ProteoWizard

[…] data file was first analyzed using the mascot distiller software (version 2.4.3.2, matrix science, london, united kingdom) and the resulting mgf files were converted into the mzml file format using msconvert (). the saprolegnia protein database (20,088 entries) was then searched using several search engines in parallel, i.e., ms-gf+ () v1.0 (v8299), myrimatch () (version 2.1.120), comet () […]

[…] events of the top 10 most intense +2 or +3 ions from the ms1 spectrum over an acquisition time of 140 minutes., the raw files obtained from lc-ms/ms were converted to mzxml format using msconvert from the proteowizard software. the resulting mzxml files were used to identify proteins by searching against human uniprotkb database on the labkey server using x!tandem algorithm–. search […]

[…] waltham, ma) as previously described (). each cross-linked sample was run four times and the data were combined before analysis (technical replicate). mass spectra were converted into mzml using msconvert from proteowizard (). standard linear peptide searches were performed using comet to identify all proteins in the sample (). cross-linked peptides were identified using the kojak version […]

[…] raw-files) were directly imported into progenesis qi (nonlinear dynamics, newcastle upon tyne, uk) for peak picking and run alignment. in addition, raw data was converted into mzxml-format using proteowizard (chambers et al. ) for processing with the ‚xcms’-package for r (https://masspec.scripps.edu/xcms/download.php) according to previously published protocols (patti et al. ; tautenhahn et […]

[…] as described in moruz et al. []. we will refer to this set as the “hm_yeast” set., converting the raw files to two separate files in the ms1 and ms2 formats [], respectively, was done with proteowizard [] with vendor peak picking for the ms2 spectra and all other options left at their default values. next, we assigned high-resolution precursor masses and charges using information […]

[…] with mass hunter (version b.05.01, agilent technologies, usa) and analyst tf (version 1.7.1, ab sciex, usa) qualitative analysis software. ms raw data files were converted to the mzxml format using proteowizard and processed by the r package xcms (version 1.41.0), which can perform peak finding, filtering, alignment, and scaling. the r package camera was used for peak annotation after xcms data […]

[…] events of the top 10 most intense +2 or +3 ions from the ms1 spectrum over an acquisition time of 140 minutes., the raw files obtained from lc-ms/ms were converted to mzxml format using msconvert from the proteowizard software. the resulting mzxml files were used to identify proteins by searching against human uniprotkb database on the labkey server using x!tandem algorithm–. search […]

[…] with a smartbeam-ii laser (355 nm). detailed instrument settings are available in si appendix., in brief, maldi-tof ms raw data were first converted to the open-source mzml format () by using proteowizard’s command-line msconvert (). the mzml files were read into r through mzr () and custom code and processed into peak lists by using maldiquant (). lastly, the peak lists informed […]

[…] repeated fragmentation. ions clustering for more than once within 25 s were excluded from the selection. mass spectrum raw files were converted to a peak list format (mgf) by ms convert software (proteowizard), and data processing was performed using mascot version 2.2 (matrix science) against the t. cruzi database downloaded from uniprot, with the following parameters: ms1 mass tolerance […]

[…] ms/ms were excluded from further fragmentation for the next 60 seconds., proteins from the lcm-derived samples were assigned by exporting features, for which ms/ms spectra were recorded, using the proteowizard software (version 3.0.9248; http://proteowizard.sourceforge.net). resulting .mgf files were submitted to mascot (version 2.3.01, matrix science, london, uk) and applied to the human […]