Corpus Engine Towards a reproducible .science file.
← All .science files

pmid:40756422

Comprehensive characterization of human aqueous humor proteomes from primary open-angle glaucoma using data-independent acquisition dataset on a TimsTOF pro mass spectrometer.

Hu Xiao · Da Qian Lu · Jimmy Ka-Wai Cheung · Ying Hon Sze · Jing Fang Bian · Chi-Wai Do · Lei Zhou · Xiao Li Xing · Thomas Chuen Lam

Data in brief · 2025 doi:10.1016/j.dib.2025.111881

Paper

complete

Experiment

partial

Data

partial

Analysis

partial

Execution

absent

Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
id
pmid:40756422
kind
science-record
content_hash
sha256:92f7aadade80ab50c3b3356381d883c6edd9e9bbff249fcc85c22c829c7fa08d
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T20:30:51Z
updated_at
2026-11-01T22:56:56Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Comprehensive characterization of human aqueous humor proteomes from primary open-angle glaucoma using data-independent acquisition dataset on a TimsTOF pro mass spectrometer.
doi
10.1016/j.dib.2025.111881
pmid
40756422
authors array · 9 items
[0]
Hu Xiao
[1]
Da Qian Lu
[2]
Jimmy Ka-Wai Cheung
[3]
Ying Hon Sze
[4]
Jing Fang Bian
[5]
Chi-Wai Do
[6]
Lei Zhou
[7]
Xiao Li Xing
[8]
Thomas Chuen Lam
journal
Data in brief
year
2025
abstract
Primary open-angle glaucoma (POAG) is the foremost cause of irreversible visual impairment, attributed to a complex array of ocular diseases. The lack of reliable prognostic indicators necessitates the development of biomarkers that can be used to detect and monitor glaucoma early in its course. In this study, human aqueous humor databases dedicated to advanced and not advanced POAG from Chinese were compiled to facilitate research on POAG, using advanced label-free quantitative proteomics technology by a TimsTOF Pro mass spectrometer. Proteins and peptides were identified and quantified by DIA-NN bioinformatics. All mass spectrometry data were deposited in the ProteomeXchange Consortium via the PRIDE partner (https://www.ebi.ac.uk/pride) with the dataset identifier PRIDE: PXD060484.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
The Mann-Whitney U test, a non-parametric method, was employed to assess differences between two independent groups. Categorical variables were analysed using the Chi-square test.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:40756422
locator
sections[6] "Clinical characteristics between advanced and non-advanced POAG groups" paragraph 3
quote
The Mann-Whitney U test, a non-parametric method, was employed to assess differences between two independent groups. Categorical variables were analysed using the Chi-square test.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
PRIDEPXD060484 (Original data)
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:40756422
locator
sections[14] "Data Availability" paragraph 2
quote
PRIDEPXD060484 (Original data)
state
complete
gaps array · 0 items
experiment object · 8 fields
state
partial
steps array · 3 items
[0] object · 13 fields
id
read_published_estimate
order
1
name
Read the published estimate from the source
kind
other
state
complete
blocked_on
null
description
The claim, method and evidence span published with the source article.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:40756422
outputs array · 1 item
[0]
the published estimate and its evidence
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
id
obtain_source_data
order
2
name
Obtain the source data from the named repository
kind
data-preparation
state
complete
blocked_on
null
description
The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:PXD060484
outputs array · 1 item
[0]
the source data with its repository provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
id
run_analysis
order
3
name
Run the published analysis
kind
analysis
state
blocked
blocked_on
method:group_comparison_mann_whitney
description
Apply the paper's statistical method to the resolved series and compare the result with the published target.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:PXD060484
outputs array · 1 item
[0]
the replicated result and its comparison
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 1 item
[0]
step:run_analysis blocked on method:group_comparison_mann_whitney
data object · 3 fields
state
partial
assets array · 2 items
[0] object · 15 fields
id
source:pmid:40756422
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1016/j.dib.2025.111881
sha256
sha256:a2142fe615a2a82776b2e38f602f89bbbc1342f7ba41f98f51f25a912546a4b2
bytes
13420
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1016/j.dib.2025.111881
version
null
note
Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.
structure object · 4 fields
pmcid
PMC12318253
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:PXD060484
role
raw
format
geo-series
media_type
application/vnd.ncbi.geo-series+json
uri
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD060484
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
PXD060484
version
null
note
PRIDEPXD060484 (Original data)
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
PRIDEPXD060484 (Original data)
access_statement_kind
data_availability_statement
sample_accessions array · 0 items
sample_count
null
group_sizes
null
group_sizes_basis
null
platform
null
taxon
null
title
A quantitative spectral library of human aqueous humor was analyzed using TimsTOFTM Pro Bruker for primary open angle glaucoma (POAG).
resolution_checked_at
2026-11-01T20:16:18Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:PXD060484 not downloaded
[1]
asset:data:geo:PXD060484 licence not read
analysis object · 4 fields
state
partial
methods array · 2 items
[0] object · 10 fields
id
method-1
family
group_comparison
specific
mann_whitney
label
Group comparison
dsl_operations array · 0 items
missing_operations array · 1 item
[0]
group_comparison_mann_whitney
expressible
false
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
1
band
verbatim
quote
The Mann-Whitney U test, a non-parametric method, was employed to assess differences between two independent groups. Categorical variables were analysed using the Chi-square test.
[1] object · 10 fields
id
method-2
family
contingency_analysis
specific
chi_square
label
Categorical (contingency table) analysis
dsl_operations array · 1 item
[0]
chi_square_test
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
categorical_cross_tabulation
evidence object · 3 fields
score
0.8
band
high
quote
Chi-square
targets array · 0 items
gaps array · 1 item
[0]
method.group_comparison_mann_whitney
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
complete
tier
R1
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
false
required_operations array · 0 items
missing_operations array · 1 item
[0]
group_comparison_mann_whitney
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: mann_whitney.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
data object · 6 fields
tier
R1
reachable
true
accessions array · 1 item
[0]
PXD060484
resolved_accessions array · 1 item
[0]
PXD060484
statements array · 1 item
[0]
PRIDEPXD060484 (Original data)
basis
The paper names PXD060484 in PRoteomics IDEntifications Database (PRIDE) and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 2 items
[0]
source:pmid:40756422
[1]
data:geo:PXD060484
steps array · 0 items
must_build object · 5 fields
dsl_operations array · 1 item
[0] object · 3 fields
operation
group_comparison_mann_whitney
priority
null
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:PXD060484
gaps array · 0 items
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-11-01T19:58:20Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
5081
completion_tokens
835
cached_tokens
264
stages array · 1 item
[0] object · 4 fields
id
extraction
state
complete
reader
MiniMax-M3.1-Flash
provider
minimax
gaps array · 3 items
[0]
review.independent_reader
[1]
review.machine_critique
[2]
review.human_critique
execution object · 5 fields
state
absent
status
not_run
mode
null
runs array · 0 items
gaps array · 1 item
[0]
execution.not_run
provenance object · 7 fields
entities array · 3 items
[0] object · 3 fields
id
pmid:40756422
type
paper
label
pmid:40756422
[1] object · 3 fields
id
source:pmid:40756422
type
manuscript
label
PMID 40756422 full text
[2] object · 3 fields
id
data:geo:PXD060484
type
dataset
label
GEO PXD060484
activities array · 3 items
[0] object · 4 fields
id
activity-reading-sci-2026-11-01
type
classification
used array · 3 items
[0] object · 3 fields
id
pmid:40756422
type
paper
label
pmid:40756422
[1] object · 3 fields
id
source:pmid:40756422
type
manuscript
label
PMID 40756422 full text
[2] object · 3 fields
id
data:geo:PXD060484
type
dataset
label
GEO PXD060484
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-40756422
type
extraction
used array · 1 item
[0]
source:pmid:40756422
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-PXD060484
type
accession_resolution
used array · 1 item
[0]
data:geo:PXD060484
agent
agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
[1] object · 3 fields
id
agent:minimax-reader
type
software
label
MiniMax literature reader
source_run_id
reading-sci-2026-11-01
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
snapshot_id
ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:40756422
parent_hash
sha256:785a78856cf6e36941a455d7602254ed23a958944a6fa9b501246ac8a33bbc15
fork_of
null
gaps array · 8 items
[0]
asset:data:geo:PXD060484 licence not read
[1]
asset:data:geo:PXD060484 not downloaded
[2]
execution.not_run
[3]
method.group_comparison_mann_whitney
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
[7]
step:run_analysis blocked on method:group_comparison_mann_whitney
assays array · 2 items
[0] object · 11 fields
role
data_generation
definition_id
mass_spectrometry
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 2 items
[0]
and quantified by DIA-NN bioinformatics. All mass spectrometry data were deposited in the ProteomeXchange C
[1]
POAG, using advanced label-free quantitative proteomics technology by a TimsTOF Pro mass spectromete
order_basis
paper_text_order:615
id
assay:1
[1] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
The Mann-Whitney U test, a non-parametric method, was employed to assess differences between two independent groups. Categorical variables were analysed using the Chi-square test.
order_basis
consumes_earlier_output
id
assay:2
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40756422", "kind": "science-record", "revision": 4, "content_hash": "sha256:92f7aadade80ab50c3b3356381d883c6edd9e9bbff249fcc85c22c829c7fa08d", "created_at": "2026-11-01T20:30:51Z", "updated_at": "2026-11-01T22:56:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive characterization of human aqueous humor proteomes from primary open-angle glaucoma using data-independent acquisition dataset on a TimsTOF pro mass spectrometer.", "doi": "10.1016/j.dib.2025.111881", "pmid": "40756422", "authors": ["Hu Xiao", "Da Qian Lu", "Jimmy Ka-Wai Cheung", "Ying Hon Sze", "Jing Fang Bian", "Chi-Wai Do", "Lei Zhou", "Xiao Li Xing", "Thomas Chuen Lam"], "journal": "Data in brief", "year": 2025, "abstract": "Primary open-angle glaucoma (POAG) is the foremost cause of irreversible visual impairment, attributed to a complex array of ocular diseases. The lack of reliable prognostic indicators necessitates the development of biomarkers that can be used to detect and monitor glaucoma early in its course. In this study, human aqueous humor databases dedicated to advanced and not advanced POAG from Chinese were compiled to facilitate research on POAG, using advanced label-free quantitative proteomics technology by a TimsTOF Pro mass spectrometer. Proteins and peptides were identified and quantified by DIA-NN bioinformatics. All mass spectrometry data were deposited in the ProteomeXchange Consortium via the PRIDE partner (https://www.ebi.ac.uk/pride) with the dataset identifier PRIDE: PXD060484.", "claims": [{"id": "claim-method", "statement": "The Mann-Whitney U test, a non-parametric method, was employed to assess differences between two independent groups. Categorical variables were analysed using the Chi-square test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40756422", "locator": "sections[6] \"Clinical characteristics between advanced and non-advanced POAG groups\" paragraph 3", "quote": "The Mann-Whitney U test, a non-parametric method, was employed to assess differences between two independent groups. Categorical variables were analysed using the Chi-square test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "PRIDEPXD060484 (Original data)", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40756422", "locator": "sections[14] \"Data Availability\" paragraph 2", "quote": "PRIDEPXD060484 (Original data)"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40756422"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD060484"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_mann_whitney", "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD060484"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_mann_whitney"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40756422", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2025.111881", "sha256": "sha256:a2142fe615a2a82776b2e38f602f89bbbc1342f7ba41f98f51f25a912546a4b2", "bytes": 13420, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2025.111881", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12318253", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD060484", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD060484", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD060484", "version": null, "note": "PRIDEPXD060484 (Original data)", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "PRIDEPXD060484 (Original data)", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "A quantitative spectral library of human aqueous humor was analyzed using TimsTOFTM Pro Bruker for primary open angle glaucoma (POAG).", "resolution_checked_at": "2026-11-01T20:16:18Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD060484 not downloaded", "asset:data:geo:PXD060484 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "mann_whitney", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Mann-Whitney U test, a non-parametric method, was employed to assess differences between two independent groups. Categorical variables were analysed using the Chi-square test."}}, {"id": "method-2", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "Chi-square"}}], "targets": [], "gaps": ["method.group_comparison_mann_whitney"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: mann_whitney."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD060484"], "resolved_accessions": ["PXD060484"], "statements": ["PRIDEPXD060484 (Original data)"], "basis": "The paper names PXD060484 in PRoteomics IDEntifications Database (PRIDE) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:40756422", "data:geo:PXD060484"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_mann_whitney", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD060484"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:58:20Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 5081, "completion_tokens": 835, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:40756422", "type": "paper", "label": "pmid:40756422"}, {"id": "source:pmid:40756422", "type": "manuscript", "label": "PMID 40756422 full text"}, {"id": "data:geo:PXD060484", "type": "dataset", "label": "GEO PXD060484"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40756422", "type": "paper", "label": "pmid:40756422"}, {"id": "source:pmid:40756422", "type": "manuscript", "label": "PMID 40756422 full text"}, {"id": "data:geo:PXD060484", "type": "dataset", "label": "GEO PXD060484"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40756422", "type": "extraction", "used": ["source:pmid:40756422"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD060484", "type": "accession_resolution", "used": ["data:geo:PXD060484"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:40756422", "parent_hash": "sha256:785a78856cf6e36941a455d7602254ed23a958944a6fa9b501246ac8a33bbc15", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PXD060484 licence not read", "asset:data:geo:PXD060484 not downloaded", "execution.not_run", "method.group_comparison_mann_whitney", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_mann_whitney"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["and quantified by DIA-NN bioinformatics. All mass spectrometry data were deposited in the ProteomeXchange C", "POAG, using advanced label-free quantitative proteomics technology by a TimsTOF Pro mass spectromete"], "order_basis": "paper_text_order:615", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The Mann-Whitney U test, a non-parametric method, was employed to assess differences between two independent groups. Categorical variables were analysed using the Chi-square test."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}