TABLE 1. LIST OF ALL PROTEINS IDENTIFIED SORTED BY GENE NAME Membrane Probability Accession GI Number Protein Name Entrez Gene Name # of Expts Peptides Fraction score number SV 0.82 10947122 NP_064693.1 ATP-binding cassette, sub-family C, member 9 isoform SUR2B ABCC9 1 EVQM[147]GAVKK SSILIMDEATASIDMATENILQK PM 0.99 21431817 P49597 Protein phosphatase 2C ABI1 (PP2C) (Abscisic acid-insensitive 1) ABI1 1 KEGKDPAAM[147]SAAEYLSK KEGKDPAAMSAAEYLSK PM 0.82 231504 P30172 ACTIN 100,ACTIN 101 AC100 1 AVFPSIVGRPR AGFAGDDAPR VSPDEHPVLLTEAPLNPK SV 1 4501853 NP_001598.1 acetyl-Coenzyme A acyltransferase 1 ACAA1 1 SITVTQDEGIRPSTTMEGLAK PM 0.86 4501855 NP_001084.1 acetyl-Coenzyme A carboxylase beta ACACB 1 VIQVENSHIILTGASALNK M[147]TVPISITNPDLLR MTVPISITNPDLLR EAISNMVVALK SV 0.75 38505218 NP_115545.3 putative acyl-CoA dehydrogenase ACAD11 1 QHSMILVPMNTPGVK QHSM[147]ILVPM[147]NTPGVK PM 1 113018 P08503 Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial precursor (MCAD) ACADM 1 VPKENVLIGEGAGFK PM 0.99 4557237 NP_000010.1 acetyl-Coenzyme A acetyltransferase 1 precursor ACAT1 1 DGLTDVYNK SV 0.89 9998948 NP_064718.1 amiloride-sensitive cation channel 3 isoform c ACCN3 1 DNEETPFEVGIR PM 1 7662238 NP_055792.1 apoptotic chromatin condensation inducer 1 ACIN1 1 VDRPSETKTEEQGIPR CEAEEAEPPAATQPQTSETQTSHL SV 0.76 30089972 NP_004026.2 acyl-coenzyme A oxidase 1 ACOX1 1 EIGTHKPLPGITVGDIGPK TSNHAIVLAQLITK PM 1 16445033 NP_443189.1 ACRC protein; putative nuclear protein ACRC 1 FAKIQIGLKVCDSADR SV 0.93 27477105 NP_055977.3 lipidosin ACSBG1 1 EVEPTSHMGVPR MELPIISNAM[147]LIGDQR PM 0.7 3182886 O18499 ACTIN 1 ACT1 1 IKIIAPPER AGFAGDDAPR GYSFTTTAER QEYDESGPSIVHR AIFPSIVGRPR QEYDESGPSIVHR PM 0.85 113242 P14883 ACTIN II ACT2 1 EEYEDSGPSIVHR VSPEEHPVLLTEAPLNPK PM 1 4501881 NP_001091.1 alpha 1 actin precursor ACTA1 1 EITALAPSTMK AGFAGDDAPR PM+SV 1 4501883 NP_001604.1 alpha 2 actin ACTA2 2 IIAPPERKVAPEEHPTLLTEAPLNPK DSYVGDEAQSK DSYVGDEAQSKR YPIEHGIITNWDDMEK AGFAGDDAPR SYELPDGQVITIGNER EITALAPSTMK VGDEAQSK YPIEHGIITNWDDM[147]EK MQKEITALAPSTMK HQGVMVGMGQKDSYVGDEAQSK M[147]QKEITALAPSTM[147]K AVFPSIVGRPR M[147]QKEITALAPSTMK SGGTTMYPGIADR MQKEITALAPSTM[147]K VAPEEHPTLLTEAPLNPK PM+SV 1 4501885 NP_001092.1 beta cytoskeletal actin ACTB 2 IIAPPERKVAPEEHPVLLTEAPLNPK GYSFTTTAER DSYVGDEAQSK DSYVGDEAQSKR AGFAGDDAPR SYELPDGQVITIGNER EITALAPSTMK VGDEAQSK MQKEITALAPSTMK HQGVMVGMGQKDSYVGDEAQSK M[147]QKEITALAPSTM[147]K AVFPSIVGRPR M[147]QKEITALAPSTMK SGGTTMYPGIADR SFTTTAEREIVR MQKEITALAPSTM[147]K VAPEEHPVLLTEAPLNPK PM+SV 1 4501887 NP_001605.1 actin, gamma 1 propeptide ACTG1 4 EITALAPSEITALAPSGILTLK IIAPPERK AVFPSIVGRPR MQKEITALAPSTMK SYELPDGQVITIGNER GYSFTTTAER AGFAGDDAPR M[147]QKEITALAPSTM[147]K M[147]QKEITALAPSTMK IKIIAPPERK IKIIAPPER ALPHAILR SYELPDGQVITIGNER TTGIVMDSGDGVTHTVPIYEGY AVFPSIVGRPR QEYDESGPSIVHR DSYVGDEAQSK EITALAPSTM[147]K GILTLK IIAPPERK PM 0.74 113284 Q00214 ACTIN, MUSCLE ACTM 1 QEYDESGPSIVHR AVFPLTVGRPR EITALAPSTMKSK PM+SV 1 4501891 NP_001093.1 actinin, alpha 1 ACTN1 3 TINEVENQILTRDAK LAILGIHNEVSK TINEVENQILTR YLDIPK DYETATLSEIK MLDAEDIVGTARPDEK GISQEQMNEFR PM+SV 1 12025678 NP_004915.2 actinin, alpha 4 ACTN4 1 TINEVENQILTRDAK GISQEQMQEFR MLDAEDIVNTARPDEK SV 1 5031573 NP_005712.1 ARP3 actin-related protein 3 homolog ACTR3 1 DREVGIPPEQSLETAK PM 0.75 47078295 NP_000013.2 adenosine deaminase ADA 1 RLNINAAKSSFLPEDEK SV 1 4557253 NP_001100.1 ADAM 8; a disintegrin and metalloproteinase domain 8 precursor ADAM8 1 GPQELVPTTHPGQPAR PM 0.99 8923417 NP_060295.1 hypothetical protein FLJ20446 ADPRHL2 1 GGDTDTIATM[147]AGAIAGAYYGM[147]DQVPESW SV 0.82 4501967 NP_000674.1 alpha-2C-adrenergic receptor; alpha2-AR-C4 ADRA2C 1 M[147]ASPALAAALAVAAAAGPNASGAGER PM 0.97 416590 P32794 AFG2 protein AFG2 1 VVVIAATNRPNSVDPALR SV 0.65 31377758 NP_060127.2 aftiphilin protein isoform 1 AFTPH 1 AWSLVDSADNSEAIR PPV PM 0.92 20140221 Q9BSE5 Agmatinase, mitochondrial precursor (AUH) AGMAT 1 GPGPGVGARPAAGLFHPGRR PM 0.78 4501993 NP_003650.1 alkylglycerone phosphate synthase precursor AGPS 1 TTSKASLNPSDTPPSVVNEDF PM 0.9 41151826 XP_372195.1 PREDICTED: agrin AGRIN 1 GPAGCEADASAPATCAEM[147]RCEFGAR FGALCEAETGR PM 0.93 7662452 NP_056054.1 ATP\GTP binding protein 1 AGTPBP1 1 GPIVVPTAGEGTSGNSGNLR PM 0.99 10947054 NP_066187.1 ankyrin 2 isoform 2 AHK2 1 GDDMPEIPPETVTEEEYIDEHGHTVVK PM 1 7706457 NP_057332.1 A-kinase anchor protein 11 isoform 1 AKAP11 1 NVIPDTPPSTPLVPSRASSEW PM 0.75 21493045 NP_004265.3 A-kinase anchor protein 6 AKAP6 1 RVSENNGNGK PM 0.91 21431604 Q9ULX6 Neighbor of A-kinase anchoring protein 95 (Homologous to AKAP95) AKAP8L 1 GIPGLDVEDDEEGGGGAP PM+SV 0.91 4502027 NP_000468.1 serum albumin precursor ALB 4 DLGEENFK KVPQVSTPTLVEVSR AEFAEVSK QTALVELVK LVAASQAALGL VPQVSTPTLVEVSR LVNEVTEFAK LVTDLTK RDAHKSEVAHR SEVAHR TPVSDR SV 1 23503239 NP_699160.1 ALDEHYDE DEHYDROGENASE 16 FAMILY MEMBER A1 ALDH16A1 1 GAVEAAHQAFPGWAGQSPGAR SV 1 4557305 NP_000025.1 aldolase A ALDOA 1 ADDGRPFPQVIK IGEHTPSALAIMENANVLAR IVAPGKGILAADESTGSIAK ELSDIAHRIVAPGK GILAADESTGSIAKR SV 0.85 40354205 NP_000026.2 aldolase B ALDOB 1 LDQGGAPLAGTNK SV 0.9 27436959 NP_055935.2 ALMS1 ALMS1 1 TGTPTVSSNSHSHSEK PM+SV 0.65 15718675 NP_001620.2 arachidonate 5-lipoxygenase-activating protein ALOX5AP 3 TQSTPGYIFGK TGTLAFER PM 0.97 10198656 NP_065434.1 anti-Mullerian hormone receptor, type II AMHR2 1 AQVEMQGCRDSDEPGCESLHCDPSPR PM 0.68 22027646 NP_570899.1 angiomotin like 1 AMOTL1 1 PCQLPFPSTM[147]QQHSPM[147]SSQTSSASGPL PM 0.87 33302598 O76262 Alpha-amylase-related protein precursor AMYREL 1 DMGSVLNYKSPRQYK SV 0.99 10947036 NP_065208.1 ankyrin 1 isoform 4 ANK1 1 ELQFSVEDINR ISEILLDHGAPIQAK PM 0.92 32967599 NP_001140.2 ankyrin 3 isoform 2 ANK3 1 LIIEETKPCVPVSM[147]K PM 0.9 51466429 XP_380018.2 ankyrin repeat and IBR domain containing 1 ANKIB1 1 EENILAGEAASQAGDSGNEAANR FHDMNPQSIALIPPATTEISADSQL SV 0.82 38683807 NP_115593.3 ankyrin repeat domain protein 17 isoform a ANKRD17 1 SSSANSKIGSSAPTTTAANTSLM[147]GIK TDEM[147]HTALMEACM[147]DGHVEVAR KSDNHSPAVVTTTVSSK VIGRGGCNINAIR PM 0.72 24233530 NP_710181.1 ankyrin repeat domain 44 ANKRD44 1 SEEAVQVLIKHSADVNAR PM 0.67 41195096 XP_048747.4 ankyrin repeat domain 50 ANKRD50 1 MLAMSYTCQAK STKASKGGK PM+SV 0.88 4502095 NP_001141.1 aminopeptidase N ANPEP 4 AQIINDAFNLASAHK DNEETGFGSGTR DHSAIPVINR ALEQALEK VVATTQM[147]QAADAR NLASAHK SIQLPTTVR EATDVIIIHSK SV 1 4502101 NP_000691.1 annexin I (lipocortin I) ANXA1 1 TPAQFDADELR GVDEATIIDILTKR SV 0.97 22165433 NP_665876.1 annexin A11; annexin XI ANXA11 1 DAQELYAAGENR GVGTDEACLIEILASR PM 0.8 4502111 NP_001147.1 annexin VII isoform 1 ANXA7 1 GFGTDEQAIVDVVANRSNDQR PM 1 14210504 NP_115882.1 clathrin coat assembly protein AP47 AP1M1 1 ELEEESIR LETGAPR PM 1 22035548 NP_001154.2 amyloid beta A4 precursor protein-binding, family A, member 1 APBA1 1 QAPAGQQRAVGPAGGGEAGQRY SV 0.68 22035550 NP_005494.2 amyloid beta A4 precursor protein-binding, family A, member 2 APBA2 1 IIEINGQSVVATAHEK PM 0.76 5031587 NP_005874.1 adenomatosis polyposis coli 2 APC2 2 GLGVEDATPSSSSENYVQETPL AIQEGANSIVTWLHQAAAATR VAAPGTTWR M[147]IAM[147]GSAAALR GVEDATPSSSSENYVQETPLVL PM 0.82 4885065 NP_005157.1 amyloid beta (A4) precursor-like protein 1 APLP1 1 RGVEYVCCPPPGTPDPSGTAVGDPSTR PM 0.8 24211473 Q9D7N9 Adipocyte plasma membrane-associated protein (Protein DD16) APMAP 1 VVKLENGEIETIAR PM 0.86 4502153 NP_000375.1 apolipoprotein B precursor; apoB-100; apoB-48 APOB 2 QANAQLSNPK HKLIDVISMYRELLK PM+SV 1 8922079 NP_061160.1 apolipoprotein B48 receptor APOB48R 2 QAQVLGTERTEEAAESQTAGR GAESEWTWHGETEGK PM+SV 0.91 4557325 NP_000032.1 apolipoprotein E3 APOE 2 GEVQAMLGQSTEELR SV 0.72 40548322 NP_954976.1 similar to Rho GTPase activating protein 12 ARHGAP27 1 VIEHGEQNRMSVQSVAIVF SV 0.89 10835002 NP_001166.1 Rho GDP dissociation inhibitor (GDI) beta ARHGDIB 1 TLLGDGPVVTDPK PM 1 21264565 NP_006006.3 AT rich interactive domain 1A (SWI- like) isoform a ARID1A 1 SPGVSTSGISSSQGEQSNPAQSPFSPHTSPHL PM+SV 0.93 22035679 NP_112739.2 AT rich interactive domain 4B (RBP1- like) isoform 2 ARID4B 3 GTNSSDSEELSAGESITK GTNSSDSEELSAGESITK PM 1 5453704 NP_006398.1 ADP-ribosylation-like factor 6 interacting protein 5 ARL6IP5 1 TPMGIVLDALEQQEEGINR SV 0.82 8922601 NP_060654.1 ADP-ribosylation factor-like 10C ARL8B 1 IWDIGGQPR GVNAIVYM[147]IDAADR GVNAIVYMIDAADR PM 1 5174393 NP_006001.1 arginine-rich protein ARMET 1 DVTFSPATIENELIK SV 0.94 5031601 NP_005711.1 actin related protein 2\3 complex subunit 1B ARPC1B 1 CSQFCTTGMDGGM[147]SIWDVK ASSEGGTAAGAGLDSLHK SV 1 13569956 NP_112240.1 actin related protein 2\3 complex, subunit 5 ARPC5L 1 PTENSSAVLLQWHEK PM 0.89 40217847 NP_054733.2 U5 snRNP-specific protein, 200-KD ASCC3L1 2 EEASDDDM[147]EGDEAVVR PM 0.76 26080431 NP_079133.3 chromosome fragility associated gene 1 ATAD5 2 GIDSDDVQDNSQLK SGYISESENSEISQQVR STNATNSNVKDVGAEEPSR ITGPTGVGKTAAVYACAQEL MVGVLAMAAAAAPPPVK DVGAEEPSR KLNTSTK QMENTTSHANSR NNSSGIK AESEASLLNVSTPK PM 1 19923287 NP_008816.2 AT-binding transcription factor 1 ATBF1 1 SVLHQTK QSPTGSDSGSVQEDSGSEPK PM 0.99 51468832 XP_058426.7 ATG16 autophagy related 16-like 2 ATG16L2 1 ESAAMAGPGVPGAPAAR GPHCTQVIPVQGR PM 0.82 17370591 Q9GKS6 Potential phospholipid-transporting ATPase VD ATP10D 1 DVSAETLM[147]QLPELYK PM 0.85 51471472 XP_085028.4 ATPase, Class VI, type 11A isoform a ATP11A 1 YPDNR TGTLTENNM[147]EFK NSDYAIPK PM 0.81 22748667 NP_689509.1 Na+\K+ -ATPase alpha 3 subunit ATP1A3 1 GVGIISEGNETVEDIAAR PM 0.96 4502281 NP_001670.1 Na+\K+ -ATPase beta 3 subunit ATP1B3 1 IIGLKPEGVPR SV 1 28373105 NP_777613.1 sarco\endoplasmic reticulum Ca2+ -ATPase isoform e ATP2A3 1 HFSVTAEGGLSPAQVTGAR AVGVAVATGLHTELGK PM 0.79 4502287 NP_001673.1 ATPase, Ca++ transporting, plasma membrane 1 ATP2B1 1 GGQVIQIPVADITVGDIAQVK