Step 1 · Data
Raw files and the search output are chosen where they are on the Mac. Every file is recognised and given its PRIDE file type; instrument, scan counts and DIA/DDA are read from the runs straight away.
A simulated dataset run through every step of PRIDE Packager: four synthetic DIA runs (two control, two treated) of 40 real human UniProt proteins, with a DIA-NN-style report. No measured data are shown. The app turned the report into an mzTab that PRIDE accepts as a COMPLETE submission, and built the folder below.
Step 2 · Results
The app says which kind of submission the files allow and creates what is missing. Here it turned the DIA-NN report into mzTab (and mzIdentML), with every identification pointing at its MS/MS spectrum, which makes the submission COMPLETE.
Step 3 · Describe
Title, protocols, species, tissue, instrument and modifications. Controlled-vocabulary terms work offline; the terms read from the files are offered with one click, and the data-processing text is drafted from the search software's own log.
Step 4 · Samples
An SDRF-Proteomics sample sheet, one row per raw file.
Step 5 · Check & build
Everything PRIDE's validator looks at, checked first; then one folder is built with PRIDE-safe file names, hard links instead of copies, checksum.txt, submission.px, the SDRF and a README.
Step 6 · Submit
The package is ready to load into PRIDE's own Submission Tool, with what happens next.
The package it built
One folder, ready to upload: every file has a unique, PRIDE-safe name, the raw files are hard links (no extra disk space), and the README records which files were the user's and which the app made.
| Folder | File | PRIDE type | What it is |
|---|---|---|---|
raw | Demo_HeLa_DIA_Ctrl_1.mzML | RAW | Peak list (mzML) (your file) |
raw | Demo_HeLa_DIA_Ctrl_2.mzML | RAW | Peak list (mzML) (your file) |
raw | Demo_HeLa_DIA_Treat_1.mzML | RAW | Peak list (mzML) (your file) |
raw | Demo_HeLa_DIA_Treat_2.mzML | RAW | Peak list (mzML) (your file) |
fasta | human_demo_40proteins.fasta | FASTA | Protein sequence database (FASTA) (your file) |
quant | report.pg_matrix.tsv | QUANT | DIA-NN protein group matrix (your file) |
quant | report.pr_matrix.tsv | QUANT | DIA-NN precursor matrix (your file) |
search | report.tsv | SEARCH | DIA-NN main report (your file) |
result | Demo_HeLa_DIA_simulated.mzTab | RESULT | mzTab made from report.tsv (made by PRIDE Packager) |
other | Demo_HeLa_DIA_simulated.mzid | OTHER | mzIdentML made from report.tsv (made by PRIDE Packager) |
experimental_design | Demo_HeLa_DIA_simulated.sdrf.tsv | EXPERIMENTAL_DESIGN | SDRF sample sheet (made by PRIDE Packager) |
submission.px
The ProteomeXchange summary file the PX Submission Tool loads: project metadata as controlled-vocabulary terms, every file with its type, and which raw files each result belongs to.
MTD submitter_name Paul H. Kim MTD submitter_email demo@example.org MTD submitter_affiliation Example lab MTD submitter_pride_login demo@example.org MTD lab_head_name Example Lab Head MTD lab_head_email head@example.org MTD lab_head_affiliation Example lab MTD project_title Simulated HeLa DIA example for PRIDE Packager MTD project_description A simulated four-run DIA experiment (two control and two treated HeLa digests) made to demonstrate PRIDE Packager. The spectra are synthetic. MTD keywords example, DIA, HeLa, simulated MTD sample_processing_protocol Simulated data: no samples were processed. The protein sequences are 40 reviewed human UniProt entries digested in silico with trypsin. MTD data_processing_protocol The data were analysed with DIA-NN (Demichev et al., Nat Methods 2020). The protein sequence database was human_demo_40proteins.fasta (40 … MTD submission_type COMPLETE MTD experiment_type [PRIDE, PRIDE:0000450, Data-independent acquisition, ] MTD species [NEWT, 9606, Homo sapiens (Human), ] MTD tissue [BTO, BTO:0001421, uterine cervix, ] MTD instrument [MS, MS:1003028, Orbitrap Exploris 480, ] MTD modification [MOD, MOD:01060, S-carboxamidomethyl-L-cysteine, ] MTD quantification [PRIDE, PRIDE:0000312, Label free, ] FMH file_id file_type file_path file_mapping FME 1 result /Users/you/Desktop/PRIDE_Demo_HeLa_DIA_simulated/result/Demo_HeLa_DIA_simulated.mzTab 3,4,5,6 FME 2 search /Users/you/Desktop/PRIDE_Demo_HeLa_DIA_simulated/search/report.tsv FME 3 raw /Users/you/Desktop/PRIDE_Demo_HeLa_DIA_simulated/raw/Demo_HeLa_DIA_Ctrl_1.mzML FME 4 raw /Users/you/Desktop/PRIDE_Demo_HeLa_DIA_simulated/raw/Demo_HeLa_DIA_Ctrl_2.mzML FME 5 raw /Users/you/Desktop/PRIDE_Demo_HeLa_DIA_simulated/raw/Demo_HeLa_DIA_Treat_1.mzML FME 6 raw /Users/you/Desktop/PRIDE_Demo_HeLa_DIA_simulated/raw/Demo_HeLa_DIA_Treat_2.mzML FME 7 quant /Users/you/Desktop/PRIDE_Demo_HeLa_DIA_simulated/quant/report.pg_matrix.tsv FME 8 quant /Users/you/Desktop/PRIDE_Demo_HeLa_DIA_simulated/quant/report.pr_matrix.tsv FME 9 fasta /Users/you/Desktop/PRIDE_Demo_HeLa_DIA_simulated/fasta/human_demo_40proteins.fasta FME 10 experimental_design /Users/you/Desktop/PRIDE_Demo_HeLa_DIA_simulated/experimental_design/Demo_HeLa_DIA_simulated.sdrf.tsv FME 11 other /Users/you/Desktop/PRIDE_Demo_HeLa_DIA_simulated/other/Demo_HeLa_DIA_simulated.mzid SMH file_id species tissue cell_type disease modification instrument quantification experimental_factor SME 1 [NEWT, 9606, Homo sapiens (Human), ] [BTO, BTO:0001421, uterine cervix, ] [MOD, MOD:01060, S-carboxamidomethyl-L-cysteine, ] [MS, MS:1003028, Orbitrap Exploris…
checksum.txt
# SHA-1 checksums written by PRIDE Packager 2026-10-29 00:46 Demo_HeLa_DIA_Ctrl_1.mzML 8839411e30f9e75974cd13d92628f04d42a0ba46 Demo_HeLa_DIA_Ctrl_2.mzML baf51ad679f7053cdf058f1ec7ec240ceafa99e1 Demo_HeLa_DIA_Treat_1.mzML 85f7a5ece34551e749dad626170928f648357ba1 Demo_HeLa_DIA_Treat_2.mzML c2152eb9568a274963b2b54d08d228f96f0435b7 human_demo_40proteins.fasta 496ea39189d5351b786b2bace304aeee839d8022 …