---
title: Proteomics inputs and parameters
description: >-
  Query formats, organism filters, instrument filters, PTM filters, and
  resolution thresholds for PRIDE and EMDB tools.
tags:
  - proteomics
  - inputs
---

You give Ivy a search keyword in your message — a protein, gene, organism, disease, or technique — plus any filters for organism, instrument, PTM, or resolution. These lookups run inside a chat turn; there is no form to fill in. The keyword itself most affects what you find, since it drives the PRIDE and EMDB matches.

## Proteomics inputs and parameters

## PRIDE Project Search: what you can ask for

| You can specify | Default | Limits and notes |
|-----------------|---------|------------------|
| A keyword: protein name, gene, organism, disease, or technique | Required | 2-200 characters |
| An organism filter | None | For example *Homo sapiens*, *Mus musculus* |
| A mass spectrometer filter | None | For example Orbitrap, Q Exactive |
| A PTM filter | None | For example phosphorylation, acetylation |
| How many results | 10 | Up to 50 |

### Common search queries

| Query Type | Examples |
|------------|---------|
| Protein/gene | `"BRCA1"`, `"p53"`, `"kinase"` |
| Disease | `"Alzheimer"`, `"breast cancer"`, `"COVID-19"` |
| Technique | `"TMT"`, `"SILAC"`, `"label-free"`, `"DIA"` |
| Tissue | `"brain"`, `"liver"`, `"plasma"` |
| PTM-focused | `"phosphoproteomics"`, `"acetylome"`, `"ubiquitome"` |

### Common instrument filters

| Instrument | Vendor | Use Case |
|-----------|--------|----------|
| `Orbitrap` | Thermo Fisher | High-resolution, high-accuracy MS |
| `Q Exactive` | Thermo Fisher | Workhorse for proteomics |
| `Orbitrap Fusion` | Thermo Fisher | Multi-mode (HCD, CID, ETD) |
| `timsTOF` | Bruker | Ion mobility + TOF |
| `TripleTOF` | SCIEX | High-speed DDA/DIA |
| `QTRAP` | SCIEX | Targeted proteomics (MRM/SRM) |

### Common PTM filters

| Modification | Description |
|-------------|-------------|
| `phosphorylation` | Serine, threonine, tyrosine phosphorylation |
| `acetylation` | Lysine acetylation |
| `ubiquitination` | Lysine ubiquitination (diGly remnant) |
| `methylation` | Arginine/lysine methylation |
| `glycosylation` | N-linked or O-linked glycosylation |
| `sumoylation` | SUMO modification |

## PRIDE Dataset Details: what you can ask for

| You can specify | Default | Limits and notes |
|-----------------|---------|------------------|
| The PRIDE project accession | Required | `PXD` followed by 6+ digits |
| The file listing (names, sizes, types) | Included | |
| Only certain file categories | All categories | For example "only the RAW files", or RAW and FASTA |
| How many files to list | 200 | Up to 500 per page |

### Accession format

PRIDE accessions follow the pattern `PXD######` where `#` is a digit:

| Example | Description |
|---------|-------------|
| `PXD000001` | First PRIDE project |
| `PXD032145` | A more recent submission |
| `PXD045678` | Typical recent accession |

## EMDB Search: what you can ask for

| You can specify | Default | Limits and notes |
|-----------------|---------|------------------|
| A keyword: protein name, complex, organism, or EMDB ID | Required | 2-200 characters |
| A resolution cutoff in Angstroms | None | For example "better than 3.0 Å" |
| An organism filter | None | Use the scientific name |
| How many results | 10 | Up to 50 |

### Resolution cutoff guide

| Cutoff (Å) | Typical Content |
|---------------|-----------------|
| `2.0` | Near-atomic resolution, rare |
| `3.0` | High resolution, well-resolved side chains |
| `4.0` | Good resolution, secondary structure clear |
| `6.0` | Medium resolution, domain-level features |
| `10.0` | Low resolution, overall shape |
| *(none)* | All resolutions |

### Common search queries

| Query Type | Examples |
|------------|---------|
| Protein complexes | `"ribosome"`, `"proteasome"`, `"spliceosome"` |
| Membrane proteins | `"ion channel"`, `"GPCR"`, `"transporter"` |
| Viruses | `"SARS-CoV-2 spike"`, `"influenza"`, `"HIV envelope"` |
| By method | `"tomography"`, `"single particle"` |
| By EMDB ID | `"EMD-13234"` |

## EMDB Entry Details: what you can ask for

Give the EMDB entry ID (for example `EMD-1234`, or just `1234`).

### ID format

Both formats are accepted and normalized:

| Input | Resolved To |
|-------|-------------|
| `EMD-1234` | `EMD-1234` |
| `1234` | `EMD-1234` |
| `emd-1234` | `EMD-1234` (case-insensitive) |

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