Top-down protein identification using isotopic envelope fingerprinting

2017 ◽  
Vol 152 ◽  
pp. 41-47 ◽  
Author(s):  
Kaijie Xiao ◽  
Fan Yu ◽  
Zhixin Tian
Keyword(s):  
Protein Identification ◽  
Top Down ◽  
Isotopic Envelope

scholarly journals Deeper Protein Identification Using Field Asymmetric Ion Mobility Spectrometry in Top-Down Proteomics

2021 ◽  
Author(s):  
Vincent R. Gerbasi ◽  
Rafael D. Melani ◽  
Susan E. Abbatiello ◽  
Michael W. Belford ◽  
Romain Huguet ◽  
...  
Keyword(s):  
Ion Mobility Spectrometry ◽  
Ion Mobility ◽  
Protein Identification ◽  
Top Down

scholarly journals Bioinformatics as a Tool for Assessing the Quality of Sub-Cellular Proteomic Strategies and Inferring Functions of Proteins: Plant Cell Wall Proteomics as a Test Case

2009 ◽  
Vol 3 ◽  
pp. BBI.S2065 ◽  
Author(s):  
Hélène San Clemente ◽  
Rafael Pont-Lezica ◽  
Elisabeth Jamet
Keyword(s):  
Cellular Localization ◽  
Protein Identification ◽  
Plant Cell Wall ◽  
Mass Spectrometry Data ◽  
Functional Domains ◽  
Test Case ◽  
Top Down ◽  
Proteomic Data ◽  
Cellular Compartments

Bioinformatics is used at three different steps of proteomic studies of sub-cellular compartments. First one is protein identification from mass spectrometry data. Second one is prediction of sub-cellular localization, and third one is the search of functional domains to predict the function of identified proteins in order to answer biological questions. The aim of the work was to get a new tool for improving the quality of proteomics of sub-cellular compartments. Starting from the analysis of problems found in databases, we designed a new Arabidopsis database named ProtAnnDB ( http://www.polebio.scsv.ups-tlse.fr/ProtAnnDB/ ). It collects in one page predictions of sub-cellular localization and of functional domains made by available software. Using this database allows not only improvement of interpretation of proteomic data (top-down analysis), but also of procedures to isolate sub-cellular compartments (bottom-up quality control).

scholarly journals ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry

2004 ◽  
Vol 32 (Web Server) ◽  
pp. W340-W345 ◽  
Author(s):  
R. D. LeDuc ◽  
G. K. Taylor ◽  
Y.-B. Kim ◽  
T. E. Januszyk ◽  
L. H. Bynum ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Identification ◽  
Top Down ◽  
Integrated Environment ◽  
Identification And Characterization ◽  
Top Down Mass Spectrometry

scholarly journals Deeper Protein Identification by Using FAIMS in Top-down Proteomics

2021 ◽  
Author(s):  
Robert Gerbasi ◽  
Rafael D. Melani ◽  
Susan E. Abbatiello ◽  
Michael W. Belford ◽  
Romain Huguet ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Molecular Weight ◽  
Gas Phase ◽  
Ion Mobility ◽  
Protein Identification ◽  
Signal To Noise ◽  
Top Down ◽  
Gas Phase Separation ◽  
Identification And Characterization

<div> <p>Field Asymmetric Ion Mobility Spectrometry (FAIMS), when used in proteomics studies, provides superior selectivity, and enables more proteins to be identified by providing additional gas phase separation. Here, we tested the performance of cylindrical FAIMS for the identification and characterization of proteoforms by top-down mass spectrometry of heterogeneous protein mixtures. Combining FAIMS with chromatographic separation resulted in a 62% increase in protein identifications and an 8% increase in proteoform identifications as compared to samples analyzed without FAIMS. This increase was attributable, in part, to improved signal-to-noise for proteoforms with similar retention times. Additionally, our results show that the optimal compensation voltage of any given proteoform was correlated with the molecular weight of the analyte. Collectively these results suggest that the addition of FAIMS can enhance top-down proteomics in both discovery and targeted applications. </p> </div>

scholarly journals Deeper Protein Identification by Using FAIMS in Top-down Proteomics

2021 ◽  
Author(s):  
Robert Gerbasi ◽  
Rafael D. Melani ◽  
Susan E. Abbatiello ◽  
Michael W. Belford ◽  
Romain Huguet ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Molecular Weight ◽  
Gas Phase ◽  
Ion Mobility ◽  
Protein Identification ◽  
Signal To Noise ◽  
Top Down ◽  
Gas Phase Separation ◽  
Identification And Characterization

<div> <p>Field Asymmetric Ion Mobility Spectrometry (FAIMS), when used in proteomics studies, provides superior selectivity, and enables more proteins to be identified by providing additional gas phase separation. Here, we tested the performance of cylindrical FAIMS for the identification and characterization of proteoforms by top-down mass spectrometry of heterogeneous protein mixtures. Combining FAIMS with chromatographic separation resulted in a 62% increase in protein identifications and an 8% increase in proteoform identifications as compared to samples analyzed without FAIMS. This increase was attributable, in part, to improved signal-to-noise for proteoforms with similar retention times. Additionally, our results show that the optimal compensation voltage of any given proteoform was correlated with the molecular weight of the analyte. Collectively these results suggest that the addition of FAIMS can enhance top-down proteomics in both discovery and targeted applications. </p> </div>

scholarly journals Top-down protein identification of proteasome proteins with nanoLC-FT-ICR-MS employing data-independent fragmentation methods

PROTEOMICS ◽  
2014 ◽  
Vol 14 (10) ◽  
pp. 1271-1282 ◽  
Author(s):  
Rajeswari Lakshmanan ◽  
Jeremy J. Wolff ◽  
Rudy Alvarado ◽  
Joseph A. Loo
Keyword(s):  
Protein Identification ◽  
Top Down ◽  
Ft Icr Ms ◽  
Ft Icr

scholarly journals ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry

2007 ◽  
Vol 35 (Web Server) ◽  
pp. W701-W706 ◽  
Author(s):  
L. Zamdborg ◽  
R. D. LeDuc ◽  
K. J. Glowacz ◽  
Y.-B. Kim ◽  
V. Viswanathan ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Identification ◽  
Top Down ◽  
Identification And Characterization ◽  
Top Down Mass Spectrometry

scholarly journals Protein Identification Using Top-Down Spectra

2011 ◽  
Vol 11 (6) ◽  
pp. M111.008524 ◽  
Author(s):  
Xiaowen Liu ◽  
Yakov Sirotkin ◽  
Yufeng Shen ◽  
Gordon Anderson ◽  
Yihsuan S. Tsai ◽  
...  
Keyword(s):  
Protein Identification ◽  
Top Down
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