Troubleshooting & FAQ

Troubleshooting and FAQ

The most common mistake

filter expects the clean summary TSV written by pxseek fetch.

pxseek fetch -o px_datasets.tsv
pxseek filter -i px_datasets.tsv -s "Homo sapiens" -o human.tsv

Do not pass the raw ProteomeCentral export directly to filter.

Quick checks

• If filter says no filters were specified, add at least one of species, repository, keyword, date, or instrument.
• If --deep fails, make sure you supplied -k or --keywords.
• If lookup fails on an identifier, confirm that it is a PXD... or RPXD... accession.
• If nothing matches, remove filters and add them back one at a time.

Cache behavior

• Summary data is cached for 24 hours.
• fetch --refresh forces a fresh summary download.
• lookup caches XML by dataset ID on disk.

Best debug sequence

1. Run pxseek fetch -o px_datasets.tsv.
2. Test one simple filter.
3. Inspect the TSV header and a few rows.
4. Add more filters gradually.
5. Use lookup or --deep only after the summary stage looks right.

FAQ

What is pxseek best at?

pxseek is best for metadata discovery and shortlist-building across ProteomeXchange datasets.

Does it download spectra or raw files?

No. It helps you find relevant datasets and capture metadata such as descriptions, identifiers, and FTP locations.

Why is fetch separate from lookup?

Because they serve different stages. fetch gives you a fast broad summary table. lookup gives you richer per-dataset detail only for the shortlist you care about.

When should I use --deep?

Use --deep when the key biological term is likely to appear in the longer description rather than in the summary title or keyword fields.

Can I start without knowing any PXD IDs?

Yes. That is the normal workflow. Start with species, repository, date, instrument, or keywords, then use lookup on the filtered shortlist.