Scaffold PTM protocols

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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



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Publication for Scaffold PTM

Scaffold PTM in pipeline

PMCID: 4890981
PMID: 26885753
DOI: 10.18632/oncotarget.7380

[…] ratios were analyzed to account for potential changes in phosphorylation of proteins that were not identified in our initial proteomic analysis., consensus motif analysis was performed using scaffold ptm (version 2.1.3) to determine overrepresented kinase motifs surrounding phosphorylation sites, using the method developed by gygi and schwartz [], as well as potential enzyme recognition […]

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Scaffold PTM in publications

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 […]

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 […]

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 […]

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 […]

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 […]

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

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