Search engine processor: Filtering and organizing peptide spectrum matches

Carvalho, Paulo C.; Fischer, Juliana de Saldanha da Gama; Xu, Tao; Cociorva, Daniel; Balbuena, Tiago Santana; Valente, Richard H.; Perales, Jonás; Yates, John R.; Barbosa, Valmir C.

doi:10.1002/pmic.201100529

Cited by 105 publications

(98 citation statements)

References 18 publications

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“…XCorr was determinate as a primary score, and ZScore was used as a secondary one. Resultant peptides were processed and evaluated by Search Engine Processor (SEPro) v3.2.0.2 using the following filter parameters: 10 ppm deviation from theoretical peptide precursor, peptides longer than six amino acid residues, and a 1% estimated protein-level FDR (46). Label free protein quantitation was performed according to the normalized spectral abundance factor (NSAF) (47).…”

Section: Methodsmentioning

confidence: 99%

Mapping Proteoforms and Protein Complexes From King Cobra Venom Using Both Denaturing and Native Top-down Proteomics

Melani¹,

Skinner

Fornelli

et al. 2016

Molecular & Cellular Proteomics

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Characterizing whole proteins by top-down proteomics avoids a step of inference encountered in the dominant bottom-up methodology when peptides are assembled computationally into proteins for identification. The direct interrogation of whole proteins and protein complexes from the venom of Ophiophagus hannah (king cobra) provides a sharply clarified view of toxin sequence variation, transit peptide cleavage sites and post-translational modifications (PTMs) likely critical for venom lethality. A tube-gel format for electrophoresis (called GELFrEE) and solution isoelectric focusing were used for protein fractionation prior to LC-MS/MS analysis resulting in 131 protein identifications (18 more than bottom-up) and a total of 184 proteoforms characterized from 14 protein toxin families. Operating both GELFrEE and mass spectrometry to preserve non-covalent interactions generated detailed information about two of the largest venom glycoprotein complexes: the homodimeric L-amino acid oxidase (ϳ130 kDa) and the multichain toxin cobra venom factor (ϳ147 kDa). The L-amino acid oxidase complex exhibited two clusters of multiproteoform complexes corresponding to the presence of 5 or 6 N-glycans moieties, each consistent with a distribution of N-acetyl hexosamines. Employing top-down proteomics in both native and denaturing modes provides unprecedented characterization of venom proteoforms and their complexes. A precise molecular inventory of venom proteins will propel the study of snake toxin variation and the targeted development of new antivenoms or other biotherapeutics. Molecular &

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Section: Methodsmentioning

confidence: 99%

Mapping Proteoforms and Protein Complexes From King Cobra Venom Using Both Denaturing and Native Top-down Proteomics

Melani¹,

Skinner

Fornelli

et al. 2016

Molecular & Cellular Proteomics

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show abstract

“…PSM validity was assessed using the search engine processor (SEPro) [26], which is embedded in PatternLab. Briefly, identifications were grouped by charge state 8 (+2 and > +3) resulting in two distinct subgroups.…”

Section: Lc-ms/ms Acquisitionmentioning

confidence: 99%

Identification of potential targets for an anticoagulant pectin

Santana¹,

Gracher²,

Rüdiger³

et al. 2017

Journal of Proteomics

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“…PSM validity was assessed using the search engine processor (SEPro), which is embedded in PatternLab version 3.0.0.30 [37]. Briefly, identifications were grouped by charge state (+2 and ≥+3) and then by tryptic status (fully tryptic, semi-tryptic), resulting in four distinct subgroups.…”

Section: Psmmentioning

confidence: 99%