#UniProt provides extremely powerful query capabilities, but the output is typically a raw FASTA file. FASTA files are ideal for sequence-based tools, but they are difficult to work with in downstream data analysis, annotation, and integration workflows.

This application fills the gap between UniProt FASTA datasets and proteomics analysis tables.

Specifically, it is designed for situations where you want to answer questions like:

• Which proteins from a curated UniProt set are actually present in my experiment?
• How many of my significant MS hits belong to a specific functional class (e.g., kinases, metal-binding proteins, reviewed human proteins)?
• Which UniProt proteins should I carry forward into structural, enrichment, or targeted analyses?

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What problem does this solve?

In many proteomics workflows, you work with two disconnected data sources:

1. A UniProt-derived FASTA set
   Examples:

   • Reviewed human proteome
   • Proteins annotated with a specific keyword (e.g., copper-binding)
   • Proteins from a specific organism or proteome
   • Proteins matching a functional or annotation-based query

2. An experimental or analytical protein list
   Examples:

   • MS-identified proteins
   • Differential abundance hits
   • LiP-MS or TPP significant proteins
   • Curated protein sets from prior analyses

This app:

• Fetches FASTA data directly from UniProt using a reproducible query
• Converts semi-structured FASTA headers into a tidy, joinable table
• Allows you to intersect UniProt-derived protein sets with your own data
• Produces outputs that are immediately usable in downstream analysis

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Why not just download FASTA manually?

Manually downloading FASTA files and inspecting headers is:

• Error-prone
• Difficult to reproduce
• Hard to integrate with data frames and pipelines
• Unscalable for iterative analysis

This app:

• Makes UniProt queries explicit and documented
• Ensures identifier parsing is consistent and deterministic
• Eliminates copy-paste and manual filtering
• Encourages reproducible, query-driven workflows

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When is this especially useful?

This tool is particularly helpful when you want to:

• Filter large UniProt protein sets down to experimentally observed proteins
• Validate whether expected functional classes appear in your data
• Prepare protein subsets for:
  • Structural modeling
  • Enrichment analysis
  • Targeted follow-up experiments
  • Custom FASTA databases
• Rapidly iterate on different UniProt queries without re-downloading files manually

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UniProt query examples

Below are example queries that can be entered directly into the app:

• Human reviewed proteome
  proteome: UP000005640 AND reviewed: true

• Human kinases (by protein name)
  organism_id:9606 AND (protein_name:kinase)

• Copper-binding proteins
  keyword: "Copper-binding" AND reviewed: true.

The application uses UniProt’s REST stream endpoint (uniprotkb/stream) to retrieve FASTA records directly from UniProt, ensuring results are up to date and reproducible.