17 tool steps across 10 unique tools, including tools inside nested subworkflows. A plus sign denotes parallel branches.
Workflow
Human UniProt Isoforms cRAP FASTA + SGPS Cut + MQ Cut→SGPS Remove Beginner + MQ Remove Beginner + PepQuery2→Collapse Collection + Concatenate datasets→Filter→Filter Remove beginning→FRB Cut→Peptide and Protein from Peptide Reports→PPPR Remove beginning→Group→Uniprot ID from verified Peptides→UniProt→Quantitation Database for MaxQuant
Complete query
The full task shown to the agent, excluding execution-condition instructions.
Perform novel-peptide validation for the supplied microbial candidate peptides using the provided tandem mass spectra. Use the supplied human UniProt sequences with isoforms and the cRAP contaminant sequences as the competing reference search space. Use a precursor mass tolerance of 10 ppm, fragment mass tolerance of 0.6 Da, tryptic digestion with at most 2 missed cleavages, precursor charge states 2 through 6, and CID/HCD fragmentation. Use fixed Carbamidomethylation on cysteine, fixed TMT 11-plex modification on lysine and the peptide N-terminus, and variable Oxidation on methionine. For each verified peptide, report every associated microbial protein assignment from the supplied peptide reports. Write `final_answer/verified_peptides.tsv` with exactly two tab-separated columns, `peptide` and `protein_id`, one peptide-protein pair per row. Peptide sequences must be uppercase and contain no modification annotations.
acc evaluator
acc compares the final output files with the reference outputs.
Metric
peptide_protein_pair_f1
Definition
Precision/recall F1 over normalized (peptide, protein_id) pairs. Peptide sequences are uppercased and stripped of modification annotations before comparison; protein identifiers are reduced to their UniProt accession. Order is irrelevant; duplicate pairs are collapsed.
Formula
Final scoreS = F1(|Q_C ∩ Q_R|, |Q_C|, |Q_R|)
Q is the set of normalized (peptide, protein accession) pairs.
A step passes when the trace directly shows that it ran. Parameter correctness and output quality are measured separately by acc.
Step 1Prepare the microbial candidate peptides and the competing human UniProt-with-isoforms plus cRAP reference space.
All supplied microbial candidate peptides and their protein associations were prepared for testing.
The competing reference space included human UniProt with isoforms and cRAP contaminants.
Step 2Test candidate peptides against the tandem mass spectra using the stated tolerances, enzyme, charge range, fragmentation mode, and modifications.
A successful spectrum-search/test execution used 10 ppm precursor and 0.6 Da fragment tolerance.
The execution used trypsin specificity with at most 2 missed cleavages and charge range 2-6.
The execution used the stated CID/HCD fragmentation handling and carbamidomethyl, TMT11, and oxidation modifications.
All candidate peptides were tested against the provided tandem mass spectra and competing reference space.
Step 3Apply a defensible validation or significance rule to retain supported peptides.
A documented validation/significance rule was applied to the search evidence rather than accepting every tested candidate.
Every retained peptide satisfies that rule and competing human/contaminant explanations were handled consistently.
Step 4Link every accepted peptide to all associated microbial protein IDs and produce the final peptide-protein table.
Every accepted peptide is linked to all supplied associated microbial protein IDs without dropping multi-protein mappings.
The required final table passes schema and final-answer checks.
Model results and score explanations
The 20 results below acc 1.000 each include a score explanation and quantitative evidence. A score below 1.000 is not automatically an error. Each replicate shows its recorded workflow, acc, step score, and Hugging Face trace. Galaxy histories can be imported by link but are not published in Galaxy's public history listing.
GPT-5.5
Open-ended code
R1acc · step score 1.000
0.982
Recorded workflow
Competitor fasta preparation→Pepquery smoke→Pepquery f10 full→Pepquery f11 chunked fallback→Pepquery f13 chunked fallback→Pepquery f15 chunked fallback→5 more steps
All 11 recorded steps
Competitor fasta preparation
Pepquery smoke
Pepquery f10 full
Pepquery f11 chunked fallback
Pepquery f13 chunked fallback
Pepquery f15 chunked fallback
Pepquery f11 full lowmem
Pepquery f13 full lowmem
Pepquery f15 full lowmem
Final tsv generation — PepQuery
Final validation — Table transformation
Score explanation
Over-permissive peptide validationThe verification criterion accepted additional peptide sequences beyond the target set. Protein assignment was then propagated for those extra accepted peptides, so precision—not recovery of target pairs—is the main loss.Evidence. The output recovered 139 of 139 target peptide-protein pairs but added 5; it reported 5 more distinct peptides than the target.
Workspace input inventory→Candidate and report mapping→Competing reference digest→Targeted competitive spectrum validation→Candidate and report mapping→Competing reference digest→2 more steps
All 8 recorded steps
Workspace input inventory
Candidate and report mapping
Competing reference digest
Targeted competitive spectrum validation
Candidate and report mapping
Competing reference digest
Targeted competitive spectrum validation
Final deliverable validation
Score explanation
Over-permissive peptide validationThe verification criterion accepted additional peptide sequences beyond the target set. Protein assignment was then propagated for those extra accepted peptides, so precision—not recovery of target pairs—is the main loss.Evidence. The output recovered 137 of 139 target peptide-protein pairs but added 50; it reported 46 more distinct peptides than the target.
Prepare candidates and competitors→Targeted spectrum validation→Final assignment export
All 3 recorded steps
Prepare candidates and competitors
Targeted spectrum validation
Final assignment export
Score explanation
Over-permissive peptide validationThe verification criterion accepted additional peptide sequences beyond the target set. Protein assignment was then propagated for those extra accepted peptides, so precision—not recovery of target pairs—is the main loss.Evidence. The output recovered 138 of 139 target peptide-protein pairs but added 47; it reported 44 more distinct peptides than the target.
Over-permissive peptide validationThe verification criterion accepted additional peptide sequences beyond the target set. Protein assignment was then propagated for those extra accepted peptides, so precision—not recovery of target pairs—is the main loss.Evidence. The output recovered 139 of 139 target peptide-protein pairs but added 5; it reported 5 more distinct peptides than the target.
Over-permissive peptide validationThe verification criterion accepted additional peptide sequences beyond the target set. Protein assignment was then propagated for those extra accepted peptides, so precision—not recovery of target pairs—is the main loss.Evidence. The output recovered 138 of 139 target peptide-protein pairs but added 27; it reported 26 more distinct peptides than the target.
Over-permissive peptide validationThe verification criterion accepted additional peptide sequences beyond the target set. Protein assignment was then propagated for those extra accepted peptides, so precision—not recovery of target pairs—is the main loss.Evidence. The output recovered 139 of 139 target peptide-protein pairs but added 5; it reported 5 more distinct peptides than the target.
Build the competing human UniProt plus cRAP reference→Test candidate peptides against tandem mass spectra with PepQuery→Apply peptide-spectrum validation or significance filtering→Link accepted peptides to microbial protein IDs
All 4 recorded steps
Build the competing human UniProt plus cRAP reference
Test candidate peptides against tandem mass spectra with PepQuery
Apply peptide-spectrum validation or significance filtering
Build the competing human UniProt plus cRAP reference→Test candidate peptides against tandem mass spectra with PepQuery→Apply peptide-spectrum validation or significance filtering→Link accepted peptides to microbial protein IDs
All 4 recorded steps
Build the competing human UniProt plus cRAP reference
Test candidate peptides against tandem mass spectra with PepQuery
Apply peptide-spectrum validation or significance filtering
Link accepted peptides to microbial protein IDs
Score explanation
Over-permissive peptide validationThe verification criterion accepted additional peptide sequences beyond the target set. Protein assignment was then propagated for those extra accepted peptides, so precision—not recovery of target pairs—is the main loss.Evidence. The output recovered 139 of 139 target peptide-protein pairs but added 15; it reported 15 more distinct peptides than the target.
Build the competing human UniProt plus cRAP reference→Test candidate peptides against tandem mass spectra with PepQuery→Apply peptide-spectrum validation or significance filtering→Link accepted peptides to microbial protein IDs
All 4 recorded steps
Build the competing human UniProt plus cRAP reference
Test candidate peptides against tandem mass spectra with PepQuery
Apply peptide-spectrum validation or significance filtering
Link accepted peptides to microbial protein IDs
Score explanation
Over-permissive peptide validationThe verification criterion accepted additional peptide sequences beyond the target set. Protein assignment was then propagated for those extra accepted peptides, so precision—not recovery of target pairs—is the main loss.Evidence. The output recovered 139 of 139 target peptide-protein pairs but added 5; it reported 5 more distinct peptides than the target.
Over-permissive peptide validationThe verification criterion accepted additional peptide sequences beyond the target set. Protein assignment was then propagated for those extra accepted peptides, so precision—not recovery of target pairs—is the main loss.Evidence. The output recovered 139 of 139 target peptide-protein pairs but added 5; it reported 5 more distinct peptides than the target.
Over-permissive peptide validationThe verification criterion accepted additional peptide sequences beyond the target set. Protein assignment was then propagated for those extra accepted peptides, so precision—not recovery of target pairs—is the main loss.Evidence. The output recovered 139 of 139 target peptide-protein pairs but added 5; it reported 5 more distinct peptides than the target.
Tp Head Tool ×3→Concatenate datasets→PepQuery ×4→Filter rows ×4→Select columns ×4→Concatenate datasets→4 more steps
All 25 recorded steps
Tp Head Tool
Tp Head Tool
Tp Head Tool
Concatenate datasets
PepQuery
PepQuery
PepQuery
PepQuery
Filter rows
Filter rows
Filter rows
Filter rows
Select columns
Select columns
Select columns
Select columns
Concatenate datasets
Sort1
Tp Uniq Tool
Tp Uniq Tool
Sort1
Sort1
Filter rows
Filter rows
Filter rows
Score explanation
Over-permissive peptide validationThe verification criterion accepted additional peptide sequences beyond the target set. Protein assignment was then propagated for those extra accepted peptides, so the main loss comes from extra results rather than missing target pairs.Evidence. The output recovered 138 of 139 target peptide-protein pairs and added 27, for 165 submitted pairs versus 139 in the target. Precision was 0.836364 and recall was 0.992806.
Build the competing human UniProt plus cRAP reference→Test candidate peptides against tandem mass spectra with PepQuery→Apply peptide-spectrum validation or significance filtering→Link accepted peptides to microbial protein IDs
All 4 recorded steps
Build the competing human UniProt plus cRAP reference
Test candidate peptides against tandem mass spectra with PepQuery
Apply peptide-spectrum validation or significance filtering
Link accepted peptides to microbial protein IDs
Score explanation
Over-permissive peptide validationThe verification criterion accepted additional peptide sequences beyond the target set. Protein assignment was then propagated for those extra accepted peptides, so precision—not recovery of target pairs—is the main loss.Evidence. The output recovered 139 of 139 target peptide-protein pairs but added 26; it reported 26 more distinct peptides than the target.
Build the competing human UniProt plus cRAP reference→Test candidate peptides against tandem mass spectra with PepQuery→Apply peptide-spectrum validation or significance filtering→Link accepted peptides to microbial protein IDs
All 4 recorded steps
Build the competing human UniProt plus cRAP reference
Test candidate peptides against tandem mass spectra with PepQuery
Apply peptide-spectrum validation or significance filtering
Link accepted peptides to microbial protein IDs
Score explanation
Peptide-pair substitutionThe total peptide and pair counts are correct, but a small set of accepted peptide-protein pairs was substituted. This points to peptide acceptance or protein-assignment decisions, not missing rows overall.Evidence. The output had 139 pairs and 134 peptides, matching the target totals, but 5 pairs were additional and 5 target pairs were absent.
Test candidate peptides against tandem mass spectra with PepQuery→Apply peptide-spectrum validation or significance filtering→Link accepted peptides to microbial protein IDs
All 3 recorded steps
Test candidate peptides against tandem mass spectra with PepQuery
Apply peptide-spectrum validation or significance filtering
Link accepted peptides to microbial protein IDs
Score explanation
Over-restrictive peptide validationThe verification and assignment criteria rejected too many target peptide-protein pairs while also accepting some alternatives. Recall loss is larger than the precision loss.Evidence. The output matched 109 of 139 target pairs, with 30 missing and 26 additional; it reported 129 peptides versus 134.
Concatenate datasets→Tp Head Tool→Filter rows→Converter Fasta To Tabular→Tp Head Tool→Table transformation→9 more steps
All 34 recorded steps
Concatenate datasets
Tp Head Tool
Filter rows
Converter Fasta To Tabular
Tp Head Tool
Table transformation
Tab2Fasta
Tab2Fasta
Tab2Fasta
Tp Head Tool
Tp Head Tool
Tp Head Tool
Tp Head Tool
Tp Head Tool
Tp Head Tool
Tp Head Tool
Tp Head Tool
Tp Head Tool
PepQuery2
PepQuery2
Tp Head Tool
Tp Head Tool
Tp Head Tool
Tp Head Tool
Table transformation
Table transformation
Table transformation
Table transformation
Concatenate datasets
Table transformation
Table transformation
Table transformation
Concatenate datasets
Table transformation
Score explanation
Over-permissive peptide validationThe verification criterion accepted additional peptide sequences beyond the target set. Protein assignment was then propagated for those extra accepted peptides, so precision—not recovery of target pairs—is the main loss.Evidence. The output recovered 139 of 139 target peptide-protein pairs but added 5; it reported 5 more distinct peptides than the target.
Over-permissive peptide validationThe verification criterion accepted additional peptide sequences beyond the target set and also missed several target pairs. Extra accepted pairs account for most of the score difference.Evidence. The output recovered 131 of 139 target peptide-protein pairs and added 32, for 163 submitted pairs. Precision was 0.803681 and recall was 0.942446.
Filter rows ×2→Concatenate datasets ×2→PepQuery2→Tp Head Tool→Filter rows ×2→Data retrieval→14 more steps
All 23 recorded steps
Filter rows
Filter rows
Concatenate datasets
Concatenate datasets
PepQuery2
Tp Head Tool
Filter rows
Filter rows
Data retrieval
PepQuery
Filter rows
PepQuery
Filter rows
PepQuery
Tp Head Tool
PepQuery2
Add Line To File
PepQuery2
PepQuery
Filter rows
Query Tabular
PepQuery2
Query Tabular
Score explanation
Over-permissive peptide validationThe verification criterion accepted additional peptide sequences beyond the target set. Protein assignment was then propagated for those extra accepted peptides, so precision—not recovery of target pairs—is the main loss.Evidence. The output recovered 139 of 139 target peptide-protein pairs but added 31; it reported 31 more distinct peptides than the target.
Test candidate peptides against tandem mass spectra with PepQuery→Apply peptide-spectrum validation or significance filtering→Link accepted peptides to microbial protein IDs
All 3 recorded steps
Test candidate peptides against tandem mass spectra with PepQuery
Apply peptide-spectrum validation or significance filtering
Link accepted peptides to microbial protein IDs
Score explanation
Additional peptide–protein pairsAll reference peptide–protein pairs were recovered; additional pairs reduced precision.Evidence. 139 matched pairs out of 144 submitted and 139 reference pairs.