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Phosphorylation site assignment software tools| MS-based untargeted proteomics

Phosphorylation site assignment of high throughput tandem mass spectrometry (LC-MS/MS) data is one of the most common and critical aspects of phosphoproteomics. Correctly assigning phosphorylated residues helps us understand their biological…
Ascore
Desktop

Ascore

Search algorithms like Sequest or Mascot often successfully identify the proper…

Search algorithms like Sequest or Mascot often successfully identify the proper peptide sequence, but fail to provide information about the presence or absence of site-determining ions. As a result,…

phosphoGigolo
Desktop

phosphoGigolo

Facilitates the assessment, validation and exploration of identified…

Facilitates the assessment, validation and exploration of identified phosphorylation sites from the acquired MS2 /MS3 level data. phosphoGigolo sorts all peptide identifications by user-defined…

PhosphoScan
Desktop

PhosphoScan

A probability-based method to unambiguously determine phosphorylation sites…

A probability-based method to unambiguously determine phosphorylation sites within phosphopeptides using MS2/3 pair information. A comparison test was performed with SEQUEST and MASCOT predictions…

PhosphoScore
Desktop

PhosphoScore

A phosphorylation assignment program that is compatible with all levels of…

A phosphorylation assignment program that is compatible with all levels of tandem mass spectrometry spectra (MSn) generated through the Bioworks/Sequest platform. The program utilizes a “cost…

ptmRS
Desktop

ptmRS

Enables automated and confident localization of modification sites within…

Enables automated and confident localization of modification sites within validated peptide sequences. ptmRS calculates individual probability values for each putatively modified site based on the…

SLoMo
Desktop

SLoMo Site Localization of Modifications

A tool which enables researchers to localise sites of post-translational…

A tool which enables researchers to localise sites of post-translational modifications to peptides identified in mass spectrometry experiments. SLoMo caters for both high and low resolution data and…

D-score
Algorithm

D-score

A generic approach for secondary hit scoring by multiple algorithms: first, we…

A generic approach for secondary hit scoring by multiple algorithms: first, we translate search engine scores of first and secondary hits in a data set derived from a multisearch engine analysis into…

PhosSA
Desktop

PhosSA

A program for phosphorylation site assignment of LC-MS/MS data. It uses a…

A program for phosphorylation site assignment of LC-MS/MS data. It uses a linear-time and linear space dynamic programming strategy for phosphorylation site assignment. The algorithm optimizes the…

Turbo SLoMo
Desktop

Turbo SLoMo

A software tool which can localise and score sites of protein modification in…

A software tool which can localise and score sites of protein modification in mass spectrometry data. Turbo SLoMo has been created to allow high throughput modification site localisation using the…

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