Paths ../tandem/taxonomy.xml /usr/local/tandem/method.xml Spectrum general 0.4 Da The value for this parameter may be 'Daltons' or 'ppm': all other values are ignored 100 100 ppm yes Spectrum conditioning 100.0 50 yes yes 15.0 466.0 500.0 150.0 15 1 Residue modification 57@C 16@M Protein general human [RK]|{P} +17.00305 +1.00794 0.0 0.0 Scoring 4 1 yes yes model refinement paramters yes yes 0.1 +42.0@[ yes 16@M,1@N,1@Q no no Output output.xml protein values = protein|spectrum (spectrum is the default) no values = yes|no tandem-style.xsl yes values = yes|no yes values = yes|no yes values = yes|no yes values = yes|no yes values = yes|no yes values = yes|no valid values = all|valid|stochastic 0.1 value is used in the valid|stochastic setting of output, results 30 values any integer greater than 0. Setting this to '1' makes cutting and pasting histograms into spread sheet programs easier.