ACR MLG INTERSECTION TKOF AT BOS. PROC NOT APPROVED BY COMPANY.

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CAPT MISTAKENLY TAXIED ONTO RWY 9 AT KBOS FROM TXWY XRAY (APPROX 500' FROM THRESHOLD) INSTEAD OF FROM TXWY S1 AT THRESHOLD. TWR ASKED IF WE WERE OK TO GO FROM THAT POINT; AND BELIEVING AN INTXN DEP WAS COMPANY APPROVED AND CONSIDERING OUR WT WAS WELL BELOW MAX FOR THE RWY (91200' VS 106600) WE ACCEPTED A TKOF CLRNC FROM THAT POINT. AFTER LEVEL OFF AT CRUISE WE CHKED THE ARPT ANALYSIS BOOK AND FOUND AN INTXN DEP FOR RWY 15R BUT NOT RWY 9 AS WE HAD THOUGHT. CONTRIBUTING TO THE EVENT WAS A LACK OF CLR TXWY AND RWY SIGNS WHICH LED TO THE USE OF THE WRONG TXWY ADJACENT TO THE CORRECT ONE. ALSO; ONCE THE ERROR HAD BEEN DISCOVERED COULD HAVE BACK-TAXIED TO THE THRESHOLD OR HELD IN POS WHILE CHKING FOR INTXN RWY ANALYSIS. WHILE CHKING FOR INTXN ANALYSIS FOUND A NOTE AT THE BOTTOM OF THE RWY 9 VFR TKOF PROC. THAT NOTE STATES THAT THE PLT MUST CONFIRM VISUALLY THAT NO SHIPS ARE TRAVERSING THE CHANNEL AND ALSO CONFIRM WITH THE TWR THAT NONE ARE TRAVERSING. WE DID CONFIRM VISUALLY BUT WERE NOT AWARE THAT THE TWR MUST ALSO BE ASKED. THIS NOTE IS NOT PROVIDED TO THE PLTS ANYWHERE EXCEPT THE ARPT ANALYSIS BOOK; WHICH IS NOT REQUIRED UNLESS OPS DOES NOT PROVIDE A TKOF WTS (TOW) MESSAGE. BELIEVE THAT SPECIAL PROCS SUCH AS THESE SHOULD BE INCLUDED IN ARPT NOTES (WITH WX) TOW MESSAGE AND WT AND BALANCE; TO INFORM THE PLTS AND INSURE COMPLIANCE.