Global analysis of the
            <i>Deinococcus radiodurans</i>
            proteome by using accurate mass tags

Lipton, Mary; Paša‐Tolić, Ljiljana; Anderson, Gordon A.; Anderson, David J.; Auberry, Deanna L.; Battista, John R.; Daly, Michael J.; Fredrickson, Jim K.; Hixson, Kim; Kostandarithes, Heather M.; Masselon, Christophe; Markillie, Lye Meng; Moore, Ronald J.; Romine, Margaret F.; Shen, Yufeng; Stritmatter, Eric; Tolić, Nikola; Udseth, Harold R.; Venkateswaran, Amudhan; Wong, Kwong-Kwok; Zhao, Rui; Smith, Richard D.

doi:10.1073/pnas.172170199

Cited by 370 publications

(354 citation statements)

References 43 publications

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“…The digested sample was ultacentrifuged and dialyzed overnight with a 500 MW cellulose ester membrane. Additional details on the sample handling are given elsewhere [26].…”

Section: Sample Preparationmentioning

confidence: 99%

“…In order to facilitate the comparison of LC retention times for peptides carried out over a series of capillary LC analyses, we have previously described the use of adjusted retention times or normalized elution times (NET) [26]. In order to determine a NET value for a particular monoisotopic mass (M mi ) obtained during an LC run, the following eq is used:…”

Section: Normalized Elution Timementioning

confidence: 99%

“…In this study, we explore using the AMT tag procedure with 10 ppm mass accuracy obtained with ESIorthogonal TOF instrument and using a set of AMT tags developed using capillary LC-FTICR measurements for Deinococcus radiodurans [26,27], an organism being studied because of its application to bioremediation. A key aspect of this work is the augmentation of accurate mass measurements with the known peptide elution times to improve the overall specificity of the analysis [13].…”

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confidence: 99%

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Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry

Strittmatter

Ferguson

Tang

et al. 2003

J. Am. Soc. Mass Spectrom.

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148

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We describe the application of capillary liquid chromatography (LC) time-of-flight (TOF) mass spectrometric instrumentation for the rapid characterization of microbial proteomes. Previously (Lipton et al., Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11049) the peptides from a series of growth conditions of Deinococcus radiodurans have been characterized using capillary LC MS/MS and accurate mass measurements which are captured as an accurate mass and time (AMT) tag database. Using this AMT tag database, detected peptides can be assigned using measurements obtained on a TOF due to the additional use of elution time data as a constraint. When peptide matches are obtained using AMT tags (i.e., using both constraints) unique matches of a mass spectral peak occurs 88% of the time. Not only are AMT tag matches unique in most cases, the coverage of the proteome is high; ϳ3500 unique peptide AMT tags are found on average per capillary LC run. From the results of the AMT tag database search, ϳ900 ORFs detected using LC-TOFMS, with ϳ500 ORFs covered by at least two AMT tags. These results indicate that AMT database searches with modest mass and elution time criteria can provide proteomic information for approximately one thousand proteins in a single run of Ͻ3 h. The advantage of this method over using MS/MS based techniques is the large number of identifications that occur in a single experiment as well as the basis for improved quantitation. For MS/MS experiments, the number of peptide identifications is severely restricted because of the time required to dissociate the peptides individually. These results demonstrate the utility of the AMT tag approach using capillary LC-TOF MS instruments, and also show that AMT tags developed using other instrumentation can be effectively utilized. (J Am Soc Mass Spectrom 2003, 14, 980 -991)

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“…The digested sample was ultacentrifuged and dialyzed overnight with a 500 MW cellulose ester membrane. Additional details on the sample handling are given elsewhere [26].…”

Section: Sample Preparationmentioning

confidence: 99%

Section: Normalized Elution Timementioning

confidence: 99%

mentioning

confidence: 99%

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Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry

Strittmatter

Ferguson

Tang

et al. 2003

J. Am. Soc. Mass Spectrom.

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148

113

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“…The utility of high MMA is particularly beneficial for the aforementioned AMT tag approach developed at our laboratory. In the initial demonstration of this approach [44] with Deinococcus radiodurans, only ϳ70% of peptides identified with SEQUEST scores above 2.0 were validated as AMT tags. An analysis of the conversion of PMT tags to AMT tags shows that almost all PMT tags having a SEQUEST cross correlation (X corr ) scores Ͼ4.0 were converted to AMT tags.…”

Section: Capillary Lc-fticr Analysesmentioning

confidence: 99%

“…particular biological system is to be examined many times (e.g., time course studies following perturbations) [43]. The approach initially involved conventional capillary LC-MS/MS studies to yield identified peptide "potential mass and time tags" (PMT tags) that were subsequently validated as "accurate mass and time tags" (AMT tags) if the predicted peptides' accurate masses were observed using FTICR (in a corresponding sample) at an equivalent elution time [44]. These peptide AMT tags thus serve as confident biomarkers to identify peptides/proteins in subsequent studies, and result in much greater throughput.…”

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confidence: 99%

An automated high performance capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometer for high-throughput proteomics

Belov

Anderson

Wingerd

et al. 2004

J. Am. Soc. Mass Spectrom.

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We describe a fully automated high performance liquid chromatography 9.4 tesla Fourier transform ion resonance cyclotron (FTICR) mass spectrometer system designed for proteomics research. A synergistic suite of ion introduction and manipulation technologies were developed and integrated as a high-performance front-end to a commercial Bruker Daltonics FTICR instrument. The developments incorporated included a dual-ESI-emitter ion source; a dualchannel electrodynamic ion funnel; tandem quadrupoles for collisional cooling and focusing, ion selection, and ion accumulation, and served to significantly improve the sensitivity, dynamic range, and mass measurement accuracy of the mass spectrometer. In addition, a novel technique for accumulating ions in the ICR cell was developed that improved both resolution and mass measurement accuracy. A new calibration methodology is also described where calibrant ions are introduced and controlled via a separate channel of the dual-channel ion funnel, allowing calibrant species to be introduced to sample spectra on a real-time basis, if needed. We also report on overall instrument automation developments that facilitate high-throughput and unattended operation. These included an automated version of the previously reported very high resolution, high pressure reversed phase gradient capillary liquid chromatography (LC) system as the separations component. A commercial autosampler was integrated to facilitate 24 h/day operation. Unattended operation of the instrument revealed exceptional overall performance: Reproducibility (1-5% deviation in uncorrected elution times), repeatability (Ͻ20% deviation in detected abundances for more abundant peptides from the same aliquot analyzed a few weeks apart), and robustness (high-throughput operation for 5 months without significant downtime). When combined with modulated-ionenergy gated trapping, the dynamic calibration of FTICR mass spectra provided decreased mass measurement errors for peptide identifications in conjunction with high resolution capillary LC separations over a dynamic range of peptide peak intensities for each spectrum of 10 3 , and Ͼ10 5 for peptide abundances in the overall separation. (J Am Soc Mass Spectrom 2004, 15, 212-232)

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Proteomics based on high-efficiency capillary separations

2002

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Identifying and quantifying in a high throughput manner the proteins expressed by cells, tissues or an organism provides the basis for understanding the functions of its constituents at a "systems" level. As a result, proteome analysis has increasingly become the focus of significant interest and research over the past decade. This is especially true following the recent stunning achievements in genomics analyses. However, unlike the static genome, the complexities and dynamism of the proteome present significant analytical challenges and demand highly efficient separations and detection technologies. A number of recent technological advancements have been in direct response to these challenges. Currently, strategically mated combinations of sophisticated separations techniques and advanced mass spectrometric detection represent the best approach to addressing the intricacies of the proteome. Liquid-phase separations, often within capillaries, are increasingly recognized as the best separations technique for this approach. In combination on-line with mass spectrometry, liquid-phase separations provide the improved analytical sensitivity, sample throughput, and quantitation capabilities necessitated by the multifaceted problems within proteomics analyses. This review focuses primarily on current high-efficiency capillary separations techniques, including both capillary liquid chromatography and capillary electrophoresis, applied to the analysis of complex proteomic samples. We emphasize developments at our laboratory and illustrate technical advances that attempt to review the role of separations within the broader context of a state-of-the-art integrated proteomics effort.

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Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags

Cited by 370 publications

References 43 publications

Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry

Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry

An automated high performance capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometer for high-throughput proteomics

Proteomics based on high-efficiency capillary separations

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