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

pmid:26977445

Validation, optimisation, and application data in support of the development of a targeted selected ion monitoring assay for degraded cardiac troponin T.

Alexander S Streng · Douwe de Boer · Freek G Bouwman · Edwin C M Mariman · Arjen Scholten · Marja P van Dieijen-Visser · Will K W H Wodzig

Data in brief · 2016 doi:10.1016/j.dib.2016.02.051

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:26977445
kind
science-record
content_hash
sha256:c13db10360db22bb5cb979d846870e0e0e21a8b02584e82051a97487703ceb78
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:16Z
updated_at
2026-11-01T21:20:26Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Validation, optimisation, and application data in support of the development of a targeted selected ion monitoring assay for degraded cardiac troponin T.
doi
10.1016/j.dib.2016.02.051
pmid
26977445
authors array · 7 items
[0]
Alexander S Streng
[1]
Douwe de Boer
[2]
Freek G Bouwman
[3]
Edwin C M Mariman
[4]
Arjen Scholten
[5]
Marja P van Dieijen-Visser
[6]
Will K W H Wodzig
journal
Data in brief
year
2016
abstract
Cardiac troponin T (cTnT) fragmentation in human serum was investigated using a newly developed targeted selected ion monitoring assay, as described in the accompanying article: "Development of a targeted selected ion monitoring assay for the elucidation of protease induced structural changes in cardiac troponin T" [1]. This article presents data describing aspects of the validation and optimisation of this assay. The data consists of several figures, an excel file containing the results of a sequence identity search, and a description of the raw mass spectrometry (MS) data files, deposited in the ProteomeXchange repository with id PRIDE: PXD003187.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
Coefficient of variation (CV) was calculated for the instrument by injecting the synthetic peptide standard 6 times while using a t-SIM method. Additionally, the CV was calculated for 6 cTnT in-gel digests prepared according to the workflow in [1].
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:26977445
locator
sections[8] "Analysis of technical replicates" paragraph 2
quote
Coefficient of variation (CV) was calculated for the instrument by injecting the synthetic peptide standard 6 times while using a t-SIM method. Additionally, the CV was calculated for 6 cTnT in-gel digests prepared according to the workflow in [1].
state
complete
[1] object · 6 fields
id
claim-data-access
statement
All figures are provided in this article. MS.raw- and.msf-files are deposited in the ProteomeXchange repository with id PRIDE: PXD003187.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:26977445
locator
sections[1] "Specifications table" paragraph 2
quote
All figures are provided in this article. MS.raw- and.msf-files are deposited in the ProteomeXchange repository with id PRIDE: PXD003187.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
The study used coefficient of variation (CV) to assess the precision of the t-SIM assay and experimental workflow; the validation and optimisation data, sequence-search Excel file, and raw mass spectrometry data are available through ProteomeXchange under PRIDE: PXD003187.
kind
quantitative
target object · 4 fields
value
6
unit
fold change
tolerance
null
source
Coefficient of variation (CV) was calculated for the instrument by injecting the synthetic peptide standard 6 times while using a t-SIM method.
evidence array · 3 items
[0] object · 3 fields
asset
source:pmid:26977445
locator
sections[3] "Data" paragraph 2
quote
The data in this article supports the validation and optimisation of a targeted selected ion monitoring (t-SIM) assay used to analyse an observed fragmentation pattern of the protein cardiac troponin T (cTnT) [1].
[1] object · 3 fields
asset
source:pmid:26977445
locator
sections[8] "Analysis of technical replicates" paragraph 2
quote
Coefficient of variation (CV) was calculated for the instrument by injecting the synthetic peptide standard 6 times while using a t-SIM method.
[2] object · 3 fields
asset
source:pmid:26977445
locator
sections[0] "Abstract" paragraph 1
quote
The data consists of several figures, an excel file containing the results of a sequence identity search, and a description of the raw mass spectrometry (MS) data files, deposited in the ProteomeXchange repository with id PRIDE: PXD003187.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
partial
objective
The study used coefficient of variation (CV) to assess the precision of the t-SIM assay and experimental workflow; the validation and optimisation data, sequence-search Excel file, and raw mass spectrometry data are available through ProteomeXchange under PRIDE: PXD003187.
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:26977445
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
blocked
blocked_on
data:accession_absent
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 · 0 items
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 · 0 items
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:obtain_source_data blocked on data:accession_absent
data object · 3 fields
state
partial
assets array · 2 items
[0] object · 15 fields
id
source:pmid:26977445
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1016/j.dib.2016.02.051
sha256
sha256:ffec84f52b8142b61b2e73cb5103c3e8fe18b6d6895199898499abf76f422f16
bytes
9055
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1016/j.dib.2016.02.051
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
PMC4782000
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 16 fields
id
asset:table:pmid:26977445:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:464a4493fa675baba7a16686eed50ac5b2318d5aa2b85d82033c81b6b95d2bf0
bytes
1104
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[1]/table-wrap[1]#t0005
version
null
note
null
structure object · 5 fields
pmcid
PMC4782000
section_index
1
section_title
Specifications table
row_count
9
column_count
2
table object · 8 fields
label
null
caption
null
rows array · 9 items
[0] array · 2 items
[0]
Subject area
[1]
Clinical chemistry.
[1] array · 2 items
[0]
More specific subject area
[1]
Cardiovascular biomarkers.
[2] array · 2 items
[0]
Type of data
[1]
Figures, graphs, table, MS data.
[3] array · 2 items
[0]
How data was acquired
[1]
SDS-PAGE with Coomassie staining, MS data acquired with the Q Exactive (Thermo Scientific), and an online database search.
[4] array · 2 items
[0]
Data format
[1]
Raw data (.raw, .msf, .xlsx) and analysed data (figures).
[5] array · 2 items
[0]
Experimental factors
[1]
cTnT fragments were created by spiking intact cTnT in human serum and incubation at 37 °C for varying amounts of time.
[6] array · 2 items
[0]
Experimental features
[1]
Intact and fragmented cTnT was purified by immunoprecipitation, separated by SDS-PAGE, manually excised and digested with trypsin followed by relative quantification using targeted-SIM.
[7] array · 2 items
[0]
Data source location
[1]
Maastricht, the Netherlands.
[8] array · 2 items
[0]
Data accessibility
[1]
All figures are provided in this article. MS.raw- and.msf-files are deposited in the ProteomeXchange repository with id PRIDE: PXD003187.
locator
section[1]/table-wrap[1]#t0005
gaps array · 0 items
analysis object · 4 fields
state
partial
methods array · 1 item
[0] object · 10 fields
id
method-1
family
null
specific
null
label
Coefficient of variation (CV)
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
Coefficient of variation (CV) was calculated for the instrument by injecting the synthetic peptide standard 6 times while using a t-SIM method. Additionally, the CV was calculated for 6 cTnT in-gel digests prepared according to the workflow in [1].
targets array · 1 item
[0] object · 8 fields
id
target-published-estimate
claim_id
claim-target-result
operation
null
unit
fold change
tolerance
null
state
complete
note
The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none.
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
blocked_on
data:accession_absent
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 (Coefficient of variation (CV)), 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
R4
reachable
false
accessions array · 1 item
[0]
PRIDE: PXD003187
resolved_accessions array · 0 items
statements array · 1 item
[0]
All figures are provided in this article. MS.raw- and.msf-files are deposited in the ProteomeXchange repository with id PRIDE: PXD003187.
basis
The paper names PRIDE: PXD003187, but the accession does not resolve in the repository (no reason recorded), so the data cannot be reached from here. 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:26977445
[1]
asset:table:pmid:26977445:1
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:None
gaps array · 1 item
[0]
data:accession_absent
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
2026-10-31T18:27:34Z
independence
same_provider
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
8
usage object · 3 fields
prompt_tokens
22222
completion_tokens
4220
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:26977445
type
paper
label
pmid:26977445
[1] object · 3 fields
id
source:pmid:26977445
type
manuscript
label
PMID 26977445 full text
[2] object · 3 fields
id
data:geo:None
type
dataset
label
GEO None
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:26977445
type
paper
label
pmid:26977445
[1] object · 3 fields
id
source:pmid:26977445
type
manuscript
label
PMID 26977445 full text
[2] object · 3 fields
id
data:geo:None
type
dataset
label
GEO None
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-26977445
type
extraction
used array · 1 item
[0]
source:pmid:26977445
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-None
type
accession_resolution
used array · 1 item
[0]
data:geo:None
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:26977445
parent_hash
sha256:a8981f1f43d66241ac4c316af1b3b1896e19f3785a7968be869df9b3e2c7b22c
fork_of
null
gaps array · 6 items
[0]
execution.not_run
[1]
method.reader_named_unmapped
[2]
review.human_critique
[3]
review.independent_reader
[4]
review.machine_critique
[5]
step:obtain_source_data blocked on data:accession_absent
assays array · 1 item
[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
0.93
evidence array · 1 item
[0]
dentity search, and a description of the raw mass spectrometry (MS) data files, deposited in the ProteomeXc
order_basis
paper_text_order:662
id
assay:1
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26977445", "kind": "science-record", "revision": 4, "content_hash": "sha256:c13db10360db22bb5cb979d846870e0e0e21a8b02584e82051a97487703ceb78", "created_at": "2026-11-01T15:40:16Z", "updated_at": "2026-11-01T21:20:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Validation, optimisation, and application data in support of the development of a targeted selected ion monitoring assay for degraded cardiac troponin T.", "doi": "10.1016/j.dib.2016.02.051", "pmid": "26977445", "authors": ["Alexander S Streng", "Douwe de Boer", "Freek G Bouwman", "Edwin C M Mariman", "Arjen Scholten", "Marja P van Dieijen-Visser", "Will K W H Wodzig"], "journal": "Data in brief", "year": 2016, "abstract": "Cardiac troponin T (cTnT) fragmentation in human serum was investigated using a newly developed targeted selected ion monitoring assay, as described in the accompanying article: \"Development of a targeted selected ion monitoring assay for the elucidation of protease induced structural changes in cardiac troponin T\" [1]. This article presents data describing aspects of the validation and optimisation of this assay. The data consists of several figures, an excel file containing the results of a sequence identity search, and a description of the raw mass spectrometry (MS) data files, deposited in the ProteomeXchange repository with id PRIDE: PXD003187.", "claims": [{"id": "claim-method", "statement": "Coefficient of variation (CV) was calculated for the instrument by injecting the synthetic peptide standard 6 times while using a t-SIM method. Additionally, the CV was calculated for 6 cTnT in-gel digests prepared according to the workflow in [1].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26977445", "locator": "sections[8] \"Analysis of technical replicates\" paragraph 2", "quote": "Coefficient of variation (CV) was calculated for the instrument by injecting the synthetic peptide standard 6 times while using a t-SIM method. Additionally, the CV was calculated for 6 cTnT in-gel digests prepared according to the workflow in [1]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All figures are provided in this article. MS.raw- and.msf-files are deposited in the ProteomeXchange repository with id PRIDE: PXD003187.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26977445", "locator": "sections[1] \"Specifications table\" paragraph 2", "quote": "All figures are provided in this article. MS.raw- and.msf-files are deposited in the ProteomeXchange repository with id PRIDE: PXD003187."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used coefficient of variation (CV) to assess the precision of the t-SIM assay and experimental workflow; the validation and optimisation data, sequence-search Excel file, and raw mass spectrometry data are available through ProteomeXchange under PRIDE: PXD003187.", "kind": "quantitative", "target": {"value": 6.0, "unit": "fold change", "tolerance": null, "source": "Coefficient of variation (CV) was calculated for the instrument by injecting the synthetic peptide standard 6 times while using a t-SIM method."}, "evidence": [{"asset": "source:pmid:26977445", "locator": "sections[3] \"Data\" paragraph 2", "quote": "The data in this article supports the validation and optimisation of a targeted selected ion monitoring (t-SIM) assay used to analyse an observed fragmentation pattern of the protein cardiac troponin T (cTnT) [1]."}, {"asset": "source:pmid:26977445", "locator": "sections[8] \"Analysis of technical replicates\" paragraph 2", "quote": "Coefficient of variation (CV) was calculated for the instrument by injecting the synthetic peptide standard 6 times while using a t-SIM method."}, {"asset": "source:pmid:26977445", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data consists of several figures, an excel file containing the results of a sequence identity search, and a description of the raw mass spectrometry (MS) data files, deposited in the ProteomeXchange repository with id PRIDE: PXD003187."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study used coefficient of variation (CV) to assess the precision of the t-SIM assay and experimental workflow; the validation and optimisation data, sequence-search Excel file, and raw mass spectrometry data are available through ProteomeXchange under PRIDE: PXD003187.", "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:26977445"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26977445", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2016.02.051", "sha256": "sha256:ffec84f52b8142b61b2e73cb5103c3e8fe18b6d6895199898499abf76f422f16", "bytes": 9055, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2016.02.051", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4782000", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:26977445:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:464a4493fa675baba7a16686eed50ac5b2318d5aa2b85d82033c81b6b95d2bf0", "bytes": 1104, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0005", "version": null, "note": null, "structure": {"pmcid": "PMC4782000", "section_index": 1, "section_title": "Specifications table", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Clinical chemistry."], ["More specific subject area", "Cardiovascular biomarkers."], ["Type of data", "Figures, graphs, table, MS data."], ["How data was acquired", "SDS-PAGE with Coomassie staining, MS data acquired with the Q Exactive (Thermo Scientific), and an online database search."], ["Data format", "Raw data (.raw, .msf, .xlsx) and analysed data (figures)."], ["Experimental factors", "cTnT fragments were created by spiking intact cTnT in human serum and incubation at 37 °C for varying amounts of time."], ["Experimental features", "Intact and fragmented cTnT was purified by immunoprecipitation, separated by SDS-PAGE, manually excised and digested with trypsin followed by relative quantification using targeted-SIM."], ["Data source location", "Maastricht, the Netherlands."], ["Data accessibility", "All figures are provided in this article. MS.raw- and.msf-files are deposited in the ProteomeXchange repository with id PRIDE: PXD003187."]], "row_count": 9, "column_count": 2, "numeric_cells": 2, "header_rows": 0, "locator": "section[1]/table-wrap[1]#t0005"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Coefficient of variation (CV)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Coefficient of variation (CV) was calculated for the instrument by injecting the synthetic peptide standard 6 times while using a t-SIM method. Additionally, the CV was calculated for 6 cTnT in-gel digests prepared according to the workflow in [1]."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 6.0, "unit": "fold change", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "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": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Coefficient of variation (CV)), 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": "R4", "reachable": false, "accessions": ["PRIDE: PXD003187"], "resolved_accessions": [], "statements": ["All figures are provided in this article. MS.raw- and.msf-files are deposited in the ProteomeXchange repository with id PRIDE: PXD003187."], "basis": "The paper names PRIDE: PXD003187, but the accession does not resolve in the repository (no reason recorded), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26977445", "asset:table:pmid:26977445:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:27:34Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 22222, "completion_tokens": 4220, "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:26977445", "type": "paper", "label": "pmid:26977445"}, {"id": "source:pmid:26977445", "type": "manuscript", "label": "PMID 26977445 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26977445", "type": "paper", "label": "pmid:26977445"}, {"id": "source:pmid:26977445", "type": "manuscript", "label": "PMID 26977445 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26977445", "type": "extraction", "used": ["source:pmid:26977445"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:26977445", "parent_hash": "sha256:a8981f1f43d66241ac4c316af1b3b1896e19f3785a7968be869df9b3e2c7b22c", "fork_of": null, "generation": 3}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "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": 0.93, "evidence": ["dentity search, and a description of the raw mass spectrometry (MS) data files, deposited in the ProteomeXc"], "order_basis": "paper_text_order:662", "id": "assay:1"}]}