Correlation of acidic and basic carrier ampholyte and immobilized pH gradient two-dimensional gel electrophoresis patterns based on mass spectrometric protein identification

1998 ◽  
Vol 19 (6) ◽  
pp. 1024-1035 ◽  
Author(s):  
Arkadiusz Nawrocki ◽  
Martin R. Larsen ◽  
Alexandre V. Podtelejnikov ◽  
Ole N. Jensen ◽  
Matthias Mann ◽  
...  
Keyword(s):  
Gel Electrophoresis ◽  
Protein Identification ◽  
Mass Spectrometric ◽  
Ph Gradient ◽  
Two Dimensional ◽  
Two Dimensional Gel Electrophoresis ◽  
Carrier Ampholyte

scholarly journals Evaluation of narrow range immobiline pH gradient gels in an automated two-dimensional gel electrophoresis machine, Auto2D

2015 ◽  
Vol 59 (1) ◽  
pp. 9-12
Author(s):  
Yuki Tani ◽  
Parlayan Cuneyd ◽  
Yoko Takai ◽  
Akira Kawai ◽  
Yutaka Unuma ◽  
...  
Keyword(s):  
Gel Electrophoresis ◽  
Narrow Range ◽  
Ph Gradient ◽  
Two Dimensional ◽  
Two Dimensional Gel Electrophoresis

ACCURATE NONLINEAR REGISTRATION FOR TWO-DIMENSIONAL GEL ELECTROPHORESIS IMAGES

2013 ◽  
Vol 21 (03) ◽  
pp. 1350020
Author(s):  
HUA-MEI XIN ◽  
YUEMIN ZHU
Keyword(s):  
Thin Plate ◽  
Gel Electrophoresis ◽  
Protein Identification ◽  
Distance Measure ◽  
Spline Interpolation ◽  
Thin Plate Spline ◽  
Two Dimensional ◽  
Registration Accuracy ◽  
Two Dimensional Gel Electrophoresis ◽  
Nonlinear Registration

Two-dimensional gel electrophoresis (2DGE) images are an important support for the analysis of proteins in proteomics. The registration of 2DGE images is considered as one of key elements in protein identification while it is a difficult problem. This paper proposes a new accurate nonlinear registration approach for 2DGE images, based on the exploitation of both spot distance measure and spot intensity. The method consists of three steps: multi-resolution affine registration, spot pairing and thin-plate spline interpolation. The results on both simulated and real gel images show that the proposed method significantly improves registration accuracy in comparison with thin-plate spline registration techniques.

scholarly journals Initial Proteome Analysis of Model Microorganism Haemophilus influenzae Strain Rd KW20

2003 ◽  
Vol 185 (15) ◽  
pp. 4593-4602 ◽  
Author(s):  
Eugene Kolker ◽  
Samuel Purvine ◽  
Michael Y. Galperin ◽  
Serg Stolyar ◽  
David R. Goodlett ◽  
...  
Keyword(s):  
Haemophilus Influenzae ◽  
Gel Electrophoresis ◽  
Ribosomal Proteins ◽  
Protein Identification ◽  
Proteome Analysis ◽  
Tandem Mass ◽  
Two Dimensional ◽  
High Confidence ◽  
Two Dimensional Gel Electrophoresis

ABSTRACT The proteome of Haemophilus influenzae strain Rd KW20 was analyzed by liquid chromatography (LC) coupled with ion trap tandem mass spectrometry (MS/MS). This approach does not require a gel electrophoresis step and provides a rapidly developed snapshot of the proteome. In order to gain insight into the central metabolism of H. influenzae, cells were grown microaerobically and anaerobically in a rich medium and soluble and membrane proteins of strain Rd KW20 were proteolyzed with trypsin and directly examined by LC-MS/MS. Several different experimental and computational approaches were utilized to optimize the proteome coverage and to ensure statistically valid protein identification. Approximately 25% of all predicted proteins (open reading frames) of H. influenzae strain Rd KW20 were identified with high confidence, as their component peptides were unambiguously assigned to tandem mass spectra. Approximately 80% of the predicted ribosomal proteins were identified with high confidence, compared to the 33% of the predicted ribosomal proteins detected by previous two-dimensional gel electrophoresis studies. The results obtained in this study are generally consistent with those obtained from computational genome analysis, two-dimensional gel electrophoresis, and whole-genome transposon mutagenesis studies. At least 15 genes originally annotated as conserved hypothetical were found to encode expressed proteins. Two more proteins, previously annotated as predicted coding regions, were detected with high confidence; these proteins also have close homologs in related bacteria. The direct proteomics approach to studying protein expression in vivo reported here is a powerful method that is applicable to proteome analysis of any (micro)organism.

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