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

pmid:26306311

Comparative analysis of cerebrospinal fluid from the meningo-encephalitic stage of T. b. gambiense and rhodesiense sleeping sickness patients using TMT quantitative proteomics.

Natalia Tiberti · Jean-Charles Sanchez

Data in brief · 2015 doi:10.1016/j.dib.2015.06.011

Paper

complete

Experiment

complete

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:26306311
kind
science-record
content_hash
sha256:e77c52e10106544c7962f3163f11adc9089e0c499594f98c0a13c2f9bc9356b3
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:10Z
updated_at
2026-11-01T21:20:05Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Comparative analysis of cerebrospinal fluid from the meningo-encephalitic stage of T. b. gambiense and rhodesiense sleeping sickness patients using TMT quantitative proteomics.
doi
10.1016/j.dib.2015.06.011
pmid
26306311
authors array · 2 items
[0]
Natalia Tiberti
[1]
Jean-Charles Sanchez
journal
Data in brief
year
2015
abstract
The quantitative proteomics data here reported are part of a research article entitled "Increased acute immune response during the meningo-encephalitic stage of Trypanosoma brucei rhodesiense sleeping sickness compared to Trypanosoma brucei gambiense", published by Tiberti et al., 2015. Transl. Proteomics 6, 1-9. Sleeping sickness (human African trypanosomiasis - HAT) is a deadly neglected tropical disease affecting mainly rural communities in sub-Saharan Africa. This parasitic disease is caused by the Trypanosoma brucei (T. b.) parasite, which is transmitted to the human host through the bite of the tse-tse fly. Two parasite sub-species, T. b. rhodesiense and T. b. gambiense, are responsible for two clinically different and geographically separated forms of sleeping sickness. The objective of the present study was to characterise and compare the cerebrospinal fluid (CSF) proteome of stage 2 (meningo-encephalitic stage) HAT patients suffering from T. b. gambiense or T. b. rhodesiense disease using high-throughput quantitative proteomics and the Tandem Mass Tag (TMT(®)) isobaric labelling. In order to evaluate the CSF proteome in the context of HAT pathophysiology, the protein dataset was then submitted to gene ontology and pathway analysis. Two significantly differentially expressed proteins (C-reactive protein and orosomucoid 1) were further verified on a larger population of patients (n=185) by ELISA, confirming the mass spectrometry results. By showing a predominant involvement of the acute immune response in rhodesiense HAT, the proteomics results obtained in this work will contribute to further understand the mechanisms of pathology occurring in HAT and to propose new biomarkers of potential clinical utility. The mass spectrometry raw data are available in the Pride Archive via ProteomeXchange through the identifier PXD001082.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
Only proteins identified with at least 2 unique peptides and with an FDR≤1% (computed at the PSM level) were considered for further quantitative analyses using Isobar quantification tool (version 1.76) [9], embedded in EasyProt.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:26306311
locator
sections[10] "Protein identification and quantification" paragraph 5
quote
Only proteins identified with at least 2 unique peptides and with an FDR≤1% (computed at the PSM level) were considered for further quantitative analyses using Isobar quantification tool (version 1.76) [9], embedded in EasyProt.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The mass spectrometry raw data are available in the Pride Archive via ProteomeXchange through the identifier PXD001082.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:26306311
locator
sections[0] "Abstract" paragraph 3
quote
The mass spectrometry raw data are available in the Pride Archive via ProteomeXchange through the identifier PXD001082.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
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:26306311
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:PXD001082
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
complete
blocked_on
null
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:PXD001082
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 · 0 items
data object · 3 fields
state
partial
assets array · 4 items
[0] object · 15 fields
id
source:pmid:26306311
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1016/j.dib.2015.06.011
sha256
sha256:db3aa2d981d7478f34518a0971daaa076547e5e81debe2820a3f0ebeae6a59c0
bytes
16437
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1016/j.dib.2015.06.011
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
PMC4534576
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:PXD001082
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=PXD001082
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
PXD001082
version
null
note
The mass spectrometry raw data are available in the Pride Archive via ProteomeXchange through the identifier PXD001082.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The mass spectrometry raw data are available in the Pride Archive via ProteomeXchange through the identifier PXD001082.
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
Quantitative comparison of CSF proteins from T. b. gambiense and T. b. rhodesiense HAT patients
resolution_checked_at
2026-10-31T18:35:55Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 16 fields
id
asset:table:pmid:26306311:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:6d86cf0233417aafb2890748d646fdf4fd106f18c01f8ca744b2eb7ab8d5ddfb
bytes
557
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[7]/table-wrap[1]#t0005
version
null
note
Demographic description of patients investigated in the TMT 6-plex experiment.
structure object · 5 fields
pmcid
PMC4534576
section_index
7
section_title
Samples
row_count
8
column_count
7
table object · 8 fields
label
Table 1
caption
Demographic description of patients investigated in the TMT 6-plex experiment.
rows array · 8 items
[0] array · 3 items
[0]
[1]
T. b. gambiense - D.R.C.
[2]
T. b. rhodesiense - UGANDA
[1] array · 7 items
[0]
[1]
Pt #1
[2]
Pt #2
[3]
Pt #3
[4]
Pt #4
[5]
Pt #5
[6]
Pt #6
[2] array · 1 item
[0]
[3] array · 7 items
[0]
Sex
[1]
F
[2]
F
[3]
F
[4]
F
[5]
F
[6]
F
[4] array · 7 items
[0]
Age
[1]
21
[2]
29
[3]
51
[4]
22
[5]
30
[6]
53
[5] array · 7 items
[0]
T+CSF
[1]
Yes
[2]
Yes
[3]
Yes
[4]
Yes
[5]
Yes
[6]
Yes
[6] array · 7 items
[0]
WBC/µL
[1]
135
[2]
217
[3]
97
[4]
119
[5]
231
[6]
70
[7] array · 7 items
[0]
TMT tag
[1]
126
[2]
127
[3]
128
[4]
129
[5]
130
[6]
131
locator
section[7]/table-wrap[1]#t0005
[3] object · 16 fields
id
asset:table:pmid:26306311:2
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:a089657e85704e986809339fe5549c95cffc5cc09ba7f6b9c04ee3b10df4d20b
bytes
1378
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[10]/table-wrap[1]#t0010
version
null
note
List of proteins significantly differentially expressed between rhodesiense and gambiense S2 CSF. Only proteins identified with at least 2 unique peptides and FDR<1% were considered for quantification.
structure object · 5 fields
pmcid
PMC4534576
section_index
10
section_title
Protein identification and quantification
row_count
12
column_count
9
table object · 8 fields
label
Table 2
caption
List of proteins significantly differentially expressed between rhodesiense and gambiense S2 CSF. Only proteins identified with at least 2 unique peptides and FDR<1% were considered for quantification.
rows array · 12 items
[0] array · 9 items
[0]
#
[1]
AC
[2]
Protein
[3]
Gene
[4]
Peptide count
[5]
Spectral count
[6]
Ratio⁎
[7]
p Value ratio
[8]
pValue sample
[1] array · 9 items
[0]
1
[1]
P06311
[2]
Ig kappa chain V–III region IARC/BL41
[3]
Na
[4]
2
[5]
2
[6]
0.69
[7]
0.007
[8]
0.002
[2] array · 9 items
[0]
2
[1]
O00584
[2]
Ribonuclease T2
[3]
RNASET2
[4]
3
[5]
3
[6]
0.69
[7]
0.006
[8]
0.019
[3] array · 9 items
[0]
3
[1]
Q9NPR2
[2]
Semaphorin-4B
[3]
SEMA4B
[4]
2
[5]
2
[6]
0.72
[7]
0.048
[8]
0.017
[4] array · 9 items
[0]
4
[1]
P04114
[2]
Apolipoprotein B-100
[3]
APOB
[4]
4
[5]
5
[6]
1.36
[7]
0.041
[8]
0.045
[5] array · 9 items
[0]
5
[1]
P19652
[2]
Alpha-1-acid glycoprotein 2
[3]
ORM2
[4]
5
[5]
10
[6]
1.49
[7]
0.005
[8]
0.017
[6] array · 9 items
[0]
6
[1]
Q03591
[2]
Complement factor H-related protein 1
[3]
CFHR1
[4]
1
[5]
1
[6]
1.52
[7]
0.023
[8]
0.036
[7] array · 9 items
[0]
7
[1]
P02748
[2]
Complement component C9
[3]
C9
[4]
8
[5]
10
[6]
1.78
[7]
0.006
[8]
0.003
[8] array · 9 items
[0]
8
[1]
Q14624
[2]
Inter-alpha-trypsin inhibitor heavy chain H4
[3]
ITIH4
[4]
10
[5]
18
[6]
1.80
[7]
0.005
[8]
0.026
[9] array · 9 items
[0]
9
[1]
P18428
[2]
Lipopolysaccharide-binding protein
[3]
LBP
[4]
2
[5]
2
[6]
2.31
[7]
0.046
[8]
0.000
[10] array · 9 items
[0]
10
[1]
P02763
[2]
Alpha-1-acid glycoprotein 1
[3]
ORM1
[4]
6
[5]
28
[6]
2.69
[7]
0.001
[8]
0.000
[11] array · 9 items
[0]
11
[1]
P02741
[2]
C-reactive protein
[3]
CRP
[4]
3
[5]
5
[6]
9.30
[7]
0.001
[8]
0.000
locator
section[10]/table-wrap[1]#t0010
gaps array · 2 items
[0]
asset:data:geo:PXD001082 not downloaded
[1]
asset:data:geo:PXD001082 licence not read
analysis object · 4 fields
state
partial
methods array · 1 item
[0] object · 10 fields
id
method-1
family
null
specific
null
label
Isobar quantification tool (version 1.76)
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
score
1
band
verbatim
quote
Only proteins identified with at least 2 unique peptides and with an FDR≤1% (computed at the PSM level) were considered for further quantitative analyses using Isobar quantification tool (version 1.76) [9], embedded in EasyProt.
targets array · 0 items
gaps array · 1 item
[0]
method.reader_named_unmapped
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
blocked
tier
R4
blocking_axis
method
blocked_on
method:not_determinable
axes object · 3 fields
method object · 5 fields
tier
R4
expressible
false
required_operations array · 0 items
missing_operations array · 0 items
basis
The reader quoted the method the paper names (Isobar quantification tool (version 1.76)), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible.
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]
PXD001082
resolved_accessions array · 1 item
[0]
PXD001082
statements array · 1 item
[0]
The mass spectrometry raw data are available in the Pride Archive via ProteomeXchange through the identifier PXD001082.
basis
The paper names PXD001082 in 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 · 4 items
[0]
source:pmid:26306311
[1]
data:geo:PXD001082
[2]
asset:table:pmid:26306311:1
[3]
asset:table:pmid:26306311:2
steps array · 1 item
[0]
run_analysis
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:PXD001082
gaps array · 1 item
[0]
method:not_determinable
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
2026-10-31T18:24:33Z
independence
same_provider
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
8
usage object · 3 fields
prompt_tokens
38388
completion_tokens
3733
cached_tokens
1840
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:26306311
type
paper
label
pmid:26306311
[1] object · 3 fields
id
source:pmid:26306311
type
manuscript
label
PMID 26306311 full text
[2] object · 3 fields
id
data:geo:PXD001082
type
dataset
label
GEO PXD001082
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:26306311
type
paper
label
pmid:26306311
[1] object · 3 fields
id
source:pmid:26306311
type
manuscript
label
PMID 26306311 full text
[2] object · 3 fields
id
data:geo:PXD001082
type
dataset
label
GEO PXD001082
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-26306311
type
extraction
used array · 1 item
[0]
source:pmid:26306311
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-PXD001082
type
accession_resolution
used array · 1 item
[0]
data:geo:PXD001082
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:26306311
parent_hash
sha256:311a9ec76f9fe5573bbaa9c0cf46e07003277db537496f83b81761ee7fce6424
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:PXD001082 licence not read
[1]
asset:data:geo:PXD001082 not downloaded
[2]
execution.not_run
[3]
method.reader_named_unmapped
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
assays array · 1 item
[0] object · 11 fields
role
data_generation
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.93
evidence array · 1 item
[0]
n a larger population of patients (n=185) by ELISA, confirming the mass spectrometry results. B
order_basis
paper_text_order:1552
id
assay:1
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26306311", "kind": "science-record", "revision": 4, "content_hash": "sha256:e77c52e10106544c7962f3163f11adc9089e0c499594f98c0a13c2f9bc9356b3", "created_at": "2026-11-01T15:40:10Z", "updated_at": "2026-11-01T21:20:05Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comparative analysis of cerebrospinal fluid from the meningo-encephalitic stage of T. b. gambiense and rhodesiense sleeping sickness patients using TMT quantitative proteomics.", "doi": "10.1016/j.dib.2015.06.011", "pmid": "26306311", "authors": ["Natalia Tiberti", "Jean-Charles Sanchez"], "journal": "Data in brief", "year": 2015, "abstract": "The quantitative proteomics data here reported are part of a research article entitled \"Increased acute immune response during the meningo-encephalitic stage of Trypanosoma brucei rhodesiense sleeping sickness compared to Trypanosoma brucei gambiense\", published by Tiberti et al., 2015. Transl. Proteomics 6, 1-9. Sleeping sickness (human African trypanosomiasis - HAT) is a deadly neglected tropical disease affecting mainly rural communities in sub-Saharan Africa. This parasitic disease is caused by the Trypanosoma brucei (T. b.) parasite, which is transmitted to the human host through the bite of the tse-tse fly. Two parasite sub-species, T. b. rhodesiense and T. b. gambiense, are responsible for two clinically different and geographically separated forms of sleeping sickness. The objective of the present study was to characterise and compare the cerebrospinal fluid (CSF) proteome of stage 2 (meningo-encephalitic stage) HAT patients suffering from T. b. gambiense or T. b. rhodesiense disease using high-throughput quantitative proteomics and the Tandem Mass Tag (TMT(®)) isobaric labelling. In order to evaluate the CSF proteome in the context of HAT pathophysiology, the protein dataset was then submitted to gene ontology and pathway analysis. Two significantly differentially expressed proteins (C-reactive protein and orosomucoid 1) were further verified on a larger population of patients (n=185) by ELISA, confirming the mass spectrometry results. By showing a predominant involvement of the acute immune response in rhodesiense HAT, the proteomics results obtained in this work will contribute to further understand the mechanisms of pathology occurring in HAT and to propose new biomarkers of potential clinical utility. The mass spectrometry raw data are available in the Pride Archive via ProteomeXchange through the identifier PXD001082.", "claims": [{"id": "claim-method", "statement": "Only proteins identified with at least 2 unique peptides and with an FDR≤1% (computed at the PSM level) were considered for further quantitative analyses using Isobar quantification tool (version 1.76) [9], embedded in EasyProt.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26306311", "locator": "sections[10] \"Protein identification and quantification\" paragraph 5", "quote": "Only proteins identified with at least 2 unique peptides and with an FDR≤1% (computed at the PSM level) were considered for further quantitative analyses using Isobar quantification tool (version 1.76) [9], embedded in EasyProt."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry raw data are available in the Pride Archive via ProteomeXchange through the identifier PXD001082.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26306311", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The mass spectrometry raw data are available in the Pride Archive via ProteomeXchange through the identifier PXD001082."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "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:26306311"], "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:PXD001082"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "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:PXD001082"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26306311", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2015.06.011", "sha256": "sha256:db3aa2d981d7478f34518a0971daaa076547e5e81debe2820a3f0ebeae6a59c0", "bytes": 16437, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2015.06.011", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4534576", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD001082", "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=PXD001082", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD001082", "version": null, "note": "The mass spectrometry raw data are available in the Pride Archive via ProteomeXchange through the identifier PXD001082.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry raw data are available in the Pride Archive via ProteomeXchange through the identifier PXD001082.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Quantitative comparison of CSF proteins from T. b. gambiense and T. b. rhodesiense HAT patients", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:26306311:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6d86cf0233417aafb2890748d646fdf4fd106f18c01f8ca744b2eb7ab8d5ddfb", "bytes": 557, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#t0005", "version": null, "note": "Demographic description of patients investigated in the TMT 6-plex experiment.", "structure": {"pmcid": "PMC4534576", "section_index": 7, "section_title": "Samples", "row_count": 8, "column_count": 7}, "table": {"label": "Table 1", "caption": "Demographic description of patients investigated in the TMT 6-plex experiment.", "rows": [["", "T. b. gambiense - D.R.C.", "T. b. rhodesiense - UGANDA"], ["", "Pt #1", "Pt #2", "Pt #3", "Pt #4", "Pt #5", "Pt #6"], [""], ["Sex", "F", "F", "F", "F", "F", "F"], ["Age", "21", "29", "51", "22", "30", "53"], ["T+CSF", "Yes", "Yes", "Yes", "Yes", "Yes", "Yes"], ["WBC/µL", "135", "217", "97", "119", "231", "70"], ["TMT tag", "126", "127", "128", "129", "130", "131"]], "row_count": 8, "column_count": 7, "numeric_cells": 24, "header_rows": 1, "locator": "section[7]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:26306311:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a089657e85704e986809339fe5549c95cffc5cc09ba7f6b9c04ee3b10df4d20b", "bytes": 1378, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#t0010", "version": null, "note": "List of proteins significantly differentially expressed between rhodesiense and gambiense S2 CSF. Only proteins identified with at least 2 unique peptides and FDR<1% were considered for quantification.", "structure": {"pmcid": "PMC4534576", "section_index": 10, "section_title": "Protein identification and quantification", "row_count": 12, "column_count": 9}, "table": {"label": "Table 2", "caption": "List of proteins significantly differentially expressed between rhodesiense and gambiense S2 CSF. Only proteins identified with at least 2 unique peptides and FDR<1% were considered for quantification.", "rows": [["#", "AC", "Protein", "Gene", "Peptide count", "Spectral count", "Ratio⁎", "p Value ratio", "pValue sample"], ["1", "P06311", "Ig kappa chain V–III region IARC/BL41", "Na", "2", "2", "0.69", "0.007", "0.002"], ["2", "O00584", "Ribonuclease T2", "RNASET2", "3", "3", "0.69", "0.006", "0.019"], ["3", "Q9NPR2", "Semaphorin-4B", "SEMA4B", "2", "2", "0.72", "0.048", "0.017"], ["4", "P04114", "Apolipoprotein B-100", "APOB", "4", "5", "1.36", "0.041", "0.045"], ["5", "P19652", "Alpha-1-acid glycoprotein 2", "ORM2", "5", "10", "1.49", "0.005", "0.017"], ["6", "Q03591", "Complement factor H-related protein 1", "CFHR1", "1", "1", "1.52", "0.023", "0.036"], ["7", "P02748", "Complement component C9", "C9", "8", "10", "1.78", "0.006", "0.003"], ["8", "Q14624", "Inter-alpha-trypsin inhibitor heavy chain H4", "ITIH4", "10", "18", "1.80", "0.005", "0.026"], ["9", "P18428", "Lipopolysaccharide-binding protein", "LBP", "2", "2", "2.31", "0.046", "0.000"], ["10", "P02763", "Alpha-1-acid glycoprotein 1", "ORM1", "6", "28", "2.69", "0.001", "0.000"], ["11", "P02741", "C-reactive protein", "CRP", "3", "5", "9.30", "0.001", "0.000"]], "row_count": 12, "column_count": 9, "numeric_cells": 82, "header_rows": 1, "locator": "section[10]/table-wrap[1]#t0010"}}], "gaps": ["asset:data:geo:PXD001082 not downloaded", "asset:data:geo:PXD001082 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Isobar quantification tool (version 1.76)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Only proteins identified with at least 2 unique peptides and with an FDR≤1% (computed at the PSM level) were considered for further quantitative analyses using Isobar quantification tool (version 1.76) [9], embedded in EasyProt."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Isobar quantification tool (version 1.76)), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["PXD001082"], "resolved_accessions": ["PXD001082"], "statements": ["The mass spectrometry raw data are available in the Pride Archive via ProteomeXchange through the identifier PXD001082."], "basis": "The paper names PXD001082 in PRIDE and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26306311", "data:geo:PXD001082", "asset:table:pmid:26306311:1", "asset:table:pmid:26306311:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD001082"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:24:33Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 38388, "completion_tokens": 3733, "cached_tokens": 1840}}, "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:26306311", "type": "paper", "label": "pmid:26306311"}, {"id": "source:pmid:26306311", "type": "manuscript", "label": "PMID 26306311 full text"}, {"id": "data:geo:PXD001082", "type": "dataset", "label": "GEO PXD001082"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26306311", "type": "paper", "label": "pmid:26306311"}, {"id": "source:pmid:26306311", "type": "manuscript", "label": "PMID 26306311 full text"}, {"id": "data:geo:PXD001082", "type": "dataset", "label": "GEO PXD001082"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26306311", "type": "extraction", "used": ["source:pmid:26306311"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD001082", "type": "accession_resolution", "used": ["data:geo:PXD001082"], "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:26306311", "parent_hash": "sha256:311a9ec76f9fe5573bbaa9c0cf46e07003277db537496f83b81761ee7fce6424", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PXD001082 licence not read", "asset:data:geo:PXD001082 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "elisa", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["n a larger population of patients (n=185) by ELISA, confirming the mass spectrometry results. B"], "order_basis": "paper_text_order:1552", "id": "assay:1"}]}