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Gang Peng
ProteomicsBrowser: MS/Proteomics Data Visualization and Investigation
ProteomicsBrowser 1
Gang Peng
Department of BiostatisticsYale School of Public Health
May 1, 2019
Gang Peng
ChallengesLarge-scaleComplexityIncreasing numbers of post-translational modifications
Advantages of Data VisualizationShow the information quick and clearIdentify the relationships and patternsShow the details of difference
Proteomic Data Analysis
ProteomicsBrowser 2
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JavaWindowsmacOSLinux
Update Database from UniProt
ProteomicsBrowser
ProteomicsBrowser 3
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Peptide Data File
Sample Data File
Input Data
ProteomicsBrowser 4
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Table View
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Browser
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PTM with Unassigned Sites
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Peptides with Multiple Matches in A Protein
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Peptides Mapped to Multiple Proteins
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Overlapping peptides Partial proteolytic cleavageMultiple charge states Post-translational modifications (PTMs)
Peptide Combination
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Sequence Based CombinationPeptides with same sequenceOther criteria
PTM Based CombinationPeptides with same PTM at selected position
Peptide Combination
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Sequence Based Combination
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A
B
C
D
A+B+C
D
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Sequence Based Combination
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+2
+2
+2
+2
+3
+3
Same PTM and Same Charge
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Sequence Based Combination
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+2
+2
+2
+2
+3
+3
Same PTM and Same Charge
A
B
C
D
E
F
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Sequence Based Combination
ProteomicsBrowser 15
+2
+2
+2
+2
+3
+3
Same PTM and Same Charge
+2
+2
+2
+2
+3
+3
+2
+2
+3
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Sequence Based Combination
ProteomicsBrowser 16
Before
After
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PTM Based Combination
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PTM Based Combination
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PTM Based Combination
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PTM Based Combination
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PTM Based Combination
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Disease_3
Normal_2
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PTM Based Combination
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Residue Frequency
Correlation
Statistic Tests
Other Functions
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Residue Frequency
Correlation
Statistic Tests
Other Functions
ProteomicsBrowser 24
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Residue Frequency
Correlation
Statistic Tests
Other Functions
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ProteomicsBrowser
ProteomicsBrowser 26
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https://medicine.yale.edu/keck/nida/proteomicsbrowser.aspx
Availability
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Gang Peng
Department of Biostatistics
Hongyu Zhao
Department of PsychiatryRashuan WilsonAngus C. NairnMelissa MonseyJane Taylor
Department of GeneticsYishuo Tang
Department of Molecular Biophysics and Biochemistry
Kenneth WilliamsTuKiet T. Lam
Acknowledgement
11/25/2019 ProteomicsBrowser 28
