Proteomics inputs and parameters
Query formats, organism filters, instrument filters, PTM filters, and resolution thresholds for PRIDE and EMDB tools.
proteomicsinputs
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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