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

pmid:26425665

SILAC-based quantification of changes in protein tyrosine phosphorylation induced by Interleukin-2 (IL-2) and IL-15 in T-lymphocytes.

Nerea Osinalde · Virginia Sánchez-Quiles · Vyacheslav Akimov · Blagoy Blagoev · Irina Kratchmarova

Data in brief · 2015 doi:10.1016/j.dib.2015.08.007

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:26425665
kind
science-record
content_hash
sha256:acc126c2345c2560c0fc6f89d104eb282027a28b5352b80922210e0da78c38d6
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:11Z
updated_at
2026-11-01T21:20:08Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
SILAC-based quantification of changes in protein tyrosine phosphorylation induced by Interleukin-2 (IL-2) and IL-15 in T-lymphocytes.
doi
10.1016/j.dib.2015.08.007
pmid
26425665
authors array · 5 items
[0]
Nerea Osinalde
[1]
Virginia Sánchez-Quiles
[2]
Vyacheslav Akimov
[3]
Blagoy Blagoev
[4]
Irina Kratchmarova
journal
Data in brief
year
2015
abstract
This data article presents the first large-scale quantitative phosphoproteomics dataset generated to decipher the signaling networks initiated by IL-2 and IL-15 in T-lymphocytes. Data was collected by combining immunoprecipitation of tyrosine phosphorylated proteins and TiO2-based phosphopeptide enrichment with SILAC-based quantitative mass spectrometry. We report all the proteins and phosphotyrosine-containing peptides identified and quantified in IL-2- and IL-15-stimulated T-lymphocytes. The gene ontology analysis of IL-2 and IL-15 effector proteins detected in the present work is also included. The data supplied in this article is related to the research work entitled "Simultaneous dissection and comparison of IL-2 and IL-15 signaling pathways by global quantitative phosphoproteomics" [1]. All mass spectrometry data have been deposited in the ProteomeXchange with the identifier PXD001129.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
For SILAC experiments, Kit225 T-cells were grown in custom-made RPMI deficient for L-Arg, and L-Lys (Gibco-Invitrogen, Carlsbad, CA), which was supplemented with 10% dyalized serum (Gibco-Invitrogen), 1% Glutamax, 1% p/s, 1% sodium pyruvate and distinct isotopes of L-Arginine (18 µg/ml) and L-Lysine (730 µg/ml).
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:26425665
locator
sections[5] "Cell culture conditions" paragraph 3
quote
For SILAC experiments, Kit225 T-cells were grown in custom-made RPMI deficient for L-Arg, and L-Lys (Gibco-Invitrogen, Carlsbad, CA), which was supplemented with 10% dyalized serum (Gibco-Invitrogen), 1% Glutamax, 1% p/s, 1% sodium pyruvate and distinct isotopes of L-Arginine (18 µg/ml) and L-Lysine (730 µg/ml).
state
complete
[1] object · 6 fields
id
claim-data-access
statement
Supplementary data associated with this article can be found in the online version at doi:10.1016/j.dib.2015.08.007.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:26425665
locator
sections[14] "fn-group" paragraph 1
quote
Supplementary data associated with this article can be found in the online version at doi:10.1016/j.dib.2015.08.007.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
partial
objective
null
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:26425665
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 · 3 items
[0] object · 15 fields
id
source:pmid:26425665
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1016/j.dib.2015.08.007
sha256
sha256:ade4ba70f05db58ba0b915b2e9a492a3c02ed875593c59ff13588124be839df4
bytes
13158
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1016/j.dib.2015.08.007
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
PMC4564383
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 16 fields
id
asset:table:pmid:26425665:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:96774573c562a0fd413d31f65bdccdc28e10996377a39e50d98737a00be7d8d2
bytes
1562
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
PMC4564383
section_index
1
section_title
p
row_count
10
column_count
2
table object · 8 fields
label
null
caption
null
rows array · 10 items
[0] array · 2 items
[0]
Subject area
[1]
Cell signaling and immunology
[1] array · 2 items
[0]
More specific subject area
[1]
Interleukin signaling and quantitative phosphoproteomics
[2] array · 2 items
[0]
Type of data
[1]
Mass spectrometry (MS) data
[3] array · 2 items
[0]
How data was acquired
[1]
MS data was acquired in a Q-Exactive (Thermo) mass spectrometer.
[4] array · 2 items
[0]
Data format
[1]
Raw (⁎raw), excel files (.xlsx)
[5] array · 2 items
[0]
Experimental factors
[1]
Kit225 T-cells were grown in light (Arg0/Lys0), medium (Arg6/Lys4) and heavy (Arg10/Lys8) media. Differentially SILAC-labeled T-cells were kept unstimulated, treated with IL-2 or stimulated with IL-15, respectively prior cell lysis.
[6] array · 2 items
[0]
Experimental features
[1]
After stimulation, cells were lysed and protein extracts derived from the three different experimental conditions were combined and enriched in tyrosine phosphorylated proteins using two antibodies. Immune complexes were fractionated in a SDS-PAGE and in-gel digested using trypsin. Resulting peptides were either directly analyzed by LC-MS/MS or enriched in phosphorylated peptides using TiO2 beads prior MS analysis.
[7] array · 2 items
[0]
Data source location
[1]
Odense, Denmark
[8] array · 2 items
[0]
Data accessibility
[1]
All MS data presented in this article are deposited in the ProteomeXchange with the identifier PXD001129 (http://proteomecentral.proteomexchange.org/datastet/PXD001129).
[9] array · 1 item
[0]
List of all proteins identified in each of the two replicas performed are provided in Supplementary material linked with this article.
locator
section[1]/table-wrap[1]#t0005
[2] object · 16 fields
id
asset:table:pmid:26425665:2
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:96774573c562a0fd413d31f65bdccdc28e10996377a39e50d98737a00be7d8d2
bytes
1562
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
PMC4564383
section_index
2
section_title
p
row_count
10
column_count
2
table object · 8 fields
label
null
caption
null
rows array · 10 items
[0] array · 2 items
[0]
Subject area
[1]
Cell signaling and immunology
[1] array · 2 items
[0]
More specific subject area
[1]
Interleukin signaling and quantitative phosphoproteomics
[2] array · 2 items
[0]
Type of data
[1]
Mass spectrometry (MS) data
[3] array · 2 items
[0]
How data was acquired
[1]
MS data was acquired in a Q-Exactive (Thermo) mass spectrometer.
[4] array · 2 items
[0]
Data format
[1]
Raw (⁎raw), excel files (.xlsx)
[5] array · 2 items
[0]
Experimental factors
[1]
Kit225 T-cells were grown in light (Arg0/Lys0), medium (Arg6/Lys4) and heavy (Arg10/Lys8) media. Differentially SILAC-labeled T-cells were kept unstimulated, treated with IL-2 or stimulated with IL-15, respectively prior cell lysis.
[6] array · 2 items
[0]
Experimental features
[1]
After stimulation, cells were lysed and protein extracts derived from the three different experimental conditions were combined and enriched in tyrosine phosphorylated proteins using two antibodies. Immune complexes were fractionated in a SDS-PAGE and in-gel digested using trypsin. Resulting peptides were either directly analyzed by LC-MS/MS or enriched in phosphorylated peptides using TiO2 beads prior MS analysis.
[7] array · 2 items
[0]
Data source location
[1]
Odense, Denmark
[8] array · 2 items
[0]
Data accessibility
[1]
All MS data presented in this article are deposited in the ProteomeXchange with the identifier PXD001129 (http://proteomecentral.proteomexchange.org/datastet/PXD001129).
[9] array · 1 item
[0]
List of all proteins identified in each of the two replicas performed are provided in Supplementary material linked with this article.
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
SILAC
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
For SILAC experiments, Kit225 T-cells were grown in custom-made RPMI deficient for L-Arg, and L-Lys (Gibco-Invitrogen, Carlsbad, CA), which was supplemented with 10% dyalized serum (Gibco-Invitrogen), 1% Glutamax, 1% p/s, 1% sodium pyruvate and distinct isotopes of L-Arginine (18 µg/ml) and L-Lysine (730 µg/ml).
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
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 (SILAC), 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 · 0 items
resolved_accessions array · 0 items
statements array · 1 item
[0]
Supplementary data associated with this article can be found in the online version at doi:10.1016/j.dib.2015.08.007.
basis
The paper names no accession to its source data, so the data has to come from the authors.
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 3 items
[0]
source:pmid:26425665
[1]
asset:table:pmid:26425665:1
[2]
asset:table:pmid:26425665:2
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: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
provider
minimax
provider_family
minimax
read_at
null
independence
same_provider
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
0
usage object · 0 fields
stages array · 1 item
[0] object · 4 fields
id
extraction
state
complete
reader
MiniMax-M3
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:26425665
type
paper
label
pmid:26425665
[1] object · 3 fields
id
source:pmid:26425665
type
manuscript
label
PMID 26425665 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:26425665
type
paper
label
pmid:26425665
[1] object · 3 fields
id
source:pmid:26425665
type
manuscript
label
PMID 26425665 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-26425665
type
extraction
used array · 1 item
[0]
source:pmid:26425665
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:26425665
parent_hash
sha256:9f3c891d31867c450c8ae7bc797b6818824700122e3cd375529a5e5f3af8dd87
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
0.99
evidence array · 3 items
[0]
ide enrichment with SILAC-based quantitative mass spectrometry. We report all the proteins and phosphotyros
[1]
bal quantitative phosphoproteomics" [1]. All mass spectrometry data have been deposited in the ProteomeXcha
[2]
ed in phosphopeptides using TiO2 beads prior mass spectrometry (MS) analysis or (E) directly analyzed by a
order_basis
paper_text_order:427
id
assay:1
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26425665", "kind": "science-record", "revision": 6, "content_hash": "sha256:acc126c2345c2560c0fc6f89d104eb282027a28b5352b80922210e0da78c38d6", "created_at": "2026-11-01T15:40:11Z", "updated_at": "2026-11-01T21:20:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "SILAC-based quantification of changes in protein tyrosine phosphorylation induced by Interleukin-2 (IL-2) and IL-15 in T-lymphocytes.", "doi": "10.1016/j.dib.2015.08.007", "pmid": "26425665", "authors": ["Nerea Osinalde", "Virginia Sánchez-Quiles", "Vyacheslav Akimov", "Blagoy Blagoev", "Irina Kratchmarova"], "journal": "Data in brief", "year": 2015, "abstract": "This data article presents the first large-scale quantitative phosphoproteomics dataset generated to decipher the signaling networks initiated by IL-2 and IL-15 in T-lymphocytes. Data was collected by combining immunoprecipitation of tyrosine phosphorylated proteins and TiO2-based phosphopeptide enrichment with SILAC-based quantitative mass spectrometry. We report all the proteins and phosphotyrosine-containing peptides identified and quantified in IL-2- and IL-15-stimulated T-lymphocytes. The gene ontology analysis of IL-2 and IL-15 effector proteins detected in the present work is also included. The data supplied in this article is related to the research work entitled \"Simultaneous dissection and comparison of IL-2 and IL-15 signaling pathways by global quantitative phosphoproteomics\" [1]. All mass spectrometry data have been deposited in the ProteomeXchange with the identifier PXD001129.", "claims": [{"id": "claim-method", "statement": "For SILAC experiments, Kit225 T-cells were grown in custom-made RPMI deficient for L-Arg, and L-Lys (Gibco-Invitrogen, Carlsbad, CA), which was supplemented with 10% dyalized serum (Gibco-Invitrogen), 1% Glutamax, 1% p/s, 1% sodium pyruvate and distinct isotopes of L-Arginine (18 µg/ml) and L-Lysine (730 µg/ml).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26425665", "locator": "sections[5] \"Cell culture conditions\" paragraph 3", "quote": "For SILAC experiments, Kit225 T-cells were grown in custom-made RPMI deficient for L-Arg, and L-Lys (Gibco-Invitrogen, Carlsbad, CA), which was supplemented with 10% dyalized serum (Gibco-Invitrogen), 1% Glutamax, 1% p/s, 1% sodium pyruvate and distinct isotopes of L-Arginine (18 µg/ml) and L-Lysine (730 µg/ml)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Supplementary data associated with this article can be found in the online version at doi:10.1016/j.dib.2015.08.007.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26425665", "locator": "sections[14] \"fn-group\" paragraph 1", "quote": "Supplementary data associated with this article can be found in the online version at doi:10.1016/j.dib.2015.08.007."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "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:26425665"], "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:26425665", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2015.08.007", "sha256": "sha256:ade4ba70f05db58ba0b915b2e9a492a3c02ed875593c59ff13588124be839df4", "bytes": 13158, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2015.08.007", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4564383", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:26425665:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:96774573c562a0fd413d31f65bdccdc28e10996377a39e50d98737a00be7d8d2", "bytes": 1562, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0005", "version": null, "note": null, "structure": {"pmcid": "PMC4564383", "section_index": 1, "section_title": "p", "row_count": 10, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Cell signaling and immunology"], ["More specific subject area", "Interleukin signaling and quantitative phosphoproteomics"], ["Type of data", "Mass spectrometry (MS) data"], ["How data was acquired", "MS data was acquired in a Q-Exactive (Thermo) mass spectrometer."], ["Data format", "Raw (⁎raw), excel files (.xlsx)"], ["Experimental factors", "Kit225 T-cells were grown in light (Arg0/Lys0), medium (Arg6/Lys4) and heavy (Arg10/Lys8) media. Differentially SILAC-labeled T-cells were kept unstimulated, treated with IL-2 or stimulated with IL-15, respectively prior cell lysis."], ["Experimental features", "After stimulation, cells were lysed and protein extracts derived from the three different experimental conditions were combined and enriched in tyrosine phosphorylated proteins using two antibodies. Immune complexes were fractionated in a SDS-PAGE and in-gel digested using trypsin. Resulting peptides were either directly analyzed by LC-MS/MS or enriched in phosphorylated peptides using TiO2 beads prior MS analysis."], ["Data source location", "Odense, Denmark"], ["Data accessibility", "All MS data presented in this article are deposited in the ProteomeXchange with the identifier PXD001129 (http://proteomecentral.proteomexchange.org/datastet/PXD001129)."], ["List of all proteins identified in each of the two replicas performed are provided in Supplementary material linked with this article."]], "row_count": 10, "column_count": 2, "numeric_cells": 2, "header_rows": 0, "locator": "section[1]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:26425665:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:96774573c562a0fd413d31f65bdccdc28e10996377a39e50d98737a00be7d8d2", "bytes": 1562, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0005", "version": null, "note": null, "structure": {"pmcid": "PMC4564383", "section_index": 2, "section_title": "p", "row_count": 10, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Cell signaling and immunology"], ["More specific subject area", "Interleukin signaling and quantitative phosphoproteomics"], ["Type of data", "Mass spectrometry (MS) data"], ["How data was acquired", "MS data was acquired in a Q-Exactive (Thermo) mass spectrometer."], ["Data format", "Raw (⁎raw), excel files (.xlsx)"], ["Experimental factors", "Kit225 T-cells were grown in light (Arg0/Lys0), medium (Arg6/Lys4) and heavy (Arg10/Lys8) media. Differentially SILAC-labeled T-cells were kept unstimulated, treated with IL-2 or stimulated with IL-15, respectively prior cell lysis."], ["Experimental features", "After stimulation, cells were lysed and protein extracts derived from the three different experimental conditions were combined and enriched in tyrosine phosphorylated proteins using two antibodies. Immune complexes were fractionated in a SDS-PAGE and in-gel digested using trypsin. Resulting peptides were either directly analyzed by LC-MS/MS or enriched in phosphorylated peptides using TiO2 beads prior MS analysis."], ["Data source location", "Odense, Denmark"], ["Data accessibility", "All MS data presented in this article are deposited in the ProteomeXchange with the identifier PXD001129 (http://proteomecentral.proteomexchange.org/datastet/PXD001129)."], ["List of all proteins identified in each of the two replicas performed are provided in Supplementary material linked with this article."]], "row_count": 10, "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": "SILAC", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "For SILAC experiments, Kit225 T-cells were grown in custom-made RPMI deficient for L-Arg, and L-Lys (Gibco-Invitrogen, Carlsbad, CA), which was supplemented with 10% dyalized serum (Gibco-Invitrogen), 1% Glutamax, 1% p/s, 1% sodium pyruvate and distinct isotopes of L-Arginine (18 µg/ml) and L-Lysine (730 µg/ml)."}}], "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": "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 (SILAC), 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": [], "resolved_accessions": [], "statements": ["Supplementary data associated with this article can be found in the online version at doi:10.1016/j.dib.2015.08.007."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26425665", "asset:table:pmid:26425665:1", "asset:table:pmid:26425665:2"], "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", "provider": "minimax", "provider_family": "minimax", "read_at": null, "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 0, "usage": {}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3", "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:26425665", "type": "paper", "label": "pmid:26425665"}, {"id": "source:pmid:26425665", "type": "manuscript", "label": "PMID 26425665 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26425665", "type": "paper", "label": "pmid:26425665"}, {"id": "source:pmid:26425665", "type": "manuscript", "label": "PMID 26425665 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26425665", "type": "extraction", "used": ["source:pmid:26425665"], "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:26425665", "parent_hash": "sha256:9f3c891d31867c450c8ae7bc797b6818824700122e3cd375529a5e5f3af8dd87", "fork_of": null, "generation": 5}, "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": 0.99, "evidence": ["ide enrichment with SILAC-based quantitative mass spectrometry. We report all the proteins and phosphotyros", "bal quantitative phosphoproteomics\" [1]. All mass spectrometry data have been deposited in the ProteomeXcha", "ed in phosphopeptides using TiO2 beads prior mass spectrometry (MS) analysis or (E) directly analyzed by a"], "order_basis": "paper_text_order:427", "id": "assay:1"}]}