Supplementary Table 2: Overview of all experiments grouped by developmental stage or cell line. Abbreviations: UC Ultracentrifugation; SCX Strong cation exchange chromatography (60 fractions) after tryptic digestion; PepFFE Free Flow Electrophoresis of peptides after tryptic digestion; PepIEF Iso Electric Focussing of peptides after tryptic digestion; ProtFFE Free Flow Electrophoresis of proteins; I cleavable ICAT; Io ICAT d0d8 isotope coded; CHCl3 Sequential extraction of proteins using chloroform. LC-MS/MS analyses were performed on a) a LTQ linear iontrap from Thermo; b) a LTQ-FT (Thermo); c) LCQ classic (Thermo). *) see also 27. 1) We use the term “sum of distinct” to refer to the total number of different peptide or protein sequences that were identified after a given number of experiments. 2) We use the term “sum of redundant” to refer to the total number of peptide or protein sequences (including multiple identifications) after a given number of experiments. 3) The term “sum of overall redundant” indicates peptide redundancy after a given number of experiments, and includes redundancy within an experiment. #) used for genomic database searches.
Protein Summary / Peptide SummaryExpGroup / Developmental Stage/ Tissue / Biochemical Fractionation / # MS runs (instrument) / sum of distinct1 proteins / sum of redund.2 proteins / sum of distinct1 peptides / sum of redund.2 peptides / sum of OVERALL red. 3 pep hits
embryo / >2h AEL; whole embryo / SCX; I / 62(a) / 2606 / 0 / 6591 / 0 / 15398
embryo / 0-24 h AEL; nuclear extract* / SDS PAGE, Pep IEF / 18(b) / 3027 / 3892 / 9383 / 10202 / 22340
embryo / 0-24 h AEL; nuclear extract* / SDS PAGE, Pep IEF / 42(a) / 3856 / 6398 / 16296 / 20393 / 42571
larvae / Fatbodies sucrose vs Normal / SCX; I / 74(a) / 4715 / 8834 / 20801 / 27084 / 57187
larvae / Fatbodies rapamycin vs Normal / SCX; I / 85(a) / 4965 / 10724 / 22199 / 31785 / 72954
larvae / Heamolymph / SCX; I / 22(a) / 5026 / 11153 / 22539 / 32620 / 76457
larvae / Total larval extract / IPG-strip pH3.8-4.9 / 72(a) / 5042 / 11512 / 22677 / 33085 / 77137
larvae# / ProtFFE / ProtFFE / 10(a) / 5063 / 11696 / 22752 / 33347 / 77510
larvae / brain, salivary glands gland / manual dissection / 5(a) / 5134 / 12530 / 23206 / 35021 / 80664
larvae / Total larval extract / PepFFE; I / 48(a) / 5273 / 13291 / 24104 / 36498 / 85261
larvae / Total larval extract / PepFFE; I / 47(a) / 5348 / 13941 / 24448 / 37814 / 88892
larvae / membranes / Hypotonic lysis; UC; SCX; I / 97(a) / 5637 / 15731 / 26132 / 41334 / 98004
larvae / Total larval extract / ProtFFE / 50(a) / 5870 / 17170 / 28622 / 46263 / 123508
larvae / Total larval extract / ProtFFE / 45(a) / 6040 / 18676 / 29908 / 51592 / 152949
Pupae# / mem; Hypotonic lysis; UC / SCX; I / 81(a) / 6563 / 21775 / 34595 / 60775 / 170905
adult / cytoplasm / Hypotonic lysis; UC; SCX; I / 16(a) / 6734 / 23106 / 35808 / 64053 / 179328
adult / cytoplasm / Hypotonic lysis; UC; SCX; I / 51(a) / 6866 / 25039 / 37171 / 70295 / 194755
adult / cytoplasm / Hypotonic lysis; UC; SCX; I / 36(a) / 6909 / 26019 / 37704 / 72085 / 197266
adult / cytoplasm / Hypotonic lysis; UC; SCX; I / 10(a) / 6943 / 26856 / 38076 / 73742 / 202465
adult / cytoplasm / Hypotonic lysis; UC; SCX; I / 82(a) / 6967 / 28932 / 38208 / 80677 / 218751
adult / Heamolymph / SCX; I / 75(a) / 7037 / 29539 / 38519 / 81916 / 221416
adult / Total extract from adult flies / CHCl3 extraction / 5(a) / 7042 / 29608 / 38543 / 82007 / 221552
adult# / insoluble / Hypotonic lysis; SCX; I / 60(a) / 7160 / 31190 / 39660 / 86123 / 229210
adult / membranes / Hypotonic lysis; UC; SCX; I / 37(a) / 7425 / 33602 / 42087 / 93057 / 241447
adult / membranes / Hypotonic lysis; UC; SCX; I / 95(a) / 7671 / 35650 / 44131 / 97996 / 252413
kc / autophag. mem / gradient centrifugation; OPT / 5(a) / 7694 / 36090 / 44474 / 98675 / 254109
kc / membranes / Hypotonic lysis; UC / 4(a) / 7718 / 36254 / 44652 / 98925 / 254980
kc / membranes / Hypotonic lysis; UC; SCX; I / 46(a) / 7988 / 38826 / 47374 / 107209 / 286306
kc / Golgi / Golgi / 5(a) / 8007 / 39496 / 47670 / 108926 / 289705
kc / total extract / gelfiltration / 10(a) / 8068 / 40690 / 48413 / 112444 / 300483
kc / chromatin / SCX; I / 89(a) / 8369 / 44336 / 54637 / 127396 / 333676
s2# / cytoplasma / Hypotonic lysis; UC; SCX; Io / 30(c) / 8383 / 44985 / 55121 / 128684 / 336866
s2 / cytoplasma / Hypotonic lysis; UC; SCX; I / 22(a) / 8428 / 46317 / 56153 / 131144 / 345588
s2# / cytoplasma / Hypotonic lysis; UC; SCX; I / 85(a) / 8720 / 50159 / 62286 / 148223 / 381830
s2 / cytoplasma / Hypotonic lysis; UC; IPG strips / 9(c) / 8722 / 50247 / 62294 / 148346 / 382054
s2 / cytoplasma; +/- insulin / Hypotonic lysis; UC; SCX; Io / 28(c) / 8724 / 50306 / 62305 / 148427 / 382152
s2 / cytoplasma / PepFFE / 23(a) / 8806 / 52318 / 64189 / 155856 / 418204
s2 / total lysate / size exclusion centrifugation / 2(a) / 8822 / 52890 / 64407 / 156829 / 419328
s2# / nuclei / Hypotonic lysis; SCX; Io / 44(c) / 8852 / 54051 / 65375 / 159233 / 427052
s2 / nuclei / Hypotonic lysis; SCX; I / 42(a) / 8948 / 57306 / 67984 / 170615 / 447240
s2 / nuclei / PepFFE / 30(a) / 8982 / 59577 / 69367 / 177947 / 463236
s2# / membranes / Hypotonic lysis; UC; SCX; Io / 21(c) / 8999 / 60505 / 69823 / 179807 / 468454
s2 / membranes / Hypotonic lysis; UC; SCX; I / 50(a) / 9124 / 63996 / 72282 / 192307 / 498587
Table 2