Scaffold Q+S protocols

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Scaffold Q+S specifications


Unique identifier OMICS_25015
Name Scaffold Q+S
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 4.0
Stability Stable
Maintained Yes



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Additional information

Scaffold Q+S in pipeline

PMCID: 4507021
PMID: 26149123
DOI: 10.1038/ncomms8285

[…] (c) and variable modifications set as oxidation (m) and phosphorylation (s/t/y). a decoy database search was performed., the output from proteome discoverer was further processed using scaffold q+s (version 4.0.5, proteome software). upon import, the data were searched using x!tandem (the global proteome machine organization). peptideprophet and proteinprophet (institute […]

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Scaffold Q+S in publications

PMCID: 5770571
PMID: 29375497
DOI: 10.3389/fmicb.2017.02586

[…] with common laboratory contaminants (downloaded from, crap project) using the mascot searching algorithm, v2.4 ( the mascot output was then analyzed using scaffold q+s, v4.3.0 ( to probabilistically validate protein identifications. assignments validated in scaffold with <1% false discovery rate were considered true. […]

PMCID: 5674068
PMID: 29109428
DOI: 10.1038/s41598-017-15132-y

[…] separately by a reverse phase c18 column coupled to a high resolution qexactive hf orbitrap mass spectrometer in positive mode via dda. the peptides and proteins were identified by mascot and scaffold q+s software using the uniprot mouse protein database., the lipidomics platform can identify and quantify lipids from 18 main lipid classes and 66 sub classes including fatty acids, […]

PMCID: 5535997
PMID: 28704956
DOI: 10.3390/ijms18071507

[…] data acquisition mode. peptides were identified using sequest algorithms, attributed to a species-specific national center for biotechnology information (ncbi) database and correlated to proteins by scaffold q+s (proteome software, portland, or, usa) using a minimum of two peptides (peptide threshold of 95% and protein threshold of 99%)., s. aureus cells were grown to saturation, titrated […]

PMCID: 5853832
DOI: 10.5334/1750-2187-12-3

[…] resolution over the m/z range 350–1250 da in positive ion mode (thermo scientific). mass spectrometry data were analysed using proteome discoverer (thermo scientific), mascot2 (matrix science ltd.), scaffold q+s4 (proteome software) and the uniprotkb-swissprot3 database., to determine if the cellular stresses associated with ischaemia-reperfusion injury affected the level of ms1 expression […]

PMCID: 5015102
PMID: 27605433
DOI: 10.1038/srep32643

[…] based on q-values at a 1% false discovery rate (fdr). with proteome discoverer, peptide identifications were grouped into proteins according to the law of parsimony and filtered to 1% fdr. scaffold q+s (v4.5.3, proteome software inc) was employed to validate ms/ms-based peptide and protein identifications from database searching. initial peptide identifications were accepted […]

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