PME7_Results_CNB

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					General
Quantitation Method
MS Instrument
Ion Source
LC Instrument

LC- Conditions
Column
Mobile Phase A
Mobile Phase B
Flow rate
Gradient profile
Total gradient time

MS conditions
Scheduled MRM used (Y/N)




Analysis
Sample load per injection (mg)
Number of replicate runs per sample

Data Analysis




Data Analysis workflow
                             MRM
                         5500 QTRAP
                           nano ESI
                     Eksigent nanoLC Ultra


Dionex Acclaim PepMap RSLC 75 mMX15cm, 2 mm size particle
                     0.1% Formic acid
               0.1% Formic acid in Acetonitrile
                        300 nl/min
       T=0 min 4% B; t=30 min 35% B; t=31 min 95% B
                          45 min


                                N
                      dwell time = 10 msec
                       Polarity = positive
                      cycle time = 2,16 sec



                              1 mg
                                2

            Analyst 1.5.1 / MultiQuant 2.1 (ABSciex)

Data were analyzed with Multiquant 2.1. Integration
parameters were set as follows:

Minimum peak width: 3 points
Noise percentage: 40%
Baseline Sub. Window: 2 min
Peak splitting: 2

Values with %CV > 20 between replicates were discarded.

Signals that could not be clearly distinguished from the
background were subjectively removed.
(MRM, iTRAQ, MSE...)




(Column type and dimensions)




( Add the rows needed to describe MS conditions/parametes relevant)




(software used)




(Briefly describe quantitation workflow, calculations performed, outline removal if any....)
For simplicity, we have included below the parameters provided by Sigma-Aldrich
Please modify them to the ones you have actually used (or just delete them and copy yours, whatever is easier)!
                              NO MODIFICATION OF THE PARAMETERS WAS CARRIED OUT
         QUANTITATIVE PROTEOMIC SAMPLE SET: MRM TRANSITIONS AND INSTRUME
                                              1
                                   PARAMETERS
Protein/NCBI                                                                 Q1         Q3
                                            MH+ RT (min)/
 Accession         Signature Peptide                      z (Q1)            Mass       Mass
                                           (mono) Segment
     No.                                                                    (Da)       (Da)
                                                                     2       493.2       774.3
                                                                     2       493.2       627.3
                       GGPFSDSYR             985.4      18.1/1
                                                                     2      493.2**     540.2**
                                                                     2      493.2*      871.4*
                                                                     2       498.2       784.4
                                                                     2       498.2       637.3
                      GGPFSDSY(R)            995.4      18.1/1
                                                                     2      498.2**     550.2**
 CAH1/P00915
                                                                     2      498.2*      881.4*
                                                                     2       485.8       871.5
                        VLDALQAIK            970.6      28.2/2       2       485.8       758.4
                                                                     2     485.8*,**   643.4*,**
                                                                     2       489.8       879.5
                       VLDALQAI(K)           978.6      28.2/2       2       489.8       766.5
                                                                     2     489.8*,**   651.4*,**
                                                                     2       658.4       976.5
                      EPISVSSEQVLK          1315.7      25.4/2       2       658.4       790.4
                                                                     2       658.4       889.5
                                                                     2       662.4       984.5
                     EPISVSSEQVL(K)         1323.7      25.4/2       2       662.4       798.4
                                                                     2       662.4       897.5
 CAH2/P00918
                                                                     2       585.3       749.4
                      SADFTNFDPR            1169.5      25.1/2       2       585.3       648.3
                                                                     2       585.3      1011.5
                                                                     2       590.3       759.4
                      SADFTNFDP(R)          1179.5      25.1/2       2       590.3       658.3
                                                                     2       590.3      1021.5
                                                                     2       742.4       978.5
                                                                     2       742.4       792.4
                   FSTVAGESGSADTVR          1483.7      17.4/1
                                                                     2      742.4*      921.4*
                                                                     2      742.4**    1049.5**
                                                                     2       747.4       988.5
                                                                     2       747.4       802.4
                  FSTVAGESGSADTV(R)         1493.7      17.4/1
                                                                     2      747.4*      931.4*
                                                                     2      747.4**    1059.5**
 CATA/P04040
                                                                     2       487.8       747.4
                                                                     2       487.8       660.3
                       NLSVEDAAR             974.5      16.2/1
                                                                     2      487.8*      860.4*
                                                                     2      487.8**     561.3**
                                                                     2       492.8       757.4
                                                                     2       492.8       670.3
                      NLSVEDAA(R)            984.5      16.2/1
                NLSVEDAA(R)      984.5    16.2/1
                                                   2    492.8*    870.4*
                                                   2    492.8**   571.3**
                                                   2     564.8     696.4
                ESDTSYVSLK       1128.5   18.6/1   2     564.8     609.4
                                                   2     564.8     797.4
                                                   2     568.8     704.4
               ESDTSYVSL(K)      1136.6   18.6/1   2     568.8     617.4
                                                   2     568.8     805.4
                                                   2     568.8     916.5
CRP/P02741
                                                   2     568.8     716.4
                GYSIFSYATK       1136.6   31.1/2
                                                   2    568.8*    1079.5*
                                                   2    568.8**   829.4**
                                                   2     572.8     924.5
                                                   2     572.8     724.4
                GYSIFSYAT(K)     1144.6   31.1/2
                                                   2    572.8*    1087.5*
                                                   2    572.8**   837.4**
                                                   3     546.6     695.4
              TFIIGELHPDDRPK     1637.9   25.8/2   3     546.6     638.8
                                                   3     546.6     727.4
                                                   3     549.3     699.4
              TFIIGELHPDDRP(K)   1645.9   25.8/2   3     549.3     642.8
                                                   3     549.3     735.4
CYB5/P00167                                        2     593.8     860.5
                 YYTLEEIQK       1186.6   41.7/2   2     593.8     759.4
                                                   2   593.8*,** 1023.5*,**
                                                   2     597.8     868.5
                YYTLEEIQ(K)      1194.6   41.7/2   2     597.8     767.4
                                                             ,          ,
                                                   2   597.8* ** 1031.5* **
                                                   2     554.8     811.4
                ALIVLAHSER       1108.7   19.6/1   2     554.8     712.4
                                                   2   554.8*,** 924.5*,**
                                                   2    559.8       821.5
                ALIVLAHSE(R)     1118.7   19.6/1   2    559.8       722.4
                                                   2   559.8*,**   934.5*,**
NQO1/P15559
                                                   3    474.9       574.3
              EGHLSPDIVAEQK      1422.7   18.2/1   3    474.9       736.3
                                                   3    474.9       899.5
                                                   3    477.6       582.3
              EGHLSPDIVAEQ(K)    1430.7   18.2/1   3    477.6       736.3
                                                   3    477.6       907.5
                                                   2    577.8       1007.5
                 FEDENFILK       1154.6   30.3/2   2    577.8       878.5
                                                   2    577.8       763.4
                                                   2    581.3       1014.6
                FEDENFI(L)K      1161.7   30.3/2   2    581.3       885.6
                                                   2    581.3       770.4
PPIA/P62937
                                                   2    528.3       956.5
                 VSFELFADK       1055.5   34.8/2   2    528.3       869.4
                                                   2    528.3       722.4
                                                   2    533.3       966.5
                VSFEL(F)ADK      1065.6   34.8/2
     PPIA/P62937




                           VSFEL(F)ADK              1065.6        34.8/2          2        533.3       879.5
                                                                                  2        533.3       732.4
                                                                                  2        447.7       579.3
                             ADEGISFR                894.4        18.5/1          2        447.7       409.2
                                                                                  2        447.7       708.4
                                                                                  2        452.7       589.3
                            ADEGISF(R)               904.4        18.5/1          2        452.7       419.2
                                                                                  2        452.7       718.4
    PRDX1/Q06830
                                                                                  2        460.8       750.4
                              GLFIIDDK               920.5        32.0/2          2        460.8       490.3
                                                                                  2        460.8       603.3
                                                                                  2        464.8       758.4
                             GLFIIDD(K)              928.5        32.0/2          2        464.8       498.3
                                                                                  2        464.8       611.3
                                                                                  2        583.3       669.4
                          DPNGLPPEAQK               1165.6        15.0/1          2        583.3       497.2
                                                                                  2       583.3**     839.5**
                                                                                  2        587.3       677.4
                         DPNGLPPEAQ(K)              1173.6        15.0/1          2        587.3       497.2
                                                                                  2       587.3**     847.5**
                                                                                  3        435.2       841.3
    RET4/P02753
                                                                                  3        435.2       507.2
                        LIVHNGYCamDGR               1303.6        15.2/1
                                                                                  2       652.3*       841.3*
                                                                                  2       652.3**     539.2**
                                                                                  3        438.6       851.3
                                                                                  3        438.6       517.2
                        LIVHNGYCamDG(R)             1313.6        15.2/1
                                                                                  2       657.3*       851.3*
                                                                                  2       657.3**     544.2**
                                                                                  3        453.9       847.4
                                                                                  2       680.3*       962.5*
                          VIGQDSSEIHFK              1359.7        19.8/1
                                                                                  2       680.3**     574.3**
                                                                                  2       680.3**     1147.5**
                                                                                  3        456.6       855.4
                                                                                  2        684.4       970.5
                         VIGQDSSEIHF(K)             1367.7        19.8/1
                                                                                  2       684.4**     578.3**
    SUMO/P63165
                                                                                  2       684.4**     1155.5**
                                                                                  2        448.7       749.4
                             FLFEGQR                 896.5        24.1/1          2       448.7*       636.3*
                                                                                  2        448.7       489.2
                                                                                  2        453.7       759.4
                             FLFEGQ(R)               906.5        24.1/1          2       453.7*       646.3*
                                                                                  2       453.7**     499.2**

1
    Instrument parameter optimization and data acquisition for data in this table were generated using an API 4000 QTRAP mass spe
2
  If transition is predicted, as indicated by a * or **, CE values are based on predictions from MRM Pilot.
3
  Values for predicted transitions use DP and CXP from other transitions of the same peptide which had been optimized by infusion or MRM Pilot.
* Transition predicted by MRM Pilot.
** Transition based on full scan MS/MS on a Thermo LTQ.
 and copy yours, whatever is easier)!
AS CARRIED OUT
RM TRANSITIONS AND INSTRUMENT
   1
 S

                      Fragment
                                CE2 DP3 CXP3 EP
                       ion type

                           y6           28   51   48   10
                           y5           28   51   16   10
                           y4           28   51   48   10
                           y7           28   51   16   10
                           y6           28   51   48   10
                           y5           28   51   16   10
                           y4           28   51   48   10
                           y7           28   51   16   10
                           y8           24   61   26   10
                           y7           24   61   24   10
                           y6           24   61   24   10
                           y8           24   61   26   10
                           y7           24   61   24   10
                           y6           24   61   24   10
                           y9           32   76   28   10
                           y7           32   76   26   10
                           y8           32   76   10   10
                           y9           32   76   28   10
                           y7           32   76   26   10
                           y8           32   76   10   10
                           y6           28   66   20   10
                           y5           28   66   18   10
                           y8           28   60   10   10
                           y6           28   66   20   10
                           y5           28   66   18   10
                           y8           28   60   10   10
                          y10           39   81   28   10
                           y8           39   81   22   10
                           y9           39   81   25   10
                          y11           39   81   25   10
                          y10           39   81   28   10
                           y8           39   81   22   10
                           y9           39   81   25   10
                          y11           39   81   25   10
                           y7           24   51   22   10
                           y6           24   51   18   10
                           y8           24   51   20   10
                           y5           24   51   20   10
                           y7           24   56   22   10
                           y6           24   56   18   10
  y8    24   56   20   10
  y5    24   56   20   10
  y6    27   61   22   10
  y5    27   61   18   10
  y7    27   60   10   10
  y6    27   61   22   10
  y5    27   61   18   10
  y7    27   60   10   10
  y8    26   61   28   10
  y6    26   61   20   10
  y9    26   61   25   10
  y7    26   61   25   10
  y8    26   61   28   10
  y6    26   61   20   10
  y9    26   61   25   10
  y7    26   61   25   10
y12++   30   65   30   10
y11++   30   65   30   10
  y6    25   60   10   10
y12++   30   65   30   10
y11++   30   65   30   10
  y6    25   60   10   10
  y7    24   60   25   10
  y6    25   60   30   10
 y8     25   60   27   10
 y7     24   60   25   10
 y6     25   60   30   10
 y8     25   60   27   10
 y7     34   91   24   10
 y6     34   91   22   10
 y8     34   91   24   10
 y7     34   91   24   10
 y6     34   91   22   10
 y8     34   91   24   10
 y5     20   41   18   10
 b7     20   41   24   10
 y8     22   41   24   10
 y5     20   41   18   10
 b7     20   41   24   10
 y8     22   41   24   10
 y8     28   76   30   10
 y7     28   76   28   10
 y6     24   60   10   10
 y8     28   76   30   10
 y7     28   76   28   10
 y6     24   60   10   10
 y8     27   76   30   10
 y7     27   76   28   10
 y6     22   60   10   10
 y8     27   56   30   10
                               y7         27     56     28   10
                               y6         22     60     10   10
                               y5         23     51     18   10
                               y3         23     51     12   10
                               y6         19     60     10   10
                               y5         23     51     18   10
                               y3         23     51     12   10
                               y6         19     60     10   10
                               y6         21     61     14   10
                               y4         21     61     16   10
                               y5         19     60     10   10
                               y6         21     61     14   10
                               y4         21     61     16   10
                               y5         19     60     10   10
                               y6         29     56     18   10
                               b5         29     56     14   10
                               y8         29     56     14   10
                               y6         29     56     18   10
                               b5         29     56     14   10
                               y8         29     56     14   10
                               y7         23     46     26   10
                               y4         23     46     16   10
                               y7         23     46     16   10
                             y9++         23     46     16   10
                               y7         23     46     26   10
                               y4         23     46     16   10
                               y7         23     46     16   10
                             y9++         23     46     16   10
                               y7         35     60     10   10
                               y8         35     60     10   10
                            y10++         35     60     10   10
                              y10         35     60     10   10
                               y7         35     60     10   10
                               y8         35     60     10   10
                            y10++         35     60     10   10
                              y10         35     60     10   10
                               y6         25     60     10   10
                               y5         19     60     10   10
                               y4         19     60     10   10
                               y6         25     60     10   10
                               y5         19     60     10   10
                               y4         19     60     10   10

e generated using an API 4000 QTRAP mass spectrometer (ABSciex).

de which had been optimized by infusion or MRM Pilot.
Provide a suitable measurement of the observed variability between the n replicate measurements for each peptide / p
Example: %CV of the measured MRM intensities for each peptide
                                        %CV (NUMBER OF REPLICATES = 2)

    Tier                   Protein                    Sample A     Sample B     Sample C
     1       CAH1/P00915_GGPFSDSYR                       0.0          8.7          1.7
     1       CAH1/P00915_VLDALQAIK                       0.0          1.5          9.0
     1       CAH2/P00918_EPISVSSEQVLK                    3.6          4.0          1.5
     1       CAH2/P00918_SADFTNFDPR                      2.0          2.4          0.9
     1       CRP/P02741_ESDTSYVSLK                       9.4          4.6          2.3
     1       CRP/P02741_GYSIFSYATK                        -          12.9          7.4
     2       NQO1/P15559_ALIVLAHSER                       -           6.1          5.8
     2       NQO1/P15559_EGHLSPDIVAEQK                   3.1         18.4          4.7
     2       PPIA/Q13427_FEDENFILK                        -            -            -
     2       PPIA/Q13427_VSFELFADK                        -            -            -
     2       SUMO/P63165_FLFEGQR                          -            -            -
     2       SUMO/P63165_VIGQDSSEIHFK                   12.9          7.4         12.1
     3       CATA/P04040_FSTVAGESGSADTVR                  -            -            -
     3       CATA/P04040_NLSVEDAAR                        -          17.4          0.6
     3       CYB5/P00167_TFIIGELHPDDRPK                   -            -            -
     3       CYB5/P00167_YYTLEEIQK                        -            -            -
     3       RETBP/P18902_DPNGLPPEAQK                     -            -            -
     3       RETBP/P18902_LIVHNGYCamDGR                   -            -            -
   Norm      PRDX1/Q06830_ADEGISFR                       3.2          0.5          5.2
   Norm      PRDX1/Q06830_GLFIIDDK                       4.2          2.7          3.1
te measurements for each peptide / protein (according to the method used). Describe it.



             Sample D      Sample E
                5.0           0.4
                3.1           1.9
                2.2           2.7
                3.8           2.1
                2.4           2.4
                2.3           1.8
                0.5           0.2
                8.6           2.3
               13.3           4.2
               13.5           7.7
                6.6            -
                1.6           1.6
               19.9           8.9
               12.8           7.2
                 -           13.4
                 -            1.1
                 -             -
                 -             -
                2.4           3.1
                6.6           6.8
The data on this and the following sheets is given as an example: delete and substitute with your data



Relative Quantitation_Fold change Table
    Tier                   Protein                     Sample A     Sample B      Sample C
     1       CAH1/P00915_GGPFSDSYR                       66.5         32.7          10.2
     1       CAH1/P00915_VLDALQAIK                       53.7         29.9          10.9
     1       CAH2/P00918_EPISVSSEQVLK                    46.2         25.4          12.7
     1       CAH2/P00918_SADFTNFDPR                      43.9         25.2           9.5
     1       CRP/P02741_ESDTSYVSLK                       38.4         23.6           9.2
     1       CRP/P02741_GYSIFSYATK                        -           21.9          12.7
     2       NQO1/P15559_ALIVLAHSER                       -           52.0          24.6
     2       NQO1/P15559_EGHLSPDIVAEQK                   23.9         23.4          14.4
     2       PPIA/Q13427_FEDENFILK                        -            -              -
     2       PPIA/Q13427_VSFELFADK                        -            -              -
     2       SUMO/P63165_FLFEGQR                          -            -              -
     2       SUMO/P63165_VIGQDSSEIHFK                    63.8         36.9          20.1
     3       CATA/P04040_FSTVAGESGSADTVR                  -            -              -
     3       CATA/P04040_NLSVEDAAR                        -           65.0          21.5
     3       CYB5/P00167_TFIIGELHPDDRPK                   -            -              -
     3       CYB5/P00167_YYTLEEIQK                        -            -              -
     3       RETBP/P18902_DPNGLPPEAQK                     -            -              -
     3       RETBP/P18902_LIVHNGYCamDGR                   -            -              -
   Norm      PRDX1/Q06830_ADEGISFR                       0.9          1.0            1.0
   Norm      PRDX1/Q06830_GLFIIDDK                       0.7          0.8            1.1

Fold change calculated as Sample E/Sample X X=A,B,C,D or E
nd substitute with your data




                     Sample D   Sample E
                       6.5        1.0
                       4.9        1.0
                       4.7        1.0
                       5.1        1.0
                       4.4        1.0
                       4.0        1.0
                       3.3        1.0
                       3.2        1.0
                       4.2        1.0
                       4.0        1.0
                        -          -
                       3.9        1.0
                       4.6        1.0
                       4.6        1.0
                        -         1.0
                        -         1.0
                        -          -
                        -          -
                       0.9        1.0
                       0.9        1.0
Absolute Quantitatio: H/L ratios
   Tier   Component Name                H/L A    H/L B    H/L C
    1     CAH1/P00915_GGPFSDSYR          62.5     30.8      9.5
    1     CAH1/P00915_VLDALQAIK          37.0     20.6      7.5
    1     CAH2/P00918_EPISVSSEQVLK       25.6     14.1      7.0
    1     CAH2/P00918_SADFTNFDPR         29.0     16.7      6.3
    1     CRP/P02741_ESDTSYVSLK          26.7     16.4      6.4
    1     CRP/P02741_GYSIFSYATK            -     181.8    105.3
    2     NQO1/P15559_ALIVLAHSER           -      58.0     27.4
    2     NQO1/P15559_EGHLSPDIVAEQK      44.4     43.5     26.8
    2     PPIA/Q13427_FEDENFILK            -        -        -
    2     PPIA/Q13427_VSFELFADK            -        -        -
    2     SUMO/P63165_FLFEGQR              -        -        -
    2     SUMO/P63165_VIGQDSSEIHFK      181.8    105.3     57.1
    3     CATA/P04040_FSTVAGESGSADTVR      -        -        -
    3     CATA/P04040_NLSVEDAAR            -      27.4      9.0
    3     CYB5/P00167_TFIIGELHPDDRPK       -        -        -
    3     CYB5/P00167_YYTLEEIQK            -        -        -
    3     RETBP/P18902_DPNGLPPEAQK         -        -        -
    3     RETBP/P18902_LIVHNGYCamDGR       -        -        -
  Norm    PRDX1/Q06830_ADEGISFR           6.5      7.4      7.4
  Norm    PRDX1/Q06830_GLFIIDDK           5.0      5.4      7.4

Absolute Quantitation: calculated fmol Light peptides based on theor. Heavy Std am

   Tier   Component Name                fmol A   fmol B   fmol C
    1     CAH1/P00915_GGPFSDSYR           4.0      8.1     26.2
    1     CAH1/P00915_VLDALQAIK           6.8     12.1     33.4
    1     CAH2/P00918_EPISVSSEQVLK        9.8     17.8     35.6
    1     CAH2/P00918_SADFTNFDPR          8.6     15.0     39.8
    1     CRP/P02741_ESDTSYVSLK           9.4     15.3     39.1
    1     CRP/P02741_GYSIFSYATK            -       1.4      2.4
    2     NQO1/P15559_ALIVLAHSER           -       1.0      2.2
    2     NQO1/P15559_EGHLSPDIVAEQK       1.4      1.4      2.2
    2     PPIA/Q13427_FEDENFILK            -        -        -
    2     PPIA/Q13427_VSFELFADK            -        -        -
    2     SUMO/P63165_FLFEGQR              -        -        -
    2     SUMO/P63165_VIGQDSSEIHFK        0.3      0.6      1.1
    3     CATA/P04040_FSTVAGESGSADTVR      -        -        -
    3     CATA/P04040_NLSVEDAAR            -       0.1      0.3
    3     CYB5/P00167_TFIIGELHPDDRPK       -        -        -
    3     CYB5/P00167_YYTLEEIQK            -        -        -
    3     RETBP/P18902_DPNGLPPEAQK         -        -        -
    3     RETBP/P18902_LIVHNGYCamDGR       -        -        -
  Norm    PRDX1/Q06830_ADEGISFR          38.6     33.9     33.8
  Norm    PRDX1/Q06830_GLFIIDDK          50.0     45.9     33.8
          H/L D    H/L E    fmol H
           6.1      0.9      250
           3.4      0.7      250
           2.6      0.6      250
           3.4      0.7      250
           3.1      0.7      250
          32.8      8.3      250
           3.7      1.1       60
           6.0      1.9       60
           2.0      0.5       60
           4.7      1.2       60
          13.2       -        60
          11.2      2.8       60
           9.5      2.1       2.5
           2.0      0.4       2.5
            -       0.6       2.5
            -       0.6       2.5
            -        -        2.5
            -        -        2.5
           6.7      7.2      250
           6.2      6.8      250

ed on theor. Heavy Std amount

          fmol D   fmol E
           40.9     265.9
           73.4     362.8
           95.8     450.8
           74.5     378.3
           81.9     359.6
            7.6      30.1
           16.4      53.8
           10.1      32.2
           30.7     128.9
           12.9      50.9
            4.5        -
            5.3      21.1
            0.3       1.2
            1.3       5.9
             -        3.9
             -        4.5
             -         -
             -         -
           37.4      34.5
           40.4      36.5
Theoretical E/X ratios

  Protein          A     B      C      D     E
   CAH1            50    25     10     5     1
   CAH1            50    25     10     5     1
   CAH2            50    25     10     5     1
   CAH2            50    25     10     5     1
   CRP             50    25     10     5     1
   CRP             50    25     10     5     1
   NQOI           100    50     25     5     1
   NQOI           100    50     25     5     1
   PPIA           100    50     25     5     1
   PPIA           100    50     25     5     1
  SUMO            100    50     25     5     1
  SUMO            100    50     25     5     1
   CATA           100    50     25     5     1
   CATA           100    50     25     5     1
   CYB5           100    50     25     5     1
   CYB5           100    50     25     5     1
  RETBP           100    50     25     5     1
  RETBP           100    50     25     5     1



Measured ratios E/X

  Protein          A      B       C     D     E
   CAH1           66.5   32.7   10.2   6.5   1.0
   CAH1           53.7   29.9   10.9   4.9   1.0
   CAH2           46.2   25.4   12.7   4.7   1.0
   CAH2           43.9   25.2    9.5   5.1   1.0
   CRP            38.4   23.6    9.2   4.4   1.0
   CRP             -     21.9   12.7   4.0   1.0
   NQOI            -     52.0   24.6   3.3   1.0
   NQOI           23.9   23.4   14.4   3.2   1.0
   PPIA            -      -       -    4.2   1.0
   PPIA            -      -       -    4.0   1.0
  SUMO             -      -       -     -     -
  SUMO            63.8   36.9   20.1   3.9   1.0
   CATA            -      -       -    4.6   1.0
   CATA            -     65.0   21.5   4.6   1.0
   CYB5            -      -       -     -    1.0
   CYB5            -      -       -     -    1.0
  RETBP            -      -       -     -     -
  RETBP            -      -       -     -     -
Change Measured
% Fold Change Measured
Theoretical Fold Change ratios

  Protein        A/B             B/C       C/D          B/C            A/C           A/C
   CAH1                 2                          2           2.5                         5
   CAH1                 2                          2           2.5                         5
   CAH2                 2                          2           2.5                         5
   CAH2                 2                          2           2.5                         5
   CRP                  2                          2           2.5                         5
   CRP                  2                          2           2.5                         5
   NQOI                 2              2                                       4
   NQOI                 2              2                                       4
   PPIA                 2              2                                       4
   PPIA                 2              2                                       4
  SUMO                  2              2                                       4
  SUMO                  2              2                                       4
   CATA                 2              2                                       4
   CATA                 2              2                                       4
   CYB5                 2              2                                       4
   CYB5                 2              2                                       4
  RETBP                 2              2                                       4
  RETBP                 2              2                                       4



Calculated Fold Change ratios

  Protein        A/B             B/C       C/D          B/C            A/C           A/C
   CAH1            2.03                          1.56         3.22                      6.55
   CAH1            1.80                          2.20         2.75                      4.94
   CAH2            1.82                          2.69         2.01                      3.65
   CAH2            1.74                          1.87         2.65                      4.61
   CRP             1.63                          2.09         2.57                      4.17
   CRP        #VALUE!                            3.21         1.73                 #VALUE!
   NQOI
   NQOI            1.02          1.62                                     1.66
   PPIA       #VALUE!       #VALUE!                                  #VALUE!
   PPIA       #VALUE!       #VALUE!                                  #VALUE!
  SUMO        #VALUE!       #VALUE!                                  #VALUE!
  SUMO             1.73          1.84                                     3.18
   CATA                     #VALUE!
   CATA                          3.03
   CYB5
   CYB5
  RETBP       #VALUE!       #VALUE!                                  #VALUE!
  RETBP       #VALUE!       #VALUE!                                  #VALUE!


% measured Fold Change / Theoretical Fold Change

  Protein        A/B             B/C       C/D          B/C            A/C           A/C
   CAH1            101.56                     78.16      128.92                       130.94
                   CAH1          89.81                         109.93       110.10                   98.89
                   CAH2          91.03                         134.39        80.28                   73.08
                   CAH2          86.96                          93.71       106.00                   92.17
                    CRP          81.33                         104.63       102.62                   83.47
                    CRP      #VALUE!                           160.53        69.09               #VALUE!
                    NQOI
                    NQOI         51.11        80.98                                      41.39
                    PPIA     #VALUE!      #VALUE!                                    #VALUE!
                    PPIA     #VALUE!      #VALUE!                                    #VALUE!
                   SUMO      #VALUE!      #VALUE!                                    #VALUE!
                   SUMO          86.36        92.11                                      79.55
                   CATA                   #VALUE!
                   CATA                      151.37
                    CYB5
                    CYB5
                   RETBP     #VALUE!      #VALUE!                                    #VALUE!
                   RETBP

            % measured FC / theoretical FC averaged per protein

                   Protein     A/B          B/C               C/D          B/C         A/C         A/C
                    CAH1          95.69                          94.04      119.51                  114.91
                    CAH2          88.99                         114.05       93.14                   82.63
                    CRP      #VALUE!                            132.58       85.86               #VALUE!
                    NQOI          51.11       80.98                                      41.39
                    PPIA     #VALUE!      #VALUE!                                    #VALUE!
                   SUMO      #VALUE!      #VALUE!                                    #VALUE!
                    CATA                  #VALUE!
                    CYB5
                   RETBP     #VALUE!      #VALUE!                                    #VALUE!

            Summary Fold Change Accuracy

            Theor. Fold       Tier 1      Stdev T1        Tier 2         Stdev T2     Tier 3     Stdev T3
                       2     #VALUE!      #VALUE!        #VALUE!         #VALUE!     #VALUE!     #VALUE!
                     2.5           99.5         17.7
                       4                                 #VALUE!         #VALUE!     #VALUE!
                       5     #VALUE!      #VALUE!        #VALUE!         #VALUE!     #VALUE!     #VALUE!
                      10     #VALUE!      #VALUE!        #VALUE!         #VALUE!     #VALUE!     #VALUE!
                      20                                 #VALUE!         #VALUE!     #VALUE!
                      25         105.8         17.6      #VALUE!         #VALUE!     #VALUE!     #VALUE!
                      50     #VALUE!      #VALUE!        #VALUE!         #VALUE!     #VALUE!     #VALUE!
                     100                                 #VALUE!         #VALUE!     #VALUE!



                                                    Series1
                  1.2
                                                    Series2
                                                    Series3
                   1
Change Measured




                  0.8
% Fold Change Measured

                         0.8


                         0.6


                         0.4


                         0.2


                          0
                               Theoretical Fold Change
B/D            C/D           D/E           A/D          B/D        C/E          A/D
        5                            5           10                      10
        5                            5           10                      10
        5                            5           10                      10
        5                            5           10                      10
        5                            5           10                      10
        5                            5           10                      10
                       5             5                        10                      20
                       5             5                        10                      20
                       5             5                        10                      20
                       5             5                        10                      20
                       5             5                        10                      20
                       5             5                        10                      20
                       5             5                        10                      20
                       5             5                        10                      20
                       5             5                        10                      20
                       5             5                        10                      20
                       5             5                        10                      20
                       5             5                        10                      20




B/D            C/D           D/E           A/D          B/D        C/E
      5.04                      6.50         10.23                   10.16
      6.05                      4.94         10.87                   10.87
      5.39                      4.71           9.82                  12.65
      4.97                      5.08           8.64                    9.52
      5.37                      4.39           8.73                    9.19
      5.55                      3.95     #VALUE!                     12.68
                                3.29
                  4.50          3.20                       7.29                    7.46
             #VALUE!            4.20                  #VALUE!                 #VALUE!
             #VALUE!            3.96                  #VALUE!                 #VALUE!
             #VALUE!       #VALUE!                    #VALUE!                 #VALUE!
                  5.09          3.94                       9.37                   16.18
             #VALUE!            4.64                  #VALUE!
                  4.62          4.65                      13.98


             #VALUE!       #VALUE!                    #VALUE!                 #VALUE!
             #VALUE!       #VALUE!                    #VALUE!                 #VALUE!




B/D            C/D           D/E           A/D          B/D        C/E
 100.77                       129.92        102.34                  101.55
 121.03                   98.88      108.70                108.69
 107.89                   94.15       98.21                126.53
  99.33                  101.54       86.38                 95.16
 107.38                   87.85       87.33                 91.92
 110.91                   79.02   #VALUE!                  126.84
                          65.71
              90.07       64.05                   72.93                 37.28
          #VALUE!         84.05               #VALUE!               #VALUE!
          #VALUE!         79.16               #VALUE!               #VALUE!
          #VALUE!     #VALUE!                 #VALUE!               #VALUE!
             101.71       78.88                   93.68                 80.91
          #VALUE!         92.89               #VALUE!
              92.35       92.99                  139.79


          #VALUE!     #VALUE!                 #VALUE!               #VALUE!




B/D         C/D         D/E         A/D         B/D       C/E
 110.90                  114.40      105.52                105.12
 103.61                   97.85       92.29                110.84
 109.14                   83.43   #VALUE!                  109.38
              90.07       64.88                   72.93                 37.28
          #VALUE!         81.61               #VALUE!               #VALUE!
          #VALUE!     #VALUE!                 #VALUE!               #VALUE!
          #VALUE!         92.94               #VALUE!

          #VALUE!     #VALUE!                 #VALUE!               #VALUE!
B/E          C/E          A/E          B/E          A/E
      25                        50
      25                        50
      25                        50
      25                        50
      25                        50
      25                        50
                   25                        50           100
                   25                        50           100
                   25                        50           100
                   25                        50           100
                   25                        50           100
                   25                        50           100
                   25                        50           100
                   25                        50           100
                   25                        50           100
                   25                        50           100
                   25                        50           100
                   25                        50           100




B/E          C/E          A/E          B/E          A/E
  32.73                     66.48
  29.92                     53.74
  25.39                     46.23
  25.22                     43.86
  23.58                     38.36
  21.91                 #VALUE!
               24.58                     52.00    #VALUE!
               14.42                     23.36        23.88
           #VALUE!                   #VALUE!      #VALUE!
           #VALUE!                   #VALUE!      #VALUE!
           #VALUE!                   #VALUE!      #VALUE!
               20.06                     36.95        63.82
           #VALUE!                   #VALUE!
               21.47                     65.00


           #VALUE!                   #VALUE!      #VALUE!
           #VALUE!                   #VALUE!      #VALUE!




B/E          C/E          A/E          B/E          A/E
 130.92                    132.97
 119.67                  107.48
 101.58                   92.46
 100.87                   87.71
  94.33                   76.72
  87.64               #VALUE!

              57.69                   46.72       23.88
          #VALUE!                 #VALUE!     #VALUE!
          #VALUE!                 #VALUE!     #VALUE!
          #VALUE!                 #VALUE!     #VALUE!
              80.23                   73.89       63.82
          #VALUE!                 #VALUE!
              85.88                  130.00


          #VALUE!                 #VALUE!     #VALUE!




B/E         C/E         A/E         B/E         A/E
 125.30                  120.23
 101.22                   90.09
  90.98               #VALUE!
              57.69                   46.72       23.88
          #VALUE!                 #VALUE!     #VALUE!
          #VALUE!                 #VALUE!     #VALUE!
          #VALUE!                 #VALUE!

          #VALUE!                 #VALUE!     #VALUE!
If available, please provide the list of identified peptides of the yeast matrix for at least 5 different runs (we'll try to ma

                                                                                      Peptide Score
Peptide sequence                      Modifications        Protein Accession          (*Score type*)
different runs (we'll try to make some statistics on peptide/protein ids)



           Column 4: Replace *score type* with the name of scoring system used (e.g., Mascot ion score, Sequest XCor, Xta
score, Sequest XCor, Xtandem E-value, Mascot E-value, q-value, PeptideProphet, etc)

				
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