Your First Protein Analysis

This guide will walk you through performing your first protein analysis on ProteinIQ. We'll use the Protein Molecular Weight Calculator as an example, but the principles apply to all tools on the platform.

What You'll Learn

By the end of this guide, you'll know how to:

• Navigate the ProteinIQ interface
• Input protein sequences correctly
• Interpret analysis results
• Export your data

Prerequisites

• A web browser (Chrome, Firefox, Safari, or Edge)
• A protein sequence to analyze (we'll provide an example)

Step 1: Access the Tool

1. Navigate to the ProteinIQ homepage
2. Click on "Tools" in the main navigation
3. Find "Protein Molecular Weight" in the Protein Analysis section
4. Click on the tool to open it

Step 2: Prepare Your Input

For this tutorial, we'll use a sample protein sequence. Copy the following FASTA sequence:

>Sample Protein - Human Insulin
MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN

Input Options

ProteinIQ accepts several input formats:

FASTA Format (recommended):

• Includes a header line starting with >
• Followed by the sequence on subsequent lines

Plain Sequence:

• Just the amino acid sequence without headers
• Useful for quick calculations

File Upload:

• Upload .fasta, .txt, or other sequence files
• Supports multiple sequences in one file

Step 3: Enter Your Sequence

1. In the input text area, paste the sample sequence above
2. The tool will automatically detect the FASTA format
3. You should see the sequence appear in the input field

Input Validation

The tool will automatically:

• Check for valid amino acid codes
• Highlight any invalid characters
• Provide suggestions for corrections

Step 4: Run the Analysis

1. Click the "Calculate Molecular Weight" button
2. Results appear instantly (no waiting for server processing!)
3. The analysis runs entirely in your browser

Step 5: Interpret Your Results

The results will show:

Primary Results

• Molecular Weight: 11,466.68 Da (approximate for our sample)
• Number of Amino Acids: 110 residues
• Formula: Complete molecular formula

Detailed Breakdown

• Amino Acid Composition: Count and percentage of each amino acid
• Physical Properties: Additional calculated properties
• Quality Metrics: Sequence validation results

Understanding the Output

Molecular Weight:

• Measured in Daltons (Da)
• Useful for protein identification and purification
• Accuracy depends on sequence quality

Amino Acid Composition:

• Shows frequency of each amino acid
• Useful for understanding protein properties
• Can indicate potential modifications needed

Step 6: Export Your Results

1. Click the "Export Results" button
2. Choose your preferred format:
   • CSV: For spreadsheet analysis
   • JSON: For programmatic use
   • PDF: For reports and documentation

Export Options

CSV Format:

• Includes all calculated values
• Easy to import into Excel or other tools
• Suitable for batch analysis comparison

JSON Format:

• Machine-readable format
• Includes metadata and parameters
• Perfect for API integration

Step 7: Next Steps

Now that you've completed your first analysis:

Try Other Tools

• Isoelectric Point Calculator: Determine protein charge
• Instability Index: Assess protein stability
• GRAVY Score: Measure hydrophobicity

Explore Advanced Features

• Batch Processing: Analyze multiple sequences
• Parameter Adjustment: Customize calculations
• Result Comparison: Compare multiple proteins

Learn More

• Read tool-specific documentation
• Explore other user guides
• Check out the API documentation

Troubleshooting

Common Issues

"Invalid amino acid code" error:

• Check for typos in your sequence
• Ensure you're using standard single-letter codes
• Remove any spaces or special characters

Empty results:

• Verify your sequence isn't empty
• Check that you've pasted the sequence correctly
• Try using the provided example sequence

Unexpected molecular weight:

• Confirm your sequence is correct
• Check for missing or extra amino acids
• Verify the sequence corresponds to your target protein

Getting Help

If you encounter issues:

1. Check the tool's help section
2. Review this guide's troubleshooting section
3. Try the provided example sequences
4. Contact support with specific error messages

Best Practices

Sequence Quality

• Always verify sequence accuracy before analysis
• Use sequences from reliable databases (UniProt, NCBI)
• Double-check for any modifications or variants

Data Management

• Keep records of your analyses
• Export results for future reference
• Document the source of your sequences

Result Validation

• Compare results with known values when possible
• Use multiple tools to cross-validate findings
• Consider experimental conditions that might affect results

Conclusion

Congratulations! You've successfully completed your first protein analysis on ProteinIQ. The same principles apply to all tools on the platform:

1. Select the appropriate tool
2. Prepare and input your data
3. Run the analysis
4. Interpret and export results

Continue exploring the platform with our other user guides, and don't hesitate to reach out if you need help along the way.