Scaffold 2

Raw files were used to generate Mascot Generic Files (MGF) through extract_msn on Mascot Daemon (version 2.2.2). Once generated, MGFs were searched with X!Tandem (Global Proteome Machine Manager; version 2006.06.01) to confer peptide identifications. Searches were conducted against the non-redundant Human IPI database (v.3.71) which contains a total of 173,490 forward and randomized protein sequences and using the following parameters for GPM: no enzyme ([X]|[X]) cleavages, 50 missed cleavage sites allowed, 7 ppm precursor ion mass tolerance, 0.4 Da fragment ion mass tolerance, fixed modifications of carbamidomethylation of cysteines, and variable modification of oxidation of methionines (oxM) and/or prolines (oxP). The X!Tandem (XML files) were then integrated through the Scaffold 2 software (version 2.06; Proteome Software Inc., Portland, Oregon). False-discovery rates (FDR) were calculated as the number of peptides identified by the randomized reverse database divided by the total number of identified peptides. To achieve a peptide FDR of 1%, X!Tandem –Log(ExpectScores) peptide scores of 2.2 or greater were accepted.

Raw files were used to generate Mascot Generic Files (MGF) through extract_msn on Mascot Daemon (version 2.2.2). Once generated, MGFs were searched with X!Tandem (Global Proteome Machine Manager; version 2006.06.01) to confer peptide identifications. Searches were conducted against the non-redundant Human IPI database (v.3.71) which contains a total of 173,490 forward and randomized protein sequences and using the following parameters for GPM: no enzyme ([X]|[X]) cleavages, 50 missed cleavage sites allowed, 7 ppm precursor ion mass tolerance, 0.4 Da fragment ion mass tolerance, fixed modifications of carbamidomethylation of cysteines, and variable modification of oxidation of methionines (oxM). The X!Tandem (XML files) were then integrated through the Scaffold 2 software (version 2.06; Proteome Software Inc., Portland, Oregon). False-discovery rates were calculated as the number of peptides identified by the randomized reverse database divided by the total number of identified peptides.

Quantitative proteomic data (Marsolais et al., 2010 (link)) were re-analyzed using Scaffold 2 software (Proteome Software Inc., Portland, OR, USA) against the UniProt database, section Viridiplantae (as of March 31, 2009).