Assuming you are working with T
(cell array) as listed in your code, you may use this code to detect the successful matches -
%%// Slightly different than yours
T={'A2P3';'NotA2P3';'A2P3';'A2P3 with (extra1)';'A2P3 with (extra1) and (extra 2)';'A2P3 with (extra1)';'B2P3';'B2P3';'NotA2P3';'B2P3 with (extra 1)';'A2P3'};
a={1 1 0 1 1 0 1 1 0 1 1 }
T(:,2)=num2cell(1);
T(3,2)=num2cell(0);
T(6,2)=num2cell(0);
T(9,2)=num2cell(0);
%%// Get the comparison results
col1_comps = ismember(char(T(:,1)),'A2P3') | ismember(char(T(:,1)),'B2P3');
comparisons = ismember(col1_comps(:,1:4),[1 1 1 1],'rows').*cell2mat(T(:,2))