#1st version Count the spectra for each phospho peptide, for both conditions. Put the counts in different columns, for all phospho peptides of each condition (not only the common ones). Replicates Separate search 2 soft replicates search 2 stiff replicates search Add prot accno + desc at counts file #2nd version added 3 more replicates for soft and 3 for stiff 1 search per condition count the peptide spectra identified in each experiment in both conditions that is: in B1 experiment count soft and stiff and in B2 experiment count soft and stiff calculate ratios between conditions but in the same experiment, averages between experiments, correlation per condition between the experiments #3rd version: we want to see if there is reproducibility between the experiments under the same condition add filters and keep the peptides that have counts >2 (arbitrarily chosen) between experiments but same condition with the same count-difference direction and count dif>=2 or ratio >=2 or ratio >=1.5 also with modified ratios: with reversed ratio for the negative direction #4th version: GO analysis run the lists through enrichr filter the GO results according to defined terms of interest, and group the terms to categories #5th version find the phosphorylated residues for specific peptides of interest in all 4 conditions, for count dif>=2 and modified_ratio >=1.5 added the mascot info for these peptides for the highest peptide for each condition, pick the transitions and plot the spectrum #6th version repeat for the old glass experiment (mascot_significant_peps_mouse_phospho), for comparison: find the phosphorylated residues for specific peptides of interest in all 4 conditions, for count dif>=2 and modified_ratio >=1.5 added the mascot info for these peptides for the highest peptide for each condition, pick the transitions and plot the spectrum #Pfind started the parser for pfind format