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<!--         I M P O R T A N T

  If you edit this file then please add an entry to
  the "changed" section below.

-->

<!--

       Changed: 2008-xx-xx XX

       Changed: 2008-06-26 JAB+PM    Added HexNAc (ST), HexNAc(N) and HexHexNAc (NST).

       Changed: 2008-06-23 PM        Added modification exclusivity defaults to all 
                                     modifications - as MSQuant would do if it creates 
                                     this file with default content.

       Changed: 2008-06-20 PM        Added exclusive peptide position definitions to all 5
                                     phosphorylation modifications:
                                         ID 5050  v.2.1              IntactPhospho(STY)
                                         ID 5051  v.2.1              phospho(STY)
                                         ID 5048  v.2.1  -and 2.2??  Phospho (ST)
                                         ID 5049  v.2.1  -and 2.2??  Phospho (Y)
                                         ID 5547  v.2.2              PhosphoIntact(STY)

       Changed: 2008-06-18 PM        Added v. 2.1 or v. 2.2 tag (comment) for all modifications.

                                     Question: are some modifications common for 2.1 and 2.2?

                                     E.g. "Phospho (ST)" / 5048 seems to be used by both.


       Changed: 2008-06-18 PM        v. 2.1 and v. 2.2 comment for the two
                                     intact phospho modifications.

                                     Added begin and end section markers
                                     for Mascot 2.1 modifications and
                                     Mascot 2.2 modifications.

       Changed: 2008-05-26 PM        Added quantmode Lys8 for v2.2.
                                     Explicit deuterium for Lys4.

       Changed: 2007-10-25 PM        Explicit start/end position for all modifications.
                                     Explicit presence of the field "GUIdoShow" - to display
                                     or hide a quantitation mode in/from the list in the options
                                     dialog.

       Changed: 2007-09-20 JA        Added quantmode Lys4 + Lys8 for v2.2

       Changed: 2007-09-18 PM        Comment formatting, indenting and white-space
                                     fixup. Comment added for each terminal specification.

       Changed: 2007-09-13 JAB       Changed HysTag masses to consistent massbase difference

       Changed: 2007-09-11 JAB       Added n-terminal specifications for all terminal modifications.
                                     Added MRKWP to allowed N-terminal modified amino acids for acetylation

       Changed: 2007-08-22 PM        Trivial changes:
                                       1. Consistent use of new XML format (as
                                          support of the old format will go
                                          away some day); mass differences.
                                          For modification IDs 5063, 5064, 5068,
                                          5069, 5546, 5552, and 5553.

                                       2. Explicit prefix and postfix strings for
                                          all (set to the same as MSQuant would
                                          display: "***").
                                          Samples: ID 5068, 5069, 5546 had a
                                                   prefix string, but no
                                                   postfix string...

       Changed: 2007-08-10 PM        Now reverse chronological order in
                                     this "changed" section. Some reformatting
                                     in comments. White-space fixup.

       Changed: 2007-08-10 JAB       Added quantmode Arg6 + Lys6 for v2.2

       Changed: 2007-08-10 JAB       Added version numbers to all quantiation
                                     modes. Prepared for official release.

       Changed: 2007-07-30 PM        Made GUInameIndex unique for quant
                                     mode "v2.2 Arg13C6 and Lys4D". Was shared
                                     with "v2.2 Arg13C6 and Lys13C615N2".

       Changed: 2007-07-05 JAB       Removed Capital letters in modifications.

       Changed: 2007-06-29 JAB       Included Deamidated (NQ) and Acetyl (Protein N-term)

       Changed: 2007-06-29 JAB       Included new definitions for Quant Arg6+K4 v2.2

       Changed: 2007-06-15 JAB       Included new definitions for ICAT C9 for v2.2

       Changed: 2007-05-14 JAB       Changed formatted string of oxidized Methionine

       Changed: 2007-05-11 JAB       Removed hyphenations in short names, added
                                     Phospho_Intact (STY), Acetyl(K) and Dioxidation(MW)

       Changed: 2007-05-03 JAB       Included quantmode Lys8 and Arg6 for v2.2

       Changed: 2007-05-01 PM        Comment formatting, indenting and white-space
                                     fixup.

       Changed: 2007-05-01 JAB       Introduced novel modification names from Mascot
                                     v2.2: ammonia-loss (C), Oxidation (P),
                                     Gln->pyroGLu (Q), Glu->pyroGlu (E) and ????

       Changed: 2007-04-11 JAB/PM    Cloned double triple-encoding labelling RK
                                     quantitation mode, made new names for default
                                     Mascot v2.2 modifications.

       Changed: 2007-04-04 JAB/PM    Changed to explicit definition of
                                     baseModification field to 0 for most
                                     quantiationmodes, except hystag and ICAT.

       Changed: 2007-03-19 PM        XML error - defined ICAT quant-mode outside
                                     of quantitation modes list.

       Changed: 2007-03-15 PM        White-space corrections in and outside comments.

       Changed: 2007-03-12 JAB/PM    Changed short-prefix for 3 out of 4 phospho-
                                     definitions.
                                     Changed string for intact phospho to ipSTY.

       Changed: 2007-03-07 JAB/KR/PM Corrected match-string for PyroQC & PyroE.

       Changed: 2007-03-06 JAB       Added Quantmode ICAT9. Added modifications
                                     ICAT_9C12 and ICAT_C13.

                                     Added peptide N-term modifications
                                     PyroQC, N-acetyl, PyroE.

                                     Added modification Ubi and hydroxyproline.

       Changed: 2006-12-14 PM        Added modification "N-Acetyl (Protein)". It is a
                                     work-around for a terminal modification - PTM
                                     scoring MUST be applied in order to get the
                                     correct masses.

                                     Added modification "Deamidation (NQ)".

                                     Enabled modification "phospho(STY)".

       Changed: 2006-09-12 PM        Defined prefix for the (hidden)
                                     modification "phospho(STY)", ID 5051.

                                     Defined prefix for the modification "Oxidation (M)":
                                       ox

       Changed: 2006-09-04 PM        Quantitation mode "LysD4 and Arg13C6", ID 7012
                                     was defined as a strange triple encoding mode.
                                     It is now the proper double encoding mode.

       Changed: 2006-09-01 CMF       Deleted extra tag causing XML syntax error

       Changed: 2006-08-01 PM        Now contains new fields (shortPrefix and
                                     shortPostfix) and the new way of specifying
                                     masses.

       Changed: 2005-11-22 PM        Prepared adding the phospho(STY) modification.
                                     It is not activated yet.

       Changed: 2005-08-10 PM        Multiple amino acids are now in field "AA" for
                                     the two phosphorylation modifications
                                     "Phospho (ST)"/ID5048 and
                                     "IntactPhospho(STY)"/ID5050. Y is in the first
                                     position for ID5050 for compatibility reasons;
                                     older versions of MSQuant with this file.

       Changed: 2005-08-08 PM        The effective content for Arginine of
                                     mode "Arg13C6 and Lys13C615N2" (ID 7101) and
                                     mode "Arg10 and Lys8"          (ID 7105) was
                                     swopped. This has been corrected.

                                     For mode "Arg10 and Lys8" (ID 7105): the label
                                     for the 2nd SILAC disc is no longer confusing.

       Changed: 2005-08-04 PM        Mode "Arg13C6 and Lys13C615N2" now really
                                     works. Truely.

       Changed: 2005-08-02 PM        Corrected mode "Arg13C6 and Lys13C615N2",
                                     ID 7101 alias "Arg6 and Lys8" -
                                     was incorrectly translated from the old
                                     standard file.
                                     Typo corrected: Arg13C65N4C10 -> Arg13C615N4.

       Changed: 2005-07-01 PM        Added HysTag mode.
                                     Changed order of modes, including GUI order.

       Changed: 2005-06-03 PM        Initial version...
-->

<QuantitationDefs>

	<!-- **************************************************************** -->
	<!-- List of quantitation modes -->

	<quantitationModes>

		<quantMode>
			<GUIname>No isotope</GUIname>
			<uniqueID>8200</uniqueID>
			<GUInameIndex>0</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
			</dishes_StartingFromDish2>
		</quantMode>

		<quantMode>
			<GUIname>v2.1 Arg13C6</GUIname>
			<uniqueID>8001</uniqueID>
			<GUInameIndex>1</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>simple double encoding</name>
					<modificationsForSILAC>
						<modification>5030</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<quantMode>
			<GUIname>v2.1 Arg13C6 and Arg13C615N4</GUIname>
			<uniqueID>8002</uniqueID>
			<GUInameIndex>2</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>Arg6</name>
					<modificationsForSILAC>
						<modification>5030</modification>
					</modificationsForSILAC>
				</SILACdish>
				<SILACdish>
					<name>higher isotope</name>
					<modificationsForSILAC>
						<modification>5031</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<quantMode>
			<GUIname>v2.1 Arg13C6 and Lys13C6</GUIname>
			<uniqueID>7006</uniqueID>
			<GUInameIndex>3</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>Arg6 and Lys6</name>
					<modificationsForSILAC>
						<modification>5030</modification>
						<modification>5040</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<quantMode>
			<GUIname>v2.1 Arg13C6 and Lys13C615N2</GUIname>
			<uniqueID>7101</uniqueID>
			<GUInameIndex>4</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>Arg6 and Lys8</name>
					<modificationsForSILAC>
						<modification>5030</modification>
						<modification>5042</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<!-- 2005-08-02. Note: systematic name: Arg13C615N4 and Lys13C615N2 -->
		<quantMode>
			<GUIname>v2.1 Arg10 and Lys8</GUIname>
			<uniqueID>7105</uniqueID>
			<GUInameIndex>5</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>Arg10 and Lys8</name>
					<modificationsForSILAC>
						<modification>5031</modification>
						<modification>5042</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<quantMode>
			<GUIname>v2.1 LeuD3</GUIname>
			<uniqueID>7099</uniqueID>
			<GUInameIndex>6</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>simple double encoding</name>
					<modificationsForSILAC>
						<modification>5044</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<quantMode>
			<GUIname>v2.1 LysD4 and Lys13C615N2</GUIname>
			<uniqueID>7004</uniqueID>
			<GUInameIndex>7</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>Lys4 - deuterium</name>
					<modificationsForSILAC>
						<modification>5041</modification>
					</modificationsForSILAC>
				</SILACdish>
				<SILACdish>
					<name>Lys8</name>
					<modificationsForSILAC>
						<modification>5042</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<!--  Corrected by PM, 2006-09-04   -->
		<quantMode>
			<GUIname>v2.1 LysD4 and Arg13C6</GUIname>
			<uniqueID>7012</uniqueID>
			<GUInameIndex>8</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>Lys4D and Arg6</name>
					<modificationsForSILAC>
						<modification>5041</modification>
						<modification>5030</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<quantMode>
			<GUIname>v2.1 LysD4</GUIname>
			<uniqueID>7010</uniqueID>
			<GUInameIndex>9</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>simple double encoding</name>
					<modificationsForSILAC>
						<modification>5041</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<quantMode>
			<GUIname>v2.1 Lys13C615N2</GUIname>
			<uniqueID>7011</uniqueID>
			<GUInameIndex>10</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>simple double encoding</name>
					<modificationsForSILAC>
						<modification>5042</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<quantMode>
			<GUIname>v2.1 Lys13C6</GUIname>
			<uniqueID>8003</uniqueID>
			<GUInameIndex>11</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>simple double encoding</name>
					<modificationsForSILAC>
						<modification>5040</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<quantMode>
			<GUIname>v2.1 HysTag</GUIname>
			<uniqueID>8007</uniqueID>
			<GUInameIndex>12</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>1</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>HysTag/ICAT like encoding, lower mass tag</name>
					<modificationsForSILAC>
						<modification>5046</modification>
					</modificationsForSILAC>
				</SILACdish>
				<SILACdish>
					<name>HysTag/ICAT like encoding, higher mass tag</name>
					<modificationsForSILAC>
						<modification>5047</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<quantMode>
			<GUIname>v2.1 RK double triple</GUIname>
			<uniqueID>7001</uniqueID>
			<GUInameIndex>13</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>middle isotope</name>
					<modificationsForSILAC>
						<modification>5041</modification>
						<modification>5030</modification>
					</modificationsForSILAC>
				</SILACdish>
				<SILACdish>
					<name>higher isotope</name>
					<modificationsForSILAC>
						<modification>5042</modification>
						<modification>5031</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<quantMode>
			<GUIname>v2.1 R6K8 vs R10K4</GUIname>
			<uniqueID>7002</uniqueID>
			<GUInameIndex>14</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>middle isotope</name>
					<modificationsForSILAC>
						<modification>5030</modification>
						<modification>5042</modification>
					</modificationsForSILAC>
				</SILACdish>
				<SILACdish>
					<name>higher isotope</name>
					<modificationsForSILAC>
						<modification>5031</modification>
						<modification>5041</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<quantMode>
			<GUIname>v2.1 R6K8 vs R10</GUIname>
			<uniqueID>7003</uniqueID>
			<GUInameIndex>15</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>middle isotope</name>
					<modificationsForSILAC>
						<modification>5030</modification>
						<modification>5042</modification>
					</modificationsForSILAC>
				</SILACdish>
				<SILACdish>
					<name>higher isotope</name>
					<modificationsForSILAC>
						<modification>5031</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<!-- PM 2006-08-01 -->
		<quantMode>
			<GUIname>v2.1 N15 labeling</GUIname>
			<uniqueID>7201</uniqueID>
			<GUInameIndex>16</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>simple double encoding</name>
					<modificationsForSILAC>
						<modification>5101</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<!-- JAB 2007-03-06 -->
		<quantMode>
			<GUIname>v2.1 ICAT_9C</GUIname>
			<uniqueID>7005</uniqueID>
			<GUInameIndex>17</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>1</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>ICAT encoding, lower mass tag</name>
					<modificationsForSILAC>
						<modification>5063</modification>
					</modificationsForSILAC>
				</SILACdish>
				<SILACdish>
					<name>ICAT encoding, higher mass tag</name>
					<modificationsForSILAC>
						<modification>5064</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<!-- JAB 2007-04-11 -->
		<!-- *************** M A S C O T    2 . 2     D E F A U L T S  ************************* -->
		<quantMode>
			<GUIname>v2.2 RK double triple</GUIname>
			<uniqueID>9001</uniqueID>
			<GUInameIndex>20</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>middle isotope</name>
					<modificationsForSILAC>
						<modification>5541</modification>
						<modification>5530</modification>
					</modificationsForSILAC>
				</SILACdish>
				<SILACdish>
					<name>higher isotope</name>
					<modificationsForSILAC>
						<modification>5542</modification>
						<modification>5531</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>


		<!-- JAB 2007-05-03 -->
		<quantMode>
			<GUIname>v2.2 Arg13C6 and Lys13C615N2</GUIname>
			<uniqueID>9002</uniqueID>
			<GUInameIndex>21</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>Arg6 and Lys8</name>
					<modificationsForSILAC>
						<modification>5530</modification>
						<modification>5542</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<!-- JAB 2007-06-15 -->
		<quantMode>
			<GUIname>v2.2 ICAT_9C</GUIname>
			<uniqueID>9003</uniqueID>
			<GUInameIndex>22</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>1</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>ICAT encoding, lower mass tag</name>
					<modificationsForSILAC>
						<modification>5552</modification>
					</modificationsForSILAC>
				</SILACdish>
				<SILACdish>
					<name>ICAT encoding, higher mass tag</name>
					<modificationsForSILAC>
						<modification>5553</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

			<!-- JAB 2007-06-29 -->
		<quantMode>
			<GUIname>v2.2 Arg13C6 and Lys4D</GUIname>
			<uniqueID>9004</uniqueID>
			<GUInameIndex>23</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>Arg6 and Lys4D</name>
					<modificationsForSILAC>
						<modification>5530</modification>
						<modification>5541</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<!-- JAB 2007-08-10 -->
		<quantMode>
			<GUIname>v2.2 Arg13C6 and Lys13C6</GUIname>
			<uniqueID>9005</uniqueID>
			<GUInameIndex>24</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>Arg6 and Lys6</name>
					<modificationsForSILAC>
						<modification>5530</modification>
						<modification>5540</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<!-- JA 2007-09-20 -->
		<quantMode>
			<GUIname>v2.2 LysD4 and Lys13C615N2</GUIname>
			<uniqueID>9006</uniqueID>
			<GUInameIndex>25</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>Lys4 - deuterium</name>
					<modificationsForSILAC>
						<modification>5541</modification>
					</modificationsForSILAC>
				</SILACdish>
				<SILACdish>
					<name>Lys8</name>
					<modificationsForSILAC>
						<modification>5542</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>

		<!-- PM 2008-05-26 -->
		<quantMode>
			<GUIname>v2.2 Lys13C615N2</GUIname>
			<uniqueID>9007</uniqueID>
			<GUInameIndex>26</GUInameIndex>
			<GUIdoShow>True</GUIdoShow>
			<baseModification>0</baseModification>
			<dishes_StartingFromDish2>
				<SILACdish>
					<name>Lys8</name>
					<modificationsForSILAC>
						<modification>5542</modification>
					</modificationsForSILAC>
				</SILACdish>
			</dishes_StartingFromDish2>
		</quantMode>


	</quantitationModes>


	<!-- **************************************************************** -->
	<!-- List of modifications that MSQuant recognises -->

	<modifications>

		<!-- *****  M O D I F I C A T I O N S,  M A S C O T    2 . 1   O R   E A R L I E R    D E F A U L T S ,  *****
		              B E G I N

		-->

		<modification>  <!-- v.2.1  -->
			<modificationName>Arginine-13C6</modificationName>
			<modificationID>5030</modificationID>
			<formattedString>Arg6</formattedString>
			<shortPrefix></shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>\S+\s+\(R-13C6\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>R</AAs>
					<massDiffFromBase>6.02012896</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.1  -->
			<modificationName>Lysine-13C6</modificationName>
			<modificationID>5040</modificationID>
			<formattedString>Lys6</formattedString>
			<shortPrefix></shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>\S+\s+\(K-13C6\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>K</AAs>
					<massDiffFromBase>6.02012896</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.1  -and 2.2??  -->
			<modificationName>Acetyl (K)</modificationName>
			<modificationID>5043</modificationID>
			<formattedString>acK</formattedString>
			<shortPrefix>ac</shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Acetyl\s+\(K\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>K</AAs>
					<massDiffFromBase>42.04695021</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.1  -->
			<modificationName>Leucine-D3</modificationName>
			<modificationID>5044</modificationID>
			<formattedString>Leu-d3</formattedString>
			<shortPrefix></shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Leu</matchString>

			<affectedAAs>
				<AAset>
					<AAs>L</AAs>
					<massDiffFromBase>3.01883023</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- PM 2006-09-12 Added postfix string. -->
		<!-- JAB 2007-05-14 Changed formatted string. -->
		<modification>  <!-- v.2.1  -and 2.2??  -->
			<modificationName>Oxidation (M)</modificationName>
			<modificationID>5045</modificationID>
			<formattedString>oxM</formattedString>
			<shortPrefix></shortPrefix>
			<shortPostfix>ox</shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Oxidation\s+\(M\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>M</AAs>
					<massDiffFromBase>15.99491463</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.1  -->
			<modificationName>Hys tag_D0</modificationName>
			<modificationID>5046</modificationID>
			<formattedString>CysHy0</formattedString>
			<shortPrefix></shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Hys\s+tag_D0</matchString>

			<affectedAAs>
				<AAset>
					<AAs>C</AAs>
					<massDiffFromBase>190.041212942</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.1  -->
			<modificationName>Hys tag_D4</modificationName>
			<modificationID>5047</modificationID>
			<formattedString>CysHy4</formattedString>
			<shortPrefix></shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Hys\s+tag_D4</matchString>

			<affectedAAs>
				<AAset>
					<AAs>C</AAs>

					<massDiffFromBase>194.06631998</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.1  -->
			<modificationName>Arginine-13C615N4</modificationName>
			<modificationID>5031</modificationID>
			<formattedString>Arg10</formattedString>
			<shortPrefix></shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>\S+\s+\(R-full\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>R</AAs>
					<massDiffFromBase>10.00826883</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.1  -->
			<modificationName>Lysine-D4</modificationName>
			<modificationID>5041</modificationID>
			<formattedString>Lys4</formattedString>
			<shortPrefix></shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Lysine\s+\(D4\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>K</AAs>
					<massDiffFromBase>4.02510698</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.1  -->
			<modificationName>Lysine-13C615N2</modificationName>
			<modificationID>5042</modificationID>
			<formattedString>Lys8</formattedString>
			<shortPrefix></shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>\S+\s+\(K-full\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>K</AAs>
					<massDiffFromBase>8.01419889</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.1  -and 2.2??  -->
			<modificationName>Phospho (ST)</modificationName>
			<modificationID>5048</modificationID>
			<formattedString>pST</formattedString>
			<shortPrefix>p</shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<!-- PM 2008-06-20 -->
			<modificationsExcludedFromSamePosition>  <!-- Note: all four may not be needed  -->
				<modID>5050</modID>  <!-- v.2.1                IntactPhospho(STY)   -->
				<modID>5051</modID>  <!-- v.2.1                phospho(STY)         -->
				<modID>5049</modID>  <!-- v.2.1  -and 2.2??    Phospho (Y)          -->
				<modID>5547</modID>  <!-- v.2.2                PhosphoIntact(STY)   -->
			</modificationsExcludedFromSamePosition>

			<matchString>Phospho\s+\(ST\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>ST</AAs>
					<massDiffFromBase>79.96633093</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.1  -and 2.2??  -->
			<modificationName>Phospho (Y)</modificationName>
			<modificationID>5049</modificationID>
			<formattedString>pY</formattedString>
			<shortPrefix>p</shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<!-- PM 2008-06-20 -->
			<modificationsExcludedFromSamePosition>  <!-- Note: all four may not be needed  -->
				<modID>5050</modID>  <!-- v.2.1                IntactPhospho(STY)   -->
				<modID>5051</modID>  <!-- v.2.1                phospho(STY)         -->
				<modID>5048</modID>  <!-- v.2.1  -and 2.2??    Phospho (ST)         -->
				<modID>5547</modID>  <!-- v.2.2                PhosphoIntact(STY)   -->
			</modificationsExcludedFromSamePosition>

			<matchString>Phospho\s+\(Y\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>Y</AAs>
					<massDiffFromBase>79.96633093</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.1  -->
			<modificationName>IntactPhospho(STY)</modificationName>
			<modificationID>5050</modificationID>
			<formattedString>ipSTY</formattedString>
			<shortPrefix>p</shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<!-- PM 2008-06-20 -->
			<modificationsExcludedFromSamePosition>  <!-- Note: all four may not be needed  -->
				<modID>5051</modID>  <!-- v.2.1                phospho(STY)         -->
				<modID>5048</modID>  <!-- v.2.1  -and 2.2??    Phospho (ST)         -->
				<modID>5049</modID>  <!-- v.2.1  -and 2.2??    Phospho (Y)          -->
				<modID>5547</modID>  <!-- v.2.2                PhosphoIntact(STY)   -->
			</modificationsExcludedFromSamePosition>


			<matchString>IntactPhospho\(STY\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>YST</AAs>
					<massDiffFromBase>79.96633093</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- PM 2006-09-12 Added postfix string. -->
		<!-- 2005-11-22 -->
		<!-- Used by BAB. Should it be here. And should the mass
		     difference be -18 Da instead?
		-->
		<modification>  <!-- v.2.1  -->
			<modificationName>phospho(STY)</modificationName>
			<modificationID>5051</modificationID>
			<formattedString>pSTY</formattedString>
			<shortPrefix>p</shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<!-- PM 2008-06-20 -->
			<modificationsExcludedFromSamePosition>  <!-- Note: all four may not be needed  -->
				<modID>5050</modID>  <!-- v.2.1                IntactPhospho(STY)   -->
				<modID>5048</modID>  <!-- v.2.1  -and 2.2??    Phospho (ST)         -->
				<modID>5049</modID>  <!-- v.2.1  -and 2.2??    Phospho (Y)          -->
				<modID>5547</modID>  <!-- v.2.2                PhosphoIntact(STY)   -->
			</modificationsExcludedFromSamePosition>

			<matchString>phospho\(STY\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>YST</AAs>
					<massDiffFromBase>79.96633093</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- PM 2006-08-01 -->
		<modification>  <!-- v.2.1  -->
			<modificationName>N15 mod</modificationName>
			<modificationID>5101</modificationID>
			<formattedString>N15</formattedString>
			<shortPrefix></shortPrefix>
			<shortPostfix>15</shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Heavy\s+Nitrogen\s+\(N15\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>ACDEFGILMPSTVY</AAs>
					<massDiffFromBase>0.997034967999999</massDiffFromBase>
				</AAset>
				<AAset>
					<AAs>KNQW</AAs>
					<massDiffFromBase>1.994069936</massDiffFromBase>
				</AAset>
				<AAset>
					<AAs>H</AAs>
					<massDiffFromBase>2.991104904</massDiffFromBase>
				</AAset>
				<AAset>
					<AAs>R</AAs>
					<massDiffFromBase>3.988139872</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- PM 2006-12-14 -->
		<modification>  <!-- v.2.1  -->
			<modificationName>N-Acetyl (Protein)</modificationName>
			<modificationID>5061</modificationID>
			<formattedString>n-ac</formattedString>
			<shortPrefix>n-ac</shortPrefix>
			<shortPostfix></shortPostfix>
			<startPosition>1</startPosition>
			<endPosition>1</endPosition>  <!--  N-term modification!!!   -->

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>N-Acetyl\s+\(Protein\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>ACDEFGHIKLMNPQRSTVWY</AAs>
					<massDiffFromBase>42.0104021</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- PM 2006-12-14 -->
		<modification>  <!-- v.2.1  -->
			<modificationName>Deamidation (NQ)</modificationName>
			<modificationID>5062</modificationID>
			<formattedString>deam</formattedString>
			<shortPrefix>deam</shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Deamidation\s+\(NQ\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>NQ</AAs>
					<massDiffFromBase>1.0062767</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- JAB 2007-03-06 -->
		<modification>  <!-- v.2.1  -->
			<modificationName>ICAT_9C12</modificationName>
			<modificationID>5063</modificationID>
			<formattedString>ICAT_l</formattedString>
			<shortPrefix>***</shortPrefix>
			<shortPostfix>***</shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>ICAT_light_9C12</matchString>

			<affectedAAs>
				<AAset>
					<AAs>C</AAs>
					<massDiffFromBase>227.126996</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.1  -->
			<modificationName>ICAT_9C13</modificationName>
			<modificationID>5064</modificationID>
			<formattedString>ICAT_H</formattedString>
			<shortPrefix>***</shortPrefix>
			<shortPostfix>***</shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>ICAT_heavy_9C13</matchString>

			<affectedAAs>
				<AAset>
					<AAs>C</AAs>
					<massDiffFromBase>236.157186</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- JAB 2007-03-06 -->
		<modification>  <!-- v.2.1  -->
			<modificationName>Pyro (N-term QC)</modificationName>
			<modificationID>5065</modificationID>
			<formattedString>npyqc</formattedString>
			<shortPrefix>npyqc</shortPrefix>
			<shortPostfix></shortPostfix>
			<startPosition>1</startPosition>
			<endPosition>1</endPosition>  <!--  N-term modification!!!   -->

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Pyro\s+\(N-term\s+QC\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>CQ</AAs>
					<massDiffFromBase>-17.026549</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- JAB 2007-03-06 -->
		<modification>  <!-- v.2.1  -and 2.2??  -->
			<modificationName>Acetyl (N-term)</modificationName>
			<modificationID>5066</modificationID>
			<formattedString>nacp</formattedString>
			<shortPrefix>nacp</shortPrefix>
			<shortPostfix></shortPostfix>
			<startPosition>1</startPosition>
			<endPosition>1</endPosition>  <!--  N-term modification!!!   -->

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Acetyl\s+\(N-term\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>ACDEFGHIKLMNPQRSTVWY</AAs>
					<massDiffFromBase>42.0104021</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- JAB 2007-03-06 -->
		<modification>  <!-- v.2.1  -->
			<modificationName>Pyro-glu (N-term E)</modificationName>
			<modificationID>5067</modificationID>
			<formattedString>npye</formattedString>
			<shortPrefix>npye</shortPrefix>
			<shortPostfix></shortPostfix>
			<startPosition>1</startPosition>
			<endPosition>1</endPosition>  <!--  N-term modification!!!   -->

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Pyro-glu\s+\(N-term\s+E\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>E</AAs>
					<massDiffFromBase>-18.0105647</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- JAB 2007-03-06 -->
		<modification>  <!-- v.2.1  -->
			<modificationName>Ubi (K)</modificationName>
			<modificationID>5068</modificationID>
			<formattedString>Ubi</formattedString>
			<shortPrefix>ub</shortPrefix>
			<shortPostfix>***</shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Ubi\s+\(K\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>K</AAs>
					<massDiffFromBase>114.0429275</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- JAB 2007-03-06 -->
		<modification>  <!-- v.2.1  -->
			<modificationName>Hydroxylation (P)</modificationName>
			<modificationID>5069</modificationID>
			<formattedString>hP</formattedString>
			<shortPrefix>h</shortPrefix>
			<shortPostfix>***</shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Hydroxylation\s+\(P\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>P</AAs>
					<massDiffFromBase>15.994919</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- *****  M O D I F I C A T I O N S,  M A S C O T   2 . 1   O R   E A R L I E R   D E F A U L T S ,  *****
		              E N D

		-->




		<!-- JAB 2007-04-11 -->
		<!-- *****  M O D I F I C A T I O N S,  M A S C O T    2 . 2   D E F A U L T S ,  *****
		              B E G I N

		-->
		<modification>  <!-- v.2.2  -->
			<modificationName>SILAC-13C6R</modificationName>
			<modificationID>5530</modificationID>
			<formattedString>Arg6</formattedString>
			<shortPrefix></shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Label:13C\(6\)\s+\(R\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>R</AAs>
					<massDiffFromBase>6.02012896</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.2  -->
			<modificationName>SILAC-13C615N4R</modificationName>
			<modificationID>5531</modificationID>
			<formattedString>Arg10</formattedString>
			<shortPrefix></shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Label:13C\(6\)15N\(4\)\s+\(R\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>R</AAs>
					<massDiffFromBase>10.00826883</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- JAB 2007-08-10 -->
		<modification>  <!-- v.2.2  -->
			<modificationName>SILAC-13C6K</modificationName>
			<modificationID>5540</modificationID>
			<formattedString>Lys6</formattedString>
			<shortPrefix></shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Label:13C\(6\)\s+\(K\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>K</AAs>
					<massDiffFromBase>6.02012896</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.2  -->
			<modificationName>SILAC-2H4K</modificationName>
			<modificationID>5541</modificationID>
			<formattedString>Lys4</formattedString>
			<shortPrefix></shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Label:2H\(4\)\s+\(K\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>K</AAs>
					<massDiffFromBase>4.02510698</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.2  -->
			<modificationName>SILAC-13C615N2K</modificationName>
			<modificationID>5542</modificationID>
			<formattedString>Lys8</formattedString>
			<shortPrefix></shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Label:13C\(6\)15N\(2\)\s+\(K\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>K</AAs>
					<massDiffFromBase>8.01419889</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- JAB 2007-05-01 -->
		<modification>  <!-- v.2.2  -->
			<modificationName>Ammonia-loss (N-term C)</modificationName>
			<modificationID>5543</modificationID>
			<formattedString>npyc</formattedString>
			<shortPrefix>npyc</shortPrefix>
			<shortPostfix></shortPostfix>
			<startPosition>1</startPosition>
			<endPosition>1</endPosition>  <!--  N-term modification!!!   -->

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Ammonia-loss\s+\(N-term\s+C\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>C</AAs>
					<massDiffFromBase>-17.026549</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.2  -->
			<modificationName>Gln->pyro-Glu (N-term Q)</modificationName>
			<modificationID>5544</modificationID>
			<formattedString>npyq</formattedString>
			<shortPrefix>npyq</shortPrefix>
			<shortPostfix></shortPostfix>
			<startPosition>1</startPosition>
			<endPosition>1</endPosition>  <!--  N-term modification!!!   -->

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Gln->pyro-Glu\s+\(N-term\s+Q\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>Q</AAs>
					<massDiffFromBase>-17.026549</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.2  -->
			<modificationName>Glu->pyro-Glu (N-term E)</modificationName>
			<modificationID>5545</modificationID>
			<formattedString>npye</formattedString>
			<shortPrefix>npye</shortPrefix>
			<shortPostfix></shortPostfix>
			<startPosition>1</startPosition>
			<endPosition>1</endPosition>  <!--  N-term modification!!!   -->

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Glu->pyro-Glu\s+\(N-term\s+E\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>E</AAs>
					<massDiffFromBase>-18.0105647</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.2  -->
			<modificationName>Oxidation (P)</modificationName>
			<modificationID>5546</modificationID>
			<formattedString>hP</formattedString>
			<shortPrefix>h</shortPrefix>
			<shortPostfix>***</shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Oxidation\s+\(P\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>P</AAs>
					<massDiffFromBase>15.994919</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- JAB 2007-05-11 -->
		<modification>  <!-- v.2.2  -->
			<modificationName>PhosphoIntact(STY)</modificationName>
			<modificationID>5547</modificationID>
			<formattedString>ipSTY</formattedString>
			<shortPrefix>p</shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<!-- PM 2008-06-20 -->
			<modificationsExcludedFromSamePosition>  <!-- Note: all four may not be needed  -->
				<modID>5050</modID>  <!-- v.2.1                IntactPhospho(STY)   -->
				<modID>5051</modID>  <!-- v.2.1                phospho(STY)         -->
				<modID>5048</modID>  <!-- v.2.1  -and 2.2??    Phospho (ST)         -->
				<modID>5049</modID>  <!-- v.2.1  -and 2.2??    Phospho (Y)          -->
			</modificationsExcludedFromSamePosition>

			<matchString>PhosphoIntact\s+\(STY\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>YST</AAs>
					<massDiffFromBase>79.96633093</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.2  -->
			<modificationName>Dioxidation (MW)</modificationName>
			<modificationID>5548</modificationID>
			<formattedString>doxMW</formattedString>
			<shortPrefix>dox</shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Dioxidation\s+\(MW\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>MW</AAs>
					<massDiffFromBase>31.989829</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.2  But not in current BMB Mascot server (??)    -->
			<modificationName>Kynurenin (W)</modificationName>
			<modificationID>5549</modificationID>
			<formattedString>kyW</formattedString>
			<shortPrefix>ky</shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Kynurenin\s+\(W\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>W</AAs>
					<massDiffFromBase>3.994915</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- JAB 2007-06-15 -->
		<modification>  <!-- v.2.2  -->
			<modificationName>ICAT_9C12</modificationName>
			<modificationID>5552</modificationID>
			<formattedString>ICAT_l</formattedString>
			<shortPrefix>***</shortPrefix>
			<shortPostfix>***</shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>ICAT-C\s+\(C\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>C</AAs>
					<massDiffFromBase>227.126996</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.2  -->
			<modificationName>ICAT_9C13</modificationName>
			<modificationID>5553</modificationID>
			<formattedString>ICAT_H</formattedString>
			<shortPrefix>***</shortPrefix>
			<shortPostfix>***</shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>ICAT-C:13C\(9\)\s+\(C\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>C</AAs>
					<massDiffFromBase>236.157186</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- JAB 2007-06-29 -->
		<modification>  <!-- v.2.2  -->
			<modificationName>Deamidated (NQ)</modificationName>
			<modificationID>5554</modificationID>
			<formattedString>deam</formattedString>
			<shortPrefix>deam</shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Deamidated\s+\(NQ\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>NQ</AAs>
					<massDiffFromBase>1.0062767</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<modification>  <!-- v.2.2  -->
			<modificationName>Acetyl (Protein N-term)</modificationName>
			<modificationID>5555</modificationID>
			<formattedString>n-ac</formattedString>
			<shortPrefix>n-ac</shortPrefix>
			<shortPostfix></shortPostfix>
			<startPosition>1</startPosition>
			<endPosition>1</endPosition>  <!--  N-term modification!!!   -->

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>Acetyl\s+\(Protein\s+N-term\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>ACDEFGHIKLMNPQRSTVWY</AAs>
					<massDiffFromBase>42.0104021</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>


		<!-- JAB 2008-06-26 -->
		<modification>  <!-- v.2.2  N-acetylhexosamine-->
			<modificationName>HexNAc (ST)</modificationName>
			<modificationID>5556</modificationID>
			<formattedString>hexnac</formattedString>
			<shortPrefix>hexnac</shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>HexNAc\s+\(ST\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>ST</AAs> <!--C8H13NO5  -->
					<massDiffFromBase>203.079372607</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- JAB 2008-06-26 -->
		<modification>  <!-- v.2.2  N-acetylhexosamine-->
			<modificationName>HexNAc (N)</modificationName>
			<modificationID>5557</modificationID>
			<formattedString>hexnac</formattedString>
			<shortPrefix>hexnac</shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>HexNAc\s+\(N\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>N</AAs> <!--C8H13NO5  -->
					<massDiffFromBase>203.079372607</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- JAB 2008-06-26 -->
		<modification>  <!-- v.2.2  hexoylN-acetylhexosamine-->
			<modificationName>HexHexNAc (NST)</modificationName>
			<modificationID>5558</modificationID>
			<formattedString>hexhexnac</formattedString>
			<shortPrefix>hexhexnac</shortPrefix>
			<shortPostfix></shortPostfix>

            <!-- Affects all of peptide; from N-terminal to C-terminal. -->
			<startPosition>1</startPosition>
			<endPosition>-1</endPosition>

			<modificationsExcludedFromSamePosition>  <!-- empty  -->
			</modificationsExcludedFromSamePosition>

			<matchString>HexHexNAc\s+\(NST\)</matchString>

			<affectedAAs>
				<AAset>
					<AAs>NST</AAs> <!--C14H23NO10  -->
					<massDiffFromBase>365.1321961</massDiffFromBase>
				</AAset>
			</affectedAAs>
		</modification>

		<!-- *****  M O D I F I C A T I O N S,  M A S C O T    2 . 2     D E F A U L T S ,  *****
		              E N D

		-->


	</modifications>
</QuantitationDefs>


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