first MS array capable of parallel high-resolution spectral acquisition. ICR cell array systems consisting of three or five cells were constructed with printed circuit boards and installed within a single superconducting magnet and vacuum system. Independent ion populations were injected and trapped within each cell in the array. Upon filling the array, all ions in all cells were simultaneously excited and ICR signals from each cell were independently amplified and recorded in parallel. Presented here are the initial results of successful parallel spectral acquisition, parallel mass spectrometry (MS) and MS/MS measurements, and parallel high-resolution acquisition with the MS array system.
Collapse
Affiliation(s)
- Sung-Gun Park
- Department of Genome Sciences, University of Washington , Seattle, Washington 98109, United States
| | - Gordon A Anderson
- GAA Custom Engineering, LLC, Benton City, Washington 99320, United States
| | - Arti T Navare
- Department of Genome Sciences, University of Washington , Seattle, Washington 98109, United States
| | - James E Bruce
- Department of Genome Sciences, University of Washington , Seattle, Washington 98109, United States
| |
Collapse
|
12
|
Dallongeville S, Garnier N, Rolando C, Tokarski C. Proteins in Art, Archaeology, and Paleontology: From Detection to Identification. Chem Rev 2015; 116:2-79. [PMID: 26709533 DOI: 10.1021/acs.chemrev.5b00037] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sophie Dallongeville
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Nicolas Garnier
- SARL Laboratoire Nicolas Garnier , 63270 Vic le Comte, France
| | - Christian Rolando
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Caroline Tokarski
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| |
Collapse
|
13
|
Three-Dimensional Electro-Sonic Flow Focusing Ionization Microfluidic Chip for Mass Spectrometry. MICROMACHINES 2015. [DOI: 10.3390/mi6121463] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
14
|
Engaging challenges in glycoproteomics: recent advances in MS-based glycopeptide analysis. Bioanalysis 2015; 7:113-31. [PMID: 25558940 DOI: 10.4155/bio.14.272] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The proteomic analysis of glycosylation is uniquely challenging. The numerous and varied biological roles of protein-linked glycans have fueled a tremendous demand for technologies that enable rapid, in-depth structural examination of glycosylated proteins in complex biological systems. In turn, this demand has driven many innovations in wide ranging fields of bioanalytical science. This review will summarize key developments in glycoprotein separation and enrichment, glycoprotein proteolysis strategies, glycopeptide separation and enrichment, the role of mass measurement accuracy in glycopeptide detection, glycopeptide ion dissociation methods for MS/MS, and informatic tools for glycoproteomic analysis. In aggregate, this selection of topics serves to encapsulate the present status of MS-based analytical technologies for engaging the challenges of glycoproteomic analysis.
Collapse
|
15
|
Zhang H, Wang DZ, Xie ZX, Zhang SF, Wang MH, Lin L. Comparative proteomics reveals highly and differentially expressed proteins in field-collected and laboratory-cultured blooming cells of the diatom S
keletonema costatum. Environ Microbiol 2015; 17:3976-91. [DOI: 10.1111/1462-2920.12914] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 05/19/2015] [Indexed: 01/09/2023]
Affiliation(s)
- Hao Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology; Xiamen University; Xiamen 361005 China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology; Xiamen University; Xiamen 361005 China
| | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology; Xiamen University; Xiamen 361005 China
| | - Shu-Fei Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology; Xiamen University; Xiamen 361005 China
| | - Ming-Hua Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology; Xiamen University; Xiamen 361005 China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology; Xiamen University; Xiamen 361005 China
| |
Collapse
|
16
|
Black WA, Stocks BB, Mellors JS, Engen JR, Ramsey JM. Utilizing Microchip Capillary Electrophoresis Electrospray Ionization for Hydrogen Exchange Mass Spectrometry. Anal Chem 2015; 87:6280-7. [PMID: 25992468 DOI: 10.1021/acs.analchem.5b01179] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Hydrogen exchange (HX) mass spectrometry (MS) of complex mixtures requires a fast, reproducible, and high peak capacity separation prior to MS detection. The current paradigm relies on liquid chromatography (LC) with fast gradients performed at low temperatures to minimize back exchange. Unfortunately, under these conditions, the efficiency of LC is limited due to resistance to mass transfer, reducing the capability to analyze complex samples. Capillary electrophoresis (CE), on the other hand, is not limited by resistance to mass transfer, enabling very rapid separations that are not adversely affected by low temperature. Previously, we have demonstrated an integrated microfluidic device coupling CE with electrospray ionization (ESI) capable of very rapid and high efficiency separations. In this work, we demonstrate the utility of this microchip CE-ESI device for HX MS. High speed CE-ESI of a bovine hemoglobin pepsin digestion was performed in 1 min with a peak capacity of 62 versus a similar LC separation performed in 7 min with peak capacity of 31. A room temperature CE method performed in 1.25 min provided similar deuterium retention as an 8.5 min LC method conducted at 0 °C. Separation of a complex mixture with CE was done with considerably better speed and nearly triple the peak capacity than the equivalent separation by LC. Overall, the results indicate the potential utility of microchip CE-ESI for HX MS.
Collapse
Affiliation(s)
| | - Bradley B Stocks
- ∥Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | | | - John R Engen
- ∥Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | | |
Collapse
|
17
|
Kim YK, Min DH. The Structural Influence of Graphene Oxide on Its Fragmentation during Laser Desorption/Ionization Mass Spectrometry for Efficient Small-Molecule Analysis. Chemistry 2015; 21:7217-23. [DOI: 10.1002/chem.201404067] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Indexed: 12/19/2022]
|
18
|
Rang J, He H, Wang T, Ding X, Zuo M, Quan M, Sun Y, Yu Z, Hu S, Xia L. Comparative analysis of genomics and proteomics in Bacillus thuringiensis 4.0718. PLoS One 2015; 10:e0119065. [PMID: 25781161 PMCID: PMC4363619 DOI: 10.1371/journal.pone.0119065] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 01/09/2015] [Indexed: 11/18/2022] Open
Abstract
Bacillus thuringiensis is a widely used biopesticide that produced various insecticidal active substances during its life cycle. Separation and purification of numerous insecticide active substances have been difficult because of the relatively short half-life of such substances. On the other hand, substances can be synthetized at different times during development, so samples at different stages have to be studied, further complicating the analysis. A dual genomic and proteomic approach would enhance our ability to identify such substances, and particularily using mass spectrometry-based proteomic methods. The comparative analysis for genomic and proteomic data have showed that not all of the products deduced from the annotated genome could be identified among the proteomic data. For instance, genome annotation results showed that 39 coding sequences in the whole genome were related to insect pathogenicity, including five cry genes. However, Cry2Ab, Cry1Ia, Cytotoxin K, Bacteriocin, Exoenzyme C3 and Alveolysin could not be detected in the proteomic data obtained. The sporulation-related proteins were also compared analysis, results showed that the great majority sporulation-related proteins can be detected by mass spectrometry. This analysis revealed Spo0A~P, SigF, SigE(+), SigK(+) and SigG(+), all known to play an important role in the process of spore formation regulatory network, also were displayed in the proteomic data. Through the comparison of the two data sets, it was possible to infer that some genes were silenced or were expressed at very low levels. For instance, found that cry2Ab seems to lack a functional promoter while cry1Ia may not be expressed due to the presence of transposons. With this comparative study a relatively complete database can be constructed and used to transform hereditary material, thereby prompting the high expression of toxic proteins. A theoretical basis is provided for constructing highly virulent engineered bacteria and for promoting the application of proteogenomics in the life sciences.
Collapse
Affiliation(s)
- Jie Rang
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
| | - Hao He
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
| | - Ting Wang
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
| | - Xuezhi Ding
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
- * E-mail: (XZD); (LQX)
| | - Mingxing Zuo
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
| | - Meifang Quan
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
| | - Yunjun Sun
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
| | - Ziquan Yu
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
| | - Shengbiao Hu
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
| | - Liqiu Xia
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
- * E-mail: (XZD); (LQX)
| |
Collapse
|
19
|
Kou Q, Wu S, Liu X. A new scoring function for top-down spectral deconvolution. BMC Genomics 2014; 15:1140. [PMID: 25523396 PMCID: PMC4378558 DOI: 10.1186/1471-2164-15-1140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 12/11/2014] [Indexed: 12/04/2022] Open
Abstract
Background Top-down mass spectrometry plays an important role in intact protein identification and characterization. Top-down mass spectra are more complex than bottom-up mass spectra because they often contain many isotopomer envelopes from highly charged ions, which may overlap with one another. As a result, spectral deconvolution, which converts a complex top-down mass spectrum into a monoisotopic mass list, is a key step in top-down spectral interpretation. Results In this paper, we propose a new scoring function, L-score, for evaluating isotopomer envelopes. By combining L-score with MS-Deconv, a new software tool, MS-Deconv+, was developed for top-down spectral deconvolution. Experimental results showed that MS-Deconv+ outperformed existing software tools in top-down spectral deconvolution. Conclusions L-score shows high discriminative ability in identification of isotopomer envelopes. Using L-score, MS-Deconv+ reports many correct monoisotopic masses missed by other software tools, which are valuable for proteoform identification and characterization. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1140) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 535 W, Michigan Street, Indianapolis, IN 46202, USA.
| |
Collapse
|
20
|
Bhandari DR, Schott M, Römpp A, Vilcinskas A, Spengler B. Metabolite localization by atmospheric pressure high-resolution scanning microprobe matrix-assisted laser desorption/ionization mass spectrometry imaging in whole-body sections and individual organs of the rove beetle Paederus riparius. Anal Bioanal Chem 2014; 407:2189-201. [PMID: 25424178 PMCID: PMC4357651 DOI: 10.1007/s00216-014-8327-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 11/04/2014] [Accepted: 11/06/2014] [Indexed: 11/25/2022]
Abstract
Mass spectrometry imaging provides for non-targeted, label-free chemical imaging. In this study, atmospheric pressure high-resolution scanning microprobe matrix-assisted laser desorption/ionization mass spectrometry imaging (AP-SMALDI MSI) was used for the first time to describe the chemical distribution of the defensive compounds pederin, pseudopederin, and pederon in tissue sections (16 μm thick) of the rove beetle Paederus riparius. The whole-insect tissue section was scanned with a 20-μm step size. Mass resolution of the orbital trapping mass spectrometer was set to 100,000 at m/z 200. Additionally, organ-specific compounds were identified for brain, nerve cord, eggs, gut, ovaries, and malpighian tubules. To confirm the distribution of the specific compounds, individual organs from the insect were dissected, and MSI experiments were performed on the dissected organs. Three ganglia of the nerve cord, with a dimension of 250–500 μm, were measured with 10-μm spatial resolution. High-quality m/z images, based on high spatial resolution and high mass accuracy were generated. These features helped to assign mass spectral peaks with high confidence. Mass accuracy of the imaging experiments was <3 ppm root mean square error, and mapping of different compound classes from a single experiment was possible. This approach improved the understanding of the biochemistry of P. riparius. Concentration differences and distributions of pederin and its analogues could be visualized in the whole-insect section. Without any labeling, we assigned key lipids for specific organs to describe their location in the body and to identify morphological structures with a specificity higher than with staining or immunohistology methods.
Collapse
Affiliation(s)
- Dhaka Ram Bhandari
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Schubertstraße 60, Building 16, 35392 Giessen, Germany
| | - Matthias Schott
- Institute of Phytopathology and Applied Zoology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Andreas Römpp
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Schubertstraße 60, Building 16, 35392 Giessen, Germany
| | - Andreas Vilcinskas
- Institute of Phytopathology and Applied Zoology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Schubertstraße 60, Building 16, 35392 Giessen, Germany
| |
Collapse
|
21
|
Laskay ÜA, Srzentić K, Monod M, Tsybin YO. Extended bottom-up proteomics with secreted aspartic protease Sap9. J Proteomics 2014; 110:20-31. [DOI: 10.1016/j.jprot.2014.07.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/04/2014] [Accepted: 07/18/2014] [Indexed: 01/21/2023]
|
22
|
Nagornov KO, Gorshkov MV, Kozhinov AN, Tsybin YO. High-Resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry with Increased Throughput for Biomolecular Analysis. Anal Chem 2014; 86:9020-8. [DOI: 10.1021/ac501579h] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Konstantin O. Nagornov
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Mikhail V. Gorshkov
- Institute
for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology (State University), 141707 Dolgoprudny,
Moscow Region, Russia
| | - Anton N. Kozhinov
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Yury O. Tsybin
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| |
Collapse
|
23
|
Ahmed FE. Utility of mass spectrometry for proteome ana lysis: part I. Conceptual and experimental approaches. Expert Rev Proteomics 2014; 5:841-64. [DOI: 10.1586/14789450.5.6.841] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
24
|
Moradian A, Kalli A, Sweredoski MJ, Hess S. The top-down, middle-down, and bottom-up mass spectrometry approaches for characterization of histone variants and their post-translational modifications. Proteomics 2013; 14:489-97. [DOI: 10.1002/pmic.201300256] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 07/30/2013] [Accepted: 08/15/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Annie Moradian
- Proteome Exploration Laboratory; Beckman Institute; California Institute of Technology; Pasadena CA USA
| | - Anastasia Kalli
- Department of Pathology and Laboratory Medicine; Children's Hospital Los Angeles; Los Angeles CA USA
| | - Michael J. Sweredoski
- Proteome Exploration Laboratory; Beckman Institute; California Institute of Technology; Pasadena CA USA
| | - Sonja Hess
- Proteome Exploration Laboratory; Beckman Institute; California Institute of Technology; Pasadena CA USA
| |
Collapse
|
25
|
Ji J, Nie L, Li Y, Yang P, Liu B. Simultaneous Online Enrichment and Identification of Trace Species Based on Microfluidic Droplets. Anal Chem 2013; 85:9617-22. [DOI: 10.1021/ac4018082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Ji Ji
- Department
of Chemistry and Institutes of Biomedical Sciences, Fudan University, 220
HanDan Road, Shanghai 200433, China
| | - Lei Nie
- Department
of Chemistry and Institutes of Biomedical Sciences, Fudan University, 220
HanDan Road, Shanghai 200433, China
- Shanghai Institute of Quality Inspection and Technical Research, Shanghai 201114, China
| | - Yixin Li
- Department
of Chemistry and Institutes of Biomedical Sciences, Fudan University, 220
HanDan Road, Shanghai 200433, China
| | - Pengyuan Yang
- Department
of Chemistry and Institutes of Biomedical Sciences, Fudan University, 220
HanDan Road, Shanghai 200433, China
| | - Baohong Liu
- Department
of Chemistry and Institutes of Biomedical Sciences, Fudan University, 220
HanDan Road, Shanghai 200433, China
| |
Collapse
|
26
|
Gao D, Liu H, Jiang Y, Lin JM. Recent advances in microfluidics combined with mass spectrometry: technologies and applications. LAB ON A CHIP 2013; 13:3309-22. [PMID: 23824006 DOI: 10.1039/c3lc50449b] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Instrument miniaturization is one of the critical issues to improve sensitivity, speed, throughput, and to reduce the cost of analysis. Microfluidics possesses the ability to handle small sample amounts, with minimal concerns related to sample loss and cross-contamination, problems typical for standard fluidic manipulations. Moreover, the native properties of microfluidics provide the potential for high-density, parallel sample processing, and high-throughput analysis. Recently, the coupling of microfluidic devices to mass spectrometry, especially electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI), has attracted an increasing interest and produced tremendous achievements. The interfaces between microfluidics and mass spectrometry are one of the primary focused problems. In this review, we summarize the latest achievements since 2008 in the field of the technologies and applications in the combining of microfluidics with ESI-MS and MALDI-MS. The integration of several analytical functions on a microfluidic device such as sample pretreatment and separations before sample introduction into the mass spectrometer is also discussed.
Collapse
Affiliation(s)
- Dan Gao
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | | | | | | |
Collapse
|
27
|
Li Y, Zhang N, Zhou Y, Wang J, Zhang Y, Wang J, Xiong C, Chen S, Nie Z. Induced dual-nanospray: a novel internal calibration method for convenient and accurate mass measurement. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1446-1449. [PMID: 23797862 DOI: 10.1007/s13361-013-0670-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 06/02/2023]
Abstract
Accurate mass information is of great importance in the determination of unknown compounds. An effective and easy-to-control internal mass calibration method will dramatically benefit accurate mass measurement. Here we reported a simple induced dual-nanospray internal calibration device which has the following three advantages: (1) the two sprayers are in the same alternating current field; thus both reference ions and sample ions can be simultaneously generated and recorded. (2) It is very simple and can be easily assembled. Just two metal tubes, two nanosprayers, and an alternating current power supply are included. (3)With the low-flow-rate character and the versatility of nanoESI, this calibration method is capable of calibrating various samples, even untreated complex samples such as urine and other biological samples with small sample volumes. The calibration errors are around 1 ppm in positive ion mode and 3 ppm in negative ion mode with good repeatability. This new internal calibration method opens up new possibilities in the determination of unknown compounds, and it has great potential for the broad applications in biological and chemical analysis.
Collapse
Affiliation(s)
- Yafeng Li
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Kalita M, Kasumov T, Brasier AR, Sadygov RG. Use of theoretical peptide distributions in phosphoproteome analysis. J Proteome Res 2013; 12:3207-14. [PMID: 23731183 PMCID: PMC3758224 DOI: 10.1021/pr4003382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The high mass accuracy and resolution of modern mass spectrometers provides new opportunities to employ theoretical peptide distributions in large-scale proteomic studies. We used theoretical distributions to study noise filtering and mass measurement errors and to examine mass-based differentiation of phosphorylated and nonphosphorylated peptides. Only the monoisotopic mass of the experimental precursor ion was necessary for this analysis. We found that peak deviations can be used to characterize the modification states of peptides in a sample. When applied to large-scale proteomic data sets, the peak deviation distribution can be used to filter chemical/electronic noise for singly charged species. Using peak deviation distributions, it is possible to separate the phosphorylated peptides from the nonphosphorylated peptides, enabling evaluation of the phosphoproteome content of a sample. Because this approach is simple, with light computational requirements, the analysis of theoretical peptide distributions has a significant potential for application to phosphoproteome analyses. For our studies we used publicly available data sets from three large-scale proteomic studies.
Collapse
Affiliation(s)
- Mridul Kalita
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77573
| | - Takhar Kasumov
- Department of Gastroenterology and Hepatology, Cleveland Clinic, 9500 Euclid, Avenue, Cleveland, OH 44195
| | - Allan R. Brasier
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77573
| | - Rovshan G. Sadygov
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77573
| |
Collapse
|
29
|
|
30
|
Cataldi TRI, Bianco G, Fonseca J, Schmitt-Kopplin P. Perceiving the chemical language of Gram-negative bacteria: listening by high-resolution mass spectrometry. Anal Bioanal Chem 2012; 405:493-507. [PMID: 22986985 DOI: 10.1007/s00216-012-6371-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 08/06/2012] [Accepted: 08/17/2012] [Indexed: 01/27/2023]
Abstract
Gram-negative bacteria use N-acylhomoserine lactones (AHLs) as their command language to coordinate population behavior during invasion and colonization of higher organisms. Although many different bacterial bioreporters are available for AHLs monitoring, in which a phenotypic response, e.g. bioluminescence, violacin production, and β-galactosidase activity, is exploited, mass spectrometry (MS) is the most versatile detector for rapid analysis of AHLs in complex microbial samples, with or without prior separation steps. In this paper we critically review recent advances in the application of high-resolution MS to analysis of the quorum sensing (QS) signaling molecules used by Gram-negative bacteria, with much emphasis on AHLs. A critical review of the use of bioreporters in the study of AHLs is followed by a short methodological survey of the capabilities of high-resolution mass spectrometry (HRMS), including Fourier-transform ion cyclotron resonance (FTICR) MS and quadrupole time-of-flight (qTOF) MS. Use of infusion electrospray ultrahigh-resolution FTICR MS (12 Tesla) enables accurate mass measurements for determination of the elemental formulas of AHLs in Acidovorax sp. N35 and Burkholderia ubonensis AB030584. Results obtained by coupling liquid chromatography with a hybrid quadrupole linear ion trap-FTICR mass spectrometer (LC-LTQ-FTICRMS, 7-T) for characterization of acylated homoserine lactones in the human pathogen Pseudomonas aeruginosa are presented. UPLC-ESI-qTOF MS has also proved to be suitable for identification of 3O-C(10)HSL in Pseudomonas putida IsoF cell culture supernatant. Aspects of sample preparation and the avoidance of analytical pitfalls are also emphasized.
Collapse
Affiliation(s)
- Tommaso R I Cataldi
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy.
| | | | | | | |
Collapse
|
31
|
Svilar L, Stankov-Jovanovic V, Lesage D, Dossmann H, Tabet JC. High-resolution mass spectrometry and hydrogen/deuterium exchange study of mitorubrin azaphilones and nitrogenized analogues. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:969-977. [PMID: 22899505 DOI: 10.1002/jms.3044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Azaphilones represent numerous groups of wild fungal secondary metabolites that exhibit exceptional tendency to bind to nitrogen atoms in various molecules, especially those containing the amine group. Nitrogenized analogues of mitorubrin azaphilones, natural secondary metabolites of Hypoxylon fragiforme fungus, have been detected in the fungal methanol extract in very low concentrations. Positive electrospray ionization interfaced with high-resolution mass spectrometry was applied for confirmation of the elemental composition of protonated species. Collision-induced dissociation (CID) experiments have been performed, and fragmentation mechanisms have been proposed. Additional information regarding both secondary metabolite analogue families has been reached by application of gas-phase proton/deuterium (H/D) exchanges performed in the collision cell of a triple quadrupole mass spectrometer. An incomplete H/D exchange with one proton less than expected was observed for both protonated mitorubrin azaphilones and their nitrogenized analogues. By means of the density functional theory, an appropriate explanation of this behavior was provided, and it revealed some information concerning gas-phase H/D exchange mechanism and protonation sites.
Collapse
Affiliation(s)
- Ljubica Svilar
- Université Pierre et Marie Curie, Institut Parisien de Chimie Moléculaire, UMR 7201-FR2769, Case Courrière 45, Bâtiment F, 716, 4, place Jussieu, 75252, Paris CEDEX 05, France
| | | | | | | | | |
Collapse
|
32
|
Zhao P, Huang J, Wang XH. Comparative Proteomics of two Vibrio anguillarum Serotype O1 Strains with Different Virulence Phenotypes. Curr Microbiol 2012; 65:262-71. [DOI: 10.1007/s00284-012-0156-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2011] [Accepted: 05/20/2012] [Indexed: 11/29/2022]
|
33
|
Miladinović SM, Kozhinov AN, Gorshkov MV, Tsybin YO. On the Utility of Isotopic Fine Structure Mass Spectrometry in Protein Identification. Anal Chem 2012; 84:4042-51. [DOI: 10.1021/ac2034584] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Saša M. Miladinović
- Biomolecular
Mass Spectrometry
Laboratory, Ecole Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| | - Anton N. Kozhinov
- Biomolecular
Mass Spectrometry
Laboratory, Ecole Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| | - Mikhail V. Gorshkov
- Institute for Energy Problems
of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Yury O. Tsybin
- Biomolecular
Mass Spectrometry
Laboratory, Ecole Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| |
Collapse
|
34
|
Kim YK, Min DH. Fabrication of alternating multilayer films of graphene oxide and carbon nanotube and its application in mechanistic study of laser desorption/ionization of small molecules. ACS APPLIED MATERIALS & INTERFACES 2012; 4:2088-2095. [PMID: 22435538 DOI: 10.1021/am300054z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Graphene, graphene oxide (GO), and multi-walled carbon nanotube (MWCNT) have been actively explored as matrix for laser desorption/ionization mass spectrometry (LDI-MS) in place of conventional organic matrix. Recently, the GO/MWCNT double layer films on a solid substrate showed excellent applicability in small molecule analysis, enzyme activity assay and tissue imaging. In the present study, LDI processes of small molecules on multilayers of alternating MWCNT and GO hybrid films were thoroughly investigated. We found that the LDI efficiency of small molecules was affected by thickness, assembly sequence and surface roughness of the hybrid films that were controlled by varying the number of layer-by-layer (LBL) assembly cycles. The study would provide useful basic information to develop an efficient LDI-MS platform based on carbon nanomaterials.
Collapse
Affiliation(s)
- Young-Kwan Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | | |
Collapse
|
35
|
Chambers AG, Ramsey JM. Microfluidic Dual Emitter Electrospray Ionization Source for Accurate Mass Measurements. Anal Chem 2012; 84:1446-51. [DOI: 10.1021/ac202603s] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Andrew G. Chambers
- Department
of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United
States
| | - J. Michael Ramsey
- Department
of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United
States
| |
Collapse
|
36
|
Mao Y, Zamdborg L, Kelleher NL, Hendrickson CL, Marshall AG. Identification of Phosphorylated Human Peptides by Accurate Mass Measurement Alone. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2011; 308:357-361. [PMID: 22866021 PMCID: PMC3409838 DOI: 10.1016/j.ijms.2011.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
At sufficiently high mass accuracy, it is possible to distinguish phosphorylated from unmodified peptides by mass measurement alone. We examine the feasibility of that idea, tested against a library of all possible in silico tryptic digest peptides from the human proteome database. The overlaps between in silico tryptic digest phosphopeptides generated from known phosphorylated proteins (1-12 sites) and all possible unmodified human peptides are considered for assumed mass error ranges of ±10, ±50, ±100, ±1,000, and ±10,000 ppb. We find that for mass error ±50 ppb, 95% of all phosphorylated human tryptic peptides can be distinguished from nonmodified peptides by accurate mass alone through the entire nominal mass range. We discuss the prospect of on-line LC MS/MS to identify phosphopeptide precursor ions in MS1 for selected dissociation in MS2 to identify the peptide and site(s) of phosphorylation.
Collapse
Affiliation(s)
- Yuan Mao
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, United States
| | - Leonid Zamdborg
- Institute for Genomic Biology, 1206 West Gregory Drive, Urbana, IL 61801
| | - Neil L. Kelleher
- Institute for Genomic Biology, 1206 West Gregory Drive, Urbana, IL 61801
| | - Christopher L. Hendrickson
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, United States
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee Florida 32310-4005, United States
| | - Alan G. Marshall
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, United States
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee Florida 32310-4005, United States
| |
Collapse
|
37
|
Wang M, Zhang P, Zong W, Xu Q, Liu R. The charge ratio between O and N on amide bonds: a new approach to the mobile proton model. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 79:1915-1919. [PMID: 21689971 DOI: 10.1016/j.saa.2011.05.088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 05/24/2011] [Accepted: 05/25/2011] [Indexed: 05/30/2023]
Abstract
The influence of charge distribution on the cleavage of the peptides was investigated by fragmentation efficiency curves and quantum chemical calculations in order to clarify the fragmentation mechanism in this paper. The peptide Arg-Gly-Asp-Cys (RGDC) was oxidized to change the charge distribution, but its main sequence was retained. Under this study, it was illustrated that the fragmentation of the peptide RGDC became easier with each addition of an O atom to the Cys hydrosulfide group and the relative charge ratios between O and N (QO/QN) in the amide bonds had much to do with the cleavage of the peptide RGDC. For each amide bond, the situations coincided with overall conclusion: the increase of the QO/QN values results in a higher fragmentation efficiency and vice versa. The methods which combined fragmentation efficiency curves with the charge distribution of peptides provided a way to refine the mobile proton model for peptide fragmentation and to probe the discrepant fragmentation of peptides in peptide/protein identification.
Collapse
Affiliation(s)
- Meijie Wang
- Shandong Key Laboratory of Water Pollution Control and Resource 4 Reuse, School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 27# Shanda South Road, Jinan 250100, PR China
| | | | | | | | | |
Collapse
|
38
|
Sun X, Kelly RT, Tang K, Smith RD. Membrane-based emitter for coupling microfluidics with ultrasensitive nanoelectrospray ionization-mass spectrometry. Anal Chem 2011; 83:5797-803. [PMID: 21657269 PMCID: PMC3139426 DOI: 10.1021/ac200960h] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
An integrated poly(dimethylsiloxane) (PDMS) membrane-based microfluidic emitter for high-performance nanoelectrospray ionization mass spectrometry has been fabricated and evaluated. The ∼100-μm-thick emitter was created by cutting a PDMS membrane that protrudes beyond the bulk substrate. The reduced surface area at the emitter enhances the electric field and reduces wetting of the surface by the electrospray solvent. As such, the emitter enables highly stable electrosprays at flow rates as low as 10 nL/min and is compatible with electrospray solvents containing a large organic component (e.g., 90% methanol). This approach enables facile emitter construction and provides excellent stability, reproducibility, and sensitivity as well as compatibility with multilayer soft lithography.
Collapse
Affiliation(s)
- Xuefei Sun
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352
| | - Ryan T. Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352
| | - Keqi Tang
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352
| |
Collapse
|
39
|
Baeumlisberger D, Rohmer M, Arrey TN, Mueller BF, Beckhaus T, Bahr U, Barka G, Karas M. Simple Dual-Spotting Procedure Enhances nLC–MALDI MS/MS Analysis of Digests with Less Specific Enzymes. J Proteome Res 2011; 10:2889-94. [DOI: 10.1021/pr2001644] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Dominic Baeumlisberger
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
| | - Marion Rohmer
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
| | - Tabiwang N. Arrey
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
| | - Benjamin F. Mueller
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
| | - Tobias Beckhaus
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
| | - Ute Bahr
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
| | - Guenes Barka
- SunChrom Wissenschaftliche Geräte GmbH, Max-Planck-Strasse 22, 61381 Friedrichsdorf, Germany
| | - Michael Karas
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
| |
Collapse
|
40
|
Wen J, Zhang H, Gross ML, Blankenship RE. Native electrospray mass spectrometry reveals the nature and stoichiometry of pigments in the FMO photosynthetic antenna protein. Biochemistry 2011; 50:3502-11. [PMID: 21449539 DOI: 10.1021/bi200239k] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The nature and stoichiometry of pigments in the Fenna-Matthews-Olson (FMO) photosynthetic antenna protein complex were determined by native electrospray mass spectrometry. The FMO antenna complex was the first chlorophyll-containing protein that was crystallized. Previous results indicate that the FMO protein forms a trimer with seven bacteriochlorophyll a in each monomer. This model has long been a working basis to understand the molecular mechanism of energy transfer through pigment/pigment and pigment/protein coupling. Recent results have suggested, however, that an eighth bacteriochlorophyll is present in some subunits. In this report, a direct mass spectrometry measurement of the molecular weight of the intact FMO protein complex clearly indicates the existence of an eighth pigment, which is assigned as a bacteriochlorophyll a by mass analysis of the complex and HPLC analysis of the pigment. The eighth pigment is found to be easily lost during purification, which results in its partial occupancy in the mass spectra of the intact complex prepared by different procedures. The results are consistent with the recent X-ray structural models. The existence of the eighth bacteriochlorophyll a in this model antenna protein gives new insights into the functional role of the FMO protein and motivates the need for new theoretical and spectroscopic assignments of spectral features of the FMO protein.
Collapse
Affiliation(s)
- Jianzhong Wen
- Department of Biology, Washington University in St. Louis, Missouri 63130, United States
| | | | | | | |
Collapse
|
41
|
Huang X, Tolmachev AV, Shen Y, Liu M, Huang L, Zhang Z, Anderson GA, Smith RD, Chan WC, Hinrichs SH, Fu K, Ding SJ. UNiquant, a program for quantitative proteomics analysis using stable isotope labeling. J Proteome Res 2011; 10:1228-37. [PMID: 21158445 DOI: 10.1021/pr1010058] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Stable isotope labeling (SIL) methods coupled with nanoscale liquid chromatography and high resolution tandem mass spectrometry are increasingly useful for elucidation of the proteome-wide differences between multiple biological samples. Development of more effective programs for the sensitive identification of peptide pairs and accurate measurement of the relative peptide/protein abundance are essential for quantitative proteomic analysis. We developed and evaluated the performance of a new program, termed UNiquant, for analyzing quantitative proteomics data using stable isotope labeling. UNiquant was compared with two other programs, MaxQuant and Mascot Distiller, using SILAC-labeled complex proteome mixtures having either known or unknown heavy/light ratios. For the SILAC-labeled Jeko-1 cell proteome digests with known heavy/light ratios (H/L = 1:1, 1:5, and 1:10), UNiquant quantified a similar number of peptide pairs as MaxQuant for the H/L = 1:1 and 1:5 mixtures. In addition, UNiquant quantified significantly more peptides than MaxQuant and Mascot Distiller in the H/L = 1:10 mixtures. UNiquant accurately measured relative peptide/protein abundance without the need for postmeasurement normalization of peptide ratios, which is required by the other programs.
Collapse
Affiliation(s)
- Xin Huang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Balch WE, Yates JR. Application of mass spectrometry to study proteomics and interactomics in cystic fibrosis. Methods Mol Biol 2011; 742:227-247. [PMID: 21547736 DOI: 10.1007/978-1-61779-120-8_14] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) does not function in isolation, but rather in a complex network of protein-protein interactions that dictate the physiology of a healthy cell and tissue and, when defective, the pathophysiology characteristic of cystic fibrosis (CF) disease. To begin to address the organization and operation of the extensive cystic fibrosis protein network dictated by simultaneous and sequential interactions, it will be necessary to understand the global protein environment (the proteome) in which CFTR functions in the cell and the local network that dictates CFTR folding, trafficking, and function at the cell surface. Emerging mass spectrometry (MS) technologies and methodologies offer an unprecedented opportunity to fully characterize both the proteome and the protein interactions directing normal CFTR function and to define what goes wrong in disease. Below we provide the CF investigator with a general introduction to the capabilities of modern mass spectrometry technologies and methodologies with the goal of inspiring further application of these technologies for development of a basic understanding of the disease and for the identification of novel pathways that may be amenable to therapeutic intervention in the clinic.
Collapse
Affiliation(s)
- William E Balch
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | | |
Collapse
|
43
|
Manes NP, Dong L, Zhou W, Du X, Reghu N, Kool AC, Choi D, Bailey CL, Petricoin EF, Liotta LA, Popov SG. Discovery of mouse spleen signaling responses to anthrax using label-free quantitative phosphoproteomics via mass spectrometry. Mol Cell Proteomics 2010; 10:M110.000927. [PMID: 21189417 DOI: 10.1074/mcp.m110.000927] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Inhalational anthrax is caused by spores of the bacterium Bacillus anthracis (B. anthracis), and is an extremely dangerous disease that can kill unvaccinated victims within 2 weeks. Modern antibiotic-based therapy can increase the survival rate to ∼50%, but only if administered presymptomatically (within 24-48 h of exposure). To discover host signaling responses to presymptomatic anthrax, label-free quantitative phosphoproteomics via liquid chromatography coupled to mass spectrometry was used to compare spleens from uninfected and spore-challenged mice over a 72 h time-course. Spleen proteins were denatured using urea, reduced using dithiothreitol, alkylated using iodoacetamide, and digested into peptides using trypsin, and the resulting phosphopeptides were enriched using titanium dioxide solid-phase extraction and analyzed by nano-liquid chromatography-Linear Trap Quadrupole-Orbitrap-MS(/MS). The fragment ion spectra were processed using DeconMSn and searched using both Mascot and SEQUEST resulting in 252,626 confident identifications of 6248 phosphopeptides (corresponding to 5782 phosphorylation sites). The precursor ion spectra were deisotoped using Decon2LS and aligned using MultiAlign resulting in the confident quantitation of 3265 of the identified phosphopeptides. ANOVAs were used to produce a q-value ranked list of host signaling responses. Late-stage (48-72 h postchallenge) Sterne strain (lethal) infections resulted in global alterations to the spleen phosphoproteome. In contrast, ΔSterne strain (asymptomatic; missing the anthrax toxin) infections resulted in 188 (5.8%) significantly altered (q<0.05) phosphopeptides. Twenty-six highly tentative phosphorylation responses to early-stage (24 h postchallenge) anthrax were discovered (q<0.5), and ten of these originated from eight proteins that have known roles in the host immune response. These tentative early-anthrax host response signaling events within mouse spleens may translate into presymptomatic diagnostic biomarkers of human anthrax detectable within circulating immune cells, and could aid in the identification of pathogenic mechanisms and therapeutic targets.
Collapse
Affiliation(s)
- Nathan P Manes
- The National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA 20110-2201, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Teeguarden JG, Webb-Robertson BJ, Waters KM, Murray AR, Kisin ER, Varnum SM, Jacobs JM, Pounds JG, Zanger RC, Shvedova AA. Comparative proteomics and pulmonary toxicity of instilled single-walled carbon nanotubes, crocidolite asbestos, and ultrafine carbon black in mice. Toxicol Sci 2010; 120:123-35. [PMID: 21135415 DOI: 10.1093/toxsci/kfq363] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Reflecting their exceptional potential to advance a range of biomedical, aeronautic, and other industrial products, carbon nanotube (CNT) production and the potential for human exposure to aerosolized CNTs are increasing. CNTs have toxicologically significant structural and chemical similarities to asbestos (AB) and have repeatedly been shown to cause pulmonary inflammation, granuloma formation, and fibrosis after inhalation/instillation/aspiration exposure in rodents, a pattern of effects similar to those observed following exposure to AB. To determine the degree to which responses to single-walled CNTs (SWCNT) and AB are similar or different, the pulmonary response of C57BL/6 mice to repeated exposures to SWCNTs, crocidolite AB, and ultrafine carbon black (UFCB) were compared using high-throughput global high performance liquid chromatography fourier transform ion cyclotron resonance mass spectrometry (HPLC-FTICR-MS) proteomics, histopathology, and bronchoalveolar lavage cytokine analyses. Mice were exposed to material suspensions (40 micrograms per mouse) twice a week for 3 weeks by pharyngeal aspiration. Histologically, the incidence and severity of inflammatory and fibrotic responses were greatest in mice treated with SWCNTs. SWCNT treatment affected the greatest changes in abundance of identified lung tissue proteins. The trend in number of proteins affected (SWCNT [376] > AB [231] > UFCB [184]) followed the potency of these materials in three biochemical assays of inflammation (cytokines). SWCNT treatment uniquely affected the abundance of 109 proteins, but these proteins largely represent cellular processes affected by AB treatment as well, further evidence of broad similarity in the tissue-level response to AB and SWCNTs. Two high-sensitivity markers of inflammation, one (S100a9) observed in humans exposed to AB, were found and may be promising biomarkers of human response to SWCNT exposure.
Collapse
|
45
|
Brown JN, Estep RD, Lopez-Ferrer D, Brewer HM, Clauss TR, Manes NP, O'Connor M, Li H, Adkins JN, Wong SW, Smith RD. Characterization of macaque pulmonary fluid proteome during monkeypox infection: dynamics of host response. Mol Cell Proteomics 2010; 9:2760-71. [PMID: 20736407 PMCID: PMC3101861 DOI: 10.1074/mcp.m110.001875] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 08/13/2010] [Indexed: 01/13/2023] Open
Abstract
Understanding viral pathogenesis is challenging because of confounding factors, including nonabrasive access to infected tissues and high abundance of inflammatory mediators that may mask mechanistic details. In diseases such as influenza and smallpox where the primary cause of mortality results from complications in the lung, the characterization of lung fluid offers a unique opportunity to study host-pathogen interactions with minimal effect on infected animals. This investigation characterizes the global proteome response in the pulmonary fluid, bronchoalveolar lavage fluid, of macaques during upper respiratory infection by monkeypox virus (MPXV), a close relative of the causative agent of smallpox, variola virus. These results are compared and contrasted against infections by vaccinia virus (VV), a low pathogenic relative of MPXV, and with extracellular fluid from MPXV-infected HeLa cells. To identify changes in the pulmonary protein compartment, macaque lung fluid was sampled twice prior to infection, serving as base line, and up to six times following intrabronchial infection with either MPXV or VV. Increased expression of inflammatory proteins was observed in response to both viruses. Although the increased expression resolved for a subset of proteins, such as C-reactive protein, S100A8, and S100A9, high expression levels persisted for other proteins, including vitamin D-binding protein and fibrinogen γ. Structural and metabolic proteins were substantially decreased in lung fluid exclusively during MPXV and not VV infection. Decreases in structural and metabolic proteins were similarly observed in the extracellular fluid of MPXV-infected HeLa cells. Results from this study suggest that the host inflammatory response may not be the only facilitator of viral pathogenesis, but rather maintaining pulmonary structural integrity could be a key factor influencing disease progression and mortality.
Collapse
Affiliation(s)
- Joseph N. Brown
- From the ‡Fundamental Science Division and Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352 and
| | - Ryan D. Estep
- §Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon 97006
| | - Daniel Lopez-Ferrer
- From the ‡Fundamental Science Division and Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352 and
| | - Heather M. Brewer
- From the ‡Fundamental Science Division and Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352 and
| | - Theresa R. Clauss
- From the ‡Fundamental Science Division and Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352 and
| | - Nathan P. Manes
- From the ‡Fundamental Science Division and Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352 and
| | - Megan O'Connor
- §Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon 97006
| | - Helen Li
- §Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon 97006
| | - Joshua N. Adkins
- From the ‡Fundamental Science Division and Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352 and
| | - Scott W. Wong
- §Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon 97006
| | - Richard D. Smith
- From the ‡Fundamental Science Division and Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352 and
| |
Collapse
|
46
|
Gorshkov MV, Good DM, Lyutvinskiy Y, Yang H, Zubarev RA. Calibration function for the Orbitrap FTMS accounting for the space charge effect. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1846-1851. [PMID: 20696596 DOI: 10.1016/j.jasms.2010.06.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 06/23/2010] [Accepted: 06/29/2010] [Indexed: 05/29/2023]
Abstract
Ion storage in an electrostatic trap has been implemented with the introduction of the Orbitrap Fourier transform mass spectrometer (FTMS), which demonstrates performance similar to high-field ion cyclotron resonance MS. High mass spectral characteristics resulted in rapid acceptance of the Orbitrap FTMS for Life Sciences applications. The basics of Orbitrap operation are well documented; however, like in any ion trap MS technology, its performance is limited by interactions between the ion clouds. These interactions result in ion cloud couplings, systematic errors in measured masses, interference between ion clouds of different size yet with close m/z ratios, etc. In this work, we have characterized the space-charge effect on the measured frequency for the Orbitrap FTMS, looking for the possibility to achieve sub-ppm levels of mass measurement accuracy (MMA) for peptides in a wide range of total ion population. As a result of this characterization, we proposed an m/z calibration law for the Orbitrap FTMS that accounts for the total ion population present in the trap during a data acquisition event. Using this law, we were able to achieve a zero-space charge MMA limit of 80 ppb for the commercial Orbitrap FTMS system and sub-ppm level of MMA over a wide range of total ion populations with the automatic gain control values varying from 10 to 10(7).
Collapse
|
47
|
Sun F, Zong W, Liu R, Wang M, Zhang P, Xu Q. The relative charge ratio between C and N atoms in amide bond acts as a key factor to determine peptide fragment efficiency in different charge states. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1857-1862. [PMID: 20688527 DOI: 10.1016/j.jasms.2010.06.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2010] [Revised: 06/24/2010] [Accepted: 06/30/2010] [Indexed: 05/29/2023]
Abstract
The influence of charge state on the peptide dissociation behavior in tandem mass spectrometry (MS/MS) is worthy of discussion. Comparative studies of singly- and doubly-protonated peptide molecules are performed to explore the effect and mechanism of charge state on peptide fragmentation. In view of the charge-directed cleavage of protonated peptides described in the mobile proton model, radiolytic oxidation was applied to change the charge distribution of peptides but retain the sequence. Experimental studies of collision energy-dependent fragmentation efficiencies coupled with quantum chemical calculations indicated that the cleavage of ARRA and its side-chain oxidation products with oxygen atoms added followed a trend that doubly-protonated peptides fragment more easily than singly-protonated forms, while the oxidation product with the guanidine group deleted showed the opposite trend. By analyzing the charge distribution around the amide bonds, we found that the relative charge ratios between C and N atoms (Q(C)/Q(N)) in the amide bonds provided a reasonable explanation for peptide fragmentation efficiencies. An increase of the Q(C)/Q(N) value of the amide bond means that a peptide fragments more easily, and vice versa. The results described in this paper provide an experimental and calculation strategy for predicting peptide fragmentation efficiency.
Collapse
Affiliation(s)
- Feng Sun
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment and Health, Jinan, PR China
| | | | | | | | | | | |
Collapse
|
48
|
Ahrné E, Müller M, Lisacek F. Unrestricted identification of modified proteins using MS/MS. Proteomics 2010; 10:671-86. [PMID: 20029840 DOI: 10.1002/pmic.200900502] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Proteins undergo PTM, which modulates their structure and regulates their function. Estimates of the PTM occurrence vary but it is safe to assume that there is an important gap between what is currently known and what remains to be discovered. The highest throughput and most comprehensive efforts to catalogue protein mixtures have so far been using MS-based shotgun proteomics. The standard approach to analyse MS/MS data is to use Peptide Fragment Fingerprinting tools such as Sequest, MASCOT or Phenyx. These tools commonly identify 5-30% of the spectra in an MS/MS data set while only a limited list of predefined protein modifications can be screened. An important part of the unidentified spectra is likely to be spectra of peptides carrying modifications not considered in the search. Bioinformatics for PTM discovery is an active area of research. In this review we focus on software solutions developed for unrestricted identification of modifications in MS/MS data, here referred to as open modification search tools. We give an overview of the conceptually different algorithmic solutions to evaluate the large number of candidate peptides per spectrum when accounting for modifications of unrestricted size and demonstrate the value of results of large-scale open modification search studies. Efficient and easy-to-use tools for protein modification discovery should prove valuable in the quest for mapping the dynamics of proteomes.
Collapse
Affiliation(s)
- Erik Ahrné
- Swiss Institute of Bioinformatics, Proteome Informatics Group, Geneva, Switzerland.
| | | | | |
Collapse
|
49
|
Sun X, Kelly RT, Tang K, Smith RD. Ultrasensitive nanoelectrospray ionization-mass spectrometry using poly(dimethylsiloxane) microchips with monolithically integrated emitters. Analyst 2010; 135:2296-302. [PMID: 20617264 DOI: 10.1039/c0an00253d] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Poly(dimethylsiloxane) (PDMS) is a widely used substrate for microfluidic devices, as it enables facile fabrication and has other distinctive properties. However, for applications requiring highly sensitive nanoelectrospray ionization mass spectrometry (nanoESI-MS) detection, the use of PDMS microdevices has been hindered by a large chemical background in the mass spectra that originates from the leaching of uncross-linked oligomers and other contaminants from the substrate. A more general challenge is that microfluidic devices containing monolithically integrated electrospray emitters are frequently unable to operate stably in the nanoflow regime where the best sensitivity is achieved. In this report, we extracted the contaminants from PDMS substrates using a series of solvents, eliminating the background observed when untreated PDMS microchips are used for nanoESI-MS, such that peptides at concentrations of 1 nM were readily detected. Optimization of the integrated emitter geometry enabled stable operation at flow rates as low as 10 nL min(-1).
Collapse
Affiliation(s)
- Xuefei Sun
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | | | | | | |
Collapse
|
50
|
Smith DJ. Mitochondrial dysfunction in mouse models of Parkinson's disease revealed by transcriptomics and proteomics. J Bioenerg Biomembr 2010; 41:487-91. [PMID: 19967437 DOI: 10.1007/s10863-009-9254-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
It has been long thought that neuronal loss in Parkinson's disease (PD) is related to reactive oxygen species from mitochondrial dysfunction. However, there have been few investigations surveying both transcriptome and proteome in PD. This review focuses on recent work using microarrays and mass spectrometry to examine neurotoxicological models of PD in the mouse. Molecular pathways involved in oxidative phosphorylation, oxidative stress, apoptosis/cell death, signal transduction and neurotransmission were highlighted. Analysis of tyrosine nitration suggested that this important post-translational modification, due to conjugation of reactive oxygen species with nitric oxide, may play an important role in signal transduction as well as the molecular pathology of PD. Thus, the combined investigations highlight known pathways in PD but also point to new directions for research, implicating particularly the role of relatively understudied classes of post-translational modifications in normal cell signaling and neurological disorders.
Collapse
Affiliation(s)
- Desmond J Smith
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, CHS 23-120, Box 951735, Los Angeles, CA 90095-1735, USA.
| |
Collapse
|