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Scaffold PTM specifications


Unique identifier OMICS_25016
Name Scaffold PTM
Software type Application/Script
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS, Windows
Programming languages Shell (Bash)
Computer skills Advanced
Version 3.1
Stability Stable
Free trial Yes
Maintained Yes




No version available



  • person_outline Scaffold Q+ Team

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Publication for Scaffold PTM

Scaffold PTM citations


Mercury alters endogenous phosphorylation profiles of SYK in murine B cells

BMC Immunol
PMCID: 5514489
PMID: 28716125
DOI: 10.1186/s12865-017-0221-0

[…] was utilized for the anti-syk immunoprecipitation experiments, except with a 0.6 da fragment tolerance. phosphorylation localization probabilities were scored with the ascore algorithm using scaffold ptm software (proteome software, ver 3.0). site localization was confirmed above a 95% probability threshold., for each sample, the area of the gel lane where syk was pre-determined […]


Phosphoproteome Analysis Reveals Phosphorylation Underpinnings in the Brains of Nurse and Forager Honeybees (Apis mellifera)

Sci Rep
PMCID: 5434016
PMID: 28512345
DOI: 10.1038/s41598-017-02192-3

[…] controlled at both the protein and peptide levels using a fusion-decoy database search strategy at a threshold ≤1.0%, an enhanced target-decoy approach that makes more conservative fdr estimations. scaffold ptm (version 2.1.3, proteome software, oregon, usa) was used to assign the phosphosites by localization probability via ascores algorithm. all ms/ms of phosphopeptides queries with an ascore […]


Phosphorylation induces sequence specific conformational switches in the RNA polymerase II C terminal domain

Nat Commun
PMCID: 5437310
PMID: 28497798
DOI: 10.1038/ncomms15233

[…] set to remove precursor peak, charge-reduced precursor peaks and peaks due to the neutral loss from charge-reduced precursors prior to the sequest search. resulting search files were exported into scaffold ptm (proteome software) where phospho-site probabilities were determined using the ascore algorithm., for nmr experiments, expression of ctd2′ was performed in m9 minimal media enriched […]


Comparative Proteomics Reveals that Phosphorylation of β Carbonic Anhydrase 1 Might be Important for Adaptation to Drought Stress in Brassica napus

Sci Rep
PMCID: 5155245
PMID: 27966654
DOI: 10.1038/srep39024

[…] usa) to validate ms/ms peptides and protein identifications. identifications were accepted if they had a greater than 95% peptide probability and contained at least one identifiable phosphopeptides. scaffold ptm (version 2.2) was used to annotate phosphorylation site located in ms/ms spectra. ascore was used to assess phosphorylation site probability. only the phosphopeptides with ascore […]


Mapping N linked glycosylation of carbohydrate active enzymes in the secretome of Aspergillus nidulans grown on lignocellulose

Biotechnol Biofuels
PMCID: 4977673
PMID: 27508003
DOI: 10.1186/s13068-016-0580-4

[…] predicted n-glyc sites in anid_02828 were validated, n225 and n365, but the peptide glycosylated at n340 was not covered.table 1, we performed an additional validation of the n-glyc sites using the scaffold ptm software with default statistical parameters pre-established by the program, based on the presence and intensity of site-specific ions compared randomly []. from the 182 sites previously […]


Relative quantification of phosphoproteomic changes in grapevine (Vitis vinifera L.) leaves in response to abscisic acid

PMCID: 4916266
PMID: 27366326
DOI: 10.1038/hortres.2016.29

[…] from the average values. finally, an unpaired t-test was assessed to test the significance of the abundance difference (p<0.0.5)., in order to identify potential enzyme recognition sites, scaffold ptm scans the data set for over-represented patterns in the amino acids surrounding modification sites. it uses the iterative statistical method described in a previous publication. sequence […]

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Scaffold PTM institution(s)
Proteome Software, Inc., Portland, OR, USA

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