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GPMAW manual v. 5.02
The GPMAW manual can now be read chapter by chapter online. Please choose the relevant chapter from the list below.
Please note that the manual layout has not been optimized for web display.
Chapter 1. Introduction.
What is GPMAW 1.1 Installation 1.2 Program layout 1.3 Starting GPMAW 1.4 Essential tables 1.5 Window menu 1.6 Recent program changes 1.7 Help 1.8 Lighthouse data 1.9
Chapter 2 Reading and saving sequences.
Open sequence 2.1 How to acquire sequences 2.2 Save sequence 2.3 Delete sequence 2.4 Import ASCII 2.5 Reading sequences from a database 2.6 Sequences from the Internet 2.7 Export sequence 2.8
Chapter 3 The sequence window.
Sequence window display 3.1 Highlight sequence 3.2 Highlight residues (motifs) 3.3 Underline residues 3.4 Cross-links 3.5 Amino acid modifications 3.6 Fragment window 3.7 Sequence information 3.8 Annotation 3.9
Chapter 4 Edit
Edit sequence 4.1 Edit mass files 4.2 Edit modification files 4.3 Composition formulas 4.4
Chapter 5 Setup
Setup system parameters - System 5.1 Peptide parameters 5.2 System colors 5.3 System directories 5.4 Digest mass search parameters 5.5 Display 5.6 BLAST 5.7 Users 5.8
Chapter 6 Mass search
Search for masses 6.1 Mass differences 6.2 Search for cross-linked peptides 6.3
Chapter 7 Search for composition/Local BLAST
Search for composition 7.1 Local BLAST 7.2
Chapter 8 Database mass search
Introduction to digest mass search 8.1 Setup digest mass databases 8.2 Digest mass search - data input 8.3 Digest mass search - status window 8.4 Digest mass search - results 8.5 Multiple digest mass search 8.6 Combine digest mass search 8.7 Protein mass search 8.8
Chapter 9 Cleavages
Automatic digest 9.1 Other cleavages 9.2 Cleavage analysis 9.3 Peptide window 9.4
Chapter 10 Fragmentation
MS/MS fragmentation 10.1 Ladder sequencing 10.2
Chapter 11 Graphs
Common graph commands 11.1 Secondary structure prediction 11.2 Hydrophobicity 11.3 Primer multiplicity 11.4 User graph 11.5 Dot-plot 11.6
Chapter 12 Utilities
MS peak analysis 12.1 Composition calculator 12.2 Database indexer (DBindex) 12.3 Simulated 2D gel 12.4
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