Supplemental Table I. Summary of tryptic peptide-to-protein correlations from the search engines X!TANDEM, OMSSA and SEQUEST along with the level of statistical significance achieved for the identification of SYK (L) NP_003168 from MS/MS spectra correlation to human amino acid sequences. Only fully tryptic 2+ or 3+ peptides with precursor intensity values greater than 1000 counts were accepted for correlation analysis.

Correlation Engine / Identification Filter / Sum Rank
0 / 1 / 2 / Parameter
TANDEM / 46 / 46 / 23 / E-207.6
OMSSA / 18 / 18 / 9 / E-78
SEQUEST / 1152 / 179 / 179 / 359.2*
Total peptide count / 1216 / 243 / 211

* An X-correlation score of 2.5 to 3.75 is considered significant.

Supplemental Table II. Comparison of fully tryptic peptide correlations to Spleen Tyrosine Kinase (SYK) long isoform SYK (L) NP_003168 and related molecules from SEQUEST algorithm. Only fully tryptic 2+ or 3+ peptides with precursor intensity values greater than 1000 counts were accepted for correlation analysis. The filter 0 indicates teh results are exactly as provided by the manufactures’ SEQUEST algorithm, filter 1 indicates that the peptide is not better explained at a different charge state, filter 2 indicates that the peptide is not better explained by another tryptic peptide sequence. The probability that the peptide frequency values were the same between the total of the some ~242 distinct correlations in filter state 2 across the treatments was low with a Chi Square value of χ2= 106.7366, df = 21, p-value = 1.821e-13 as calculated by the R statistical Analysis System.

Peptide / Tryptic / Tryptic STYP
Filter method / 0 / 1 / 2 / 0 / 1 / 2
Live anti CD36_IgA / 53 / 8 / 8 / 107 / 12 / 12
Crude anti CD 36_IgA / 49 / 17 / 15 / 92 / 11 / 10
Live antiCD36_IgG / 15 / 4 / 4 / 42 / 7 / 7
Crude antiCD36_IgG / 24 / 10 / 7 / 34 / 8 / 6
Live human IgG / 54 / 24 / 17 / 50 / 16 / 12
Crude human IgG / 26 / 5 / 3 / 48 / 8 / 6
Media human IgG / 8 / 2 / 1 / 12 / 2 / 1
Live oxLDL / 110 / 21 / 21 / 152 / 21 / 21
Crude oxLDL / 95 / 22 / 19 / 119 / 22 / 20
Media oxLDL / 5 / 0 / 0 / 6 / 0 / 0
Live None / 4 / 1 / 1 / 8 / 2 / 2
Crude None / 34 / 6 / 5 / 50 / 14 / 13

Supplemental Table III. A summary of the peptides, families of overlapping peptides, phosphopeptides and family of overlapping phosphopeptide observed from the affinity chromatography and mass spectrometry experiments to SYK (L) NP_003168 and related molecules. Families of peptides amino acid sequences shared by more than one peptide are shown. The Serine Threonine or Tyrosine phosphorylation columns (STYP) tabulates the maximum number of phosphorylations observed in the amino acid sequence. Note some phosphorylations are confirmed by double or triple overlapping peptides sequences. The chance that so many peptides would correlate to the same overlapping peptide sequences by random change is essentially zero [60, 64]. The maximum number of PO3 (80 Da) observed to satisfy the delta/mz reported is listed.

Peptide / delta m/z / MH / z / PO3 / N
ADGLLRVLTVPCQKIGTQGNVNFGGRPQLPGSHPATWSAGGIISR / 0.246 / 4629.299 / 3 / 0 / 1
ALRADENYYKAQTHGK / -0.114 / 1866.043 / 3 / 0 / 3
AQTHGKWPVK / 0.172 / 1152.341 / 3 / 1 / 2
AQTHGKWPVKWYAPECINYYK / -0.856 / 2583.969 / 3 / 0 / 1
DKNIIELVHQVSMGMK / -0.504 / 1843.209 / 3 / 1 / 3
DKTGKLSIPEGK / -0.435 / 1273.472 / 3 / 2 / 1
DLAARNVLLVTQHYAK / -0.935 / 1813.109 / 3 / 0 / 1
DNNGSYALCLLHEGKVLHYRIDK / 1.732 / 2660.022 / 3 / 3 / 1
EALPMDTEVYESPYADPEEIRPK / 0.139 / 2680.943 / 3 / 0 / 17
EESEQIVLIGSK / 0.258 / 1332.493 / 2,3 / 0 / 3
EESEQIVLIGSKTNGK / 0.461 / 1732.928 / 3 / 0 / 4
EESEQIVLIGSKTNGKFLIR / -3.058 / 2262.611 / 3 / 3 / 1
EESEQIVLIGSKTNGKFLIRAR / 0.123 / 2489.877 / 3 / 1 / 3
ELGSGNFGTVK / -0.673 / 1109.224 / 3 / 2 / 4
ELGSGNFGTVKK / 0.832 / 1237.398 / 3 / 0 / 1
ELGSGNFGTVKKGYYQMK / -1.517 / 2008.299 / 3 / 2 / 2
EVYLDRK / 2.556 / 923.056 / 3 / 0 / 1
EVYLDRKLLTLEDKELGSGNFGTVK / -1.298 / 2826.219 / 3 / 4 / 1
FSSKSDVWSFGVLMWEAFSYGQKPYRGMK / 0.304 / 3420.928 / 3 / 0 / 1
GERMGCPAGCPR / -0.820 / 1234.451 / 3 / 0 / 2
GMKGSEVTAMLEKGER / -2.577 / 1724.000 / 3 / 0 / 1
GMKGSEVTAMLEKGERMGCPAGCPR / 1.463 / 2597.074 / 3 / 2 / 1
GSEVTAMLEK / -0.541 / 1065.226 / 2,3 / 0 / 6
GSEVTAMLEKGER / 1.291 / 1407.581 / 3 / 3 / 3
IDKDKTGKLSIPEGK / -0.942 / 1407.581 / 3 / 5 / 1
IKSYSFPKPGHR / 0.399 / 1407.581 / 3 / 3 / 7
ILKNEANDPALK / 0.957 / 1326.535 / 3 / 0 / 6
ILKNEANDPALKDELLAEANVMQQLDNPYIVR / -2.366 / 3640.146 / 3 / 1 / 1
ISDFGLSKALR / 0.512 / 1207.415 / 3 / 2 / 3
ISREESEQIVLIGSK / 0.544 / 1688.918 / 3 / 0 / 1
ISREESEQIVLIGSKTNGK / 0.396 / 2089.353 / 3 / 4 / 1
KAHHYTIER / 1.099 / 1155.301 / 3 / 2 / 1
KFDTLWQLVEHYSYK / 0.451 / 1958.223 / 3 / 0 / 5
KGYYQMKK / -0.271 / 1046.272 / 3 / 0 / 1
KGYYQMKKVVK / 0.815 / 1372.712 / 3 / 0 / 4
KLLTLEDKELGSGNFGTVK / 0.140 / 2050.359 / 2,3 / 3 / 7
KPFNRPQGVQPK / -0.658 / 1396.635 / 3 / 0 / 14
KPFNRPQGVQPKTGPFEDLKENLIR / 2.065 / 2910.348 / 3 / 0 / 1
KSSPAQGNR / 0.488 / 945.023 / 3 / 0 / 1
KVVKTVAVK / 1.274 / 972.259 / 3 / 0 / 11
KVVKTVAVKILK / 1.203 / 1326.752 / 2,3 / 1 / 6
LIATTAHEKMPWFHGK / 0.260 / 1868.206 / 3 / 0 / 1
LIATTAHEKMPWFHGKISR / -2.489 / 2224.631 / 3 / 3 / 1
LLTLEDK / -0.359 / 831.984 / 3 / 1 / 1
LLTLEDKELGSGNFGTVK / -0.417 / 1922.185 / 3 / 3 / 12
LLTLEDKELGSGNFGTVKK / 0.039 / 2050.359 / 3 / 3 / 8
LLTLEDKELGSGNFGTVKKGYYQMK / 1.073 / 2821.261 / 3 / 0 / 1
MASSGMADSANHLPFFFGNITR / 0.124 / 2372.678 / 3 / 3 / 6
MGCPAGCPR / 2.407 / 892.096 / 2 / 0 / 1
MIGICEAESWMLVMEMAELGPLNK / -1.550 / 2697.271 / 3 / 1 / 1
MPWFHGK / 2.524 / 903.089 / 3 / 0 / 1
MPWFHGKISREESEQIVLIGSKTNGK / 0.324 / 2973.419 / 3 / 0 / 1
NEANDPALK / -0.326 / 972.042 / 2 / 0 / 4
QESTVSFNPYEPELAPWAADKGPQR / 0.291 / 2819.059 / 3 / 0 / 17
QSRNYLGGFALSVAHGR / -2.811 / 1834.047 / 3 / 0 / 1
QSRNYLGGFALSVAHGRK / 0.654 / 1962.221 / 3 / 2 / 2
QSRNYLGGFALSVAHGRKAHHYTIER / -2.230 / 2970.326 / 3 / 0 / 1
QTWNLQGQALEQAIISQKPQLEK / 0.491 / 2653.010 / 3 / 0 / 12
TGKLSIPEGK / -0.038 / 1030.209 / 3 / 2 / 2
TGKLSIPEGKK / -1.123 / 1158.383 / 3 / 2 / 8
TGPFEDLK / 0.899 / 907.011 / 3 / 1 / 2
TGPFEDLKENLIR / 0.089 / 1532.736 / 3 / 1 / 3
TGPFEDLKENLIREYVK / -1.296 / 2052.334 / 3 / 2 / 3
THASPADLCHYHSQESDGLVCLLK / -0.375 / 2625.933 / 3 / 5 / 2
TNGKFLIR / -1.106 / 949.141 / 3 / 0 / 1
TVAVKILKNEANDPALK / -0.074 / 1825.158 / 3 / 1 / 1
VLHYRIDK / 2.328 / 1044.241 / 3 / 0 / 1
VVKTVAVK / -0.858 / 844.085 / 2 / 1 / 1
VVKTVAVKILK / -0.362 / 1198.578 / 3 / 0 / 2
VVKTVAVKILKNEANDPALK / 0.295 / 2151.598 / 3 / 1 / 4
WPVKWYAPECINYYK / -3.203 / 1961.288 / 3 / 0 / 1
WYAPECINYYK / -0.154 / 1450.651 / 3 / 3 / 2
YLEESNFVHRDLAAR / -1.140 / 1821.002 / 3 / 2 / 3
YLQQNRHVK / -2.045 / 1186.359 / 3 / 1 / 1

Supplementary Figure 1. The quantile plot of the log precursor intensity of the SYK binding proteins from Table I compared across affinity treatments where significant differences are shown by a different lower case letter as determined by the Tukey Kramer (HSD) test.

Df Sum Sq Mean Sq F value Pr(>F)

TreatmentName 25 5785 231.39 909.7 <2e-16 ***

Residuals 286713 72931 0.25

1_LARC_antiCD36_IgA 10_LARC_oxLDL_CONTROLS_RUNS_1_To_4
"j" "d"
11_LARC_UncoatedBeads_Extract 12_LARC_LIVE_CELLS_UNTREATED_BEADS
"kl" "c"
13_OXLDLReRuns 15_LARC_antiCD36_IgA_STYP
"b" "h"
16_LARC_antiCD36_IgA_CONTROLS_STYP 17_LARC_antiCD36_IgG_STYP
"f" "jk"
18_LARC_antiCD36_IgG_CONTROLS_STYP 19_LARC_oxLDL_Media_Beads_Blanks_STYP
"d" "a"
2_LARC_antiCD36_IgA_CONTROLS 20_LARC_IgG_STYP
"g" "c"
21_LARC_IgG_CONTROLS_STYP 22_LARC_IgG_Media_Beads_Blanks_STYP
"e" "a"
23_LARC_oxLDL__STYP 24_LARC_oxLDL_CONTROLS__STYP
"i" "c"
25_LARC_UncoatedBeads_Extract_STYP 26_LARC_LIVE_CELLS_UNTREATED_BEADS_STYP
"hi" "de"
27_OXLDLReRuns_STYP 3_LARC_antiCD36_IgG
"b" "l"
4_LARC_antiCD36_IgG_CONTROLS 5_LARC_oxLDL_Media_Beads_Blanks
"e" "b"
6_LARC_IgG 7_LARC_IgG_CONTROLS
"d" "f"
8_LARC_IgG_Media_Beads_Blanks 9_LARC_oxLDL_
"b" "k"

1