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Database NCBInr.2009.03.24 NCBInr.2009.03.24.random.concat NCBInr.2009.07.10 NCBInr.refseq.2009.09.14 NCBInr.refseq.2009.09.14.random SwissProt.2009.03.24 SwissProt.2009.03.24.random.concat SwissProt.2009.07.07 UniProtKB.2009.03.24 UniProtKB.2009.03.24.random.concat UniProtKB.2009.07.07 DNA Frame Translation 6 3 -3 1 -1 Taxonomy All HUMAN MOUSE HUMAN RODENT RODENT ROACH LOCUST BEETLE MICROORGANISMS ARABIDOPSIS THALIANA ARCHAEOGLOBUS FULGIDUS BACILLUS SUBTILIS BACULOVIRIDAE BORRELIA BURGDORFERI BOS TAURUS BOTHROPS INSULARIS BRASSICA BRUGIA MALAYI CAENORHABDITIS ELEGANS CANDIDA CANIS FAMILIARIS CAPRA HIRCUS CERCOPITHECUS AETHIOPS CHLAMYDIA TRACHOMATIS CHLAMYDOPHILA PNEUMONIAE DANIO RERIO DICTYOSTELIUM DISCOIDEUM DROSOPHILA MELANOGASTER EQUUS CABALLUS ESCHERICHIA COLI FELIS CATUS FRANCISELLA TULARENSIS GALLUS GALLUS GLYCINE MAX GREEN PLANTS GORILLA GORILLA HAEMOPHILUS HAEMOPHILUS INFLUENZAE HELICOBACTER PYLORI HOMO SAPIENS MACACA MAMMALS METHANOCOCCUS JANNASCHII HUMAN ADENOVIRUS 5 MUS MUSCULUS MYCOBACTERIUM MYCOPLASMA NEISSERIA ORYCTOLAGUS CUNICULUS ORYZA SATIVA OVIS ARIES PAN TROGLODYTES PSEUDOMONAS AERUGINOSA RATTUS NORVEGICUS SACCHAROMYCES SACCHAROMYCES CEREVISIAE SALMONELLA SCHIZOSACCHAROMYCES POMBE SHEWANELLA ONEIDENSIS SUS SCROFA SYNECHOCYSTIS TOXOPLASMA GONDII TREPONEMA PALLIDUM TRYPANOSOMA UNKNOWN UNREADABLE XENOPUS LAEVIS Output HTML XML Hits to file Name	Digest No enzyme Trypsin TrypsinPro SlymotrypsinFYWKR Chymotrypsin Chymotrypsin FYW ChymotrypsinFWYMEDLN V8 DE V8 E Lys-C Lys-N Arg-C Asp-N Asp-C DE-N CNBr Pepsin(porcine gastric) Glu-C Tyr-C Thermolysin Full Protein Pro-C CNBr/Trypsin CNBr/V8 DE CNBr/V8 E CNBr/Lys-C CNBr/Asp-N CNBr/Asp-C CNBr/Arg-C CNBr/V8 E CNBr/Trypsin/V8 DE CNBr/Trypsin/V8 E CNBr/Arg-C/V8 E CNBr/Lys-C/V8 E Trypsin/Asp-N Trypsin/DE-N Trypsin/V8 DE Trypsin/V8 E Trypsin/Glu-C Chymotrypsin/Arg-C Lys-C/Trypsin Lys-C/V8 DE Lys-C/V8 E Lys-C/Asp-N V8 DE/Chymotrypsin Arg-C/V8 E Non-Specific at 0 termini at 1 termini at 2 termini at N termini at C termini N termini-1=D Max. Missed Cleavages Constant Mods Acetohydrazide (C-term) Acetohydrazide (DE) Acetyl (K) Acetyl (N-term) Acetyl:2H(3) (K) Acetyl:2H(3) (N-term) Amidated (C-term) Amidated+iTRAQ8plex (C-term) Amino (Y) Asn->Succinimide (N) Biotin (N-term) Carbamidomethyl (C) Carbamidomethyl (N-term) Carbamyl (K) Carbamyl (N-term) Carboxy (W) Carboxymethyl (C) Cys->Dha (C) Deamidated (N) Deamidated (Q) Dehydrated (D) Dehydrated (ST) Dehydro (C) Delta:2H(6)C(3) (K) Delta:2H(6)C(3) (N-term) Delta:H(2)C(3) (K) Delta:H(4)C(3)O(1) (C) Delta:H(4)C(3)O(1) (CHK) Delta:H(4)C(6) (K) Delta:H(6)C(3) (K) Delta:H(6)C(3) (N-term) Delta:H(6)C(6)O(1) (K) Delta:H(8)C(6)O(2) (K) Dethiomethyl (M) Dimethyl (N-term) Dioxidation (M) Dioxidation (W) DTT_C (C) DTT_C:2H(6) (C) DTT_ST (ST) DTT_ST:2H(6) (ST) Formyl (K) Formyl (N-term) GirardT (N) GlyGly (C) GlyGly (N-term) GlyTyr (N-term) Guanidinyl (K) HexNAc (ST) HexNAcHex (ST) HexNAcHexSA (ST) Hydroxymethyl (CRWHKNQY) ICAT-C (C) ICAT-C:13C(9) (C) ICAT-D (C) ICAT-D:2H(8) (C) IDEnT (C) iTRAQ4plex (K) iTRAQ4plex (N-term) iTRAQ4plex (Y) iTRAQ8plex (K) iTRAQ8plex (N-term) Label:13C(6) (K) Label:13C(6) (L) Label:13C(6) (R) Label:13C(6)15N(1) (L) Label:13C(6)15N(2) (K) Label:13C(6)15N(2)+Carbamyl (K) Label:13C(6)15N(4) (R) Label:18O(1) (C-term) Label:18O(2) (C-term) Label:2H(3) (L) Methyl (C-term) Methyl (DE) Methyl (E) Methyl (H) Methyl (K) Methyl (R) Methyl:13C(1)2H(3) (C-term) Methyl:13C(1)2H(3) (DE) Methylthiol (C) Nethylmaleimide (C) Nitro (Y) Oxidation (M) Oxidation (P) Oxidation (PWY) Oxidation (W) Oxidation (Y) PEO-Iodoacetyl-LC-Biotin (C) Phospho (ST) Phospho (STY) Phospho (Y) Propionamide (C) Pyridylethyl (C) Quinone (W) SerTyr (N-term) SerTyr+iTRAQ (N-term) SerTyrLys(OAc) (N-term) SerTyrLys(OAcs) (N-term) Sulfo (Y) TMT (K) TMT (N-term) TMT2plex (K) TMT2plex (N-term) TMT6plex (K) TMT6plex (N-term) Trioxidation (C) Trp->Hydroxykynurenin (W) Trp->Kynurenin (W) Xlink:BSSA1 (N-term) Xlink:BSSA2 (N-term) Xlink:DSS1 (N-term) Xlink:DSS2 (N-term) Xlink:FCXL1-1 (N-term) Xlink:FCXL1-2 (N-term)
[-] Pre-Search Parameters Protein MW (Da) to All Protein pI to All Hits From msfit mspattern mshomology mstag msseq Name Remove Selected Taxonomy Taxonomy Names Accession Numbers Names Additional Accession Numbers
	Sample ID (comment) Maximum Reported Hits Expectation Calc Method None Linear Tail Fit
Variable Mods Acetohydrazide (C-term) Acetohydrazide (DE) Acetyl (K) Acetyl (Protein N-term) Acetyl+Oxidation (Protein N-term M) Acetyl:2H(3) (K) Acetyl:2H(3) (N-term) Amidated (C-term) Amidated+iTRAQ8plex (C-term) Amino (Y) Asn->Succinimide (N) Biotin (N-term) Biotin (Uncleaved K) Carbamidomethyl (C) Carbamidomethyl (N-term) Carbamidomethyl (Uncleaved DEHKM) Carbamidomethyl (Uncleaved HKM) Carbamyl (K) Carbamyl (N-term) Carboxy (W) Carboxymethyl (C) Cation:N(1)H(4) (Neutral loss) Cys->Dha (C) Deamidated (N) Deamidated (Q) Dehydrated (D) Dehydrated (ST) Dehydro (C) Delta:2H(6)C(3) (K) Delta:2H(6)C(3) (N-term) Delta:H(2)C(3) (K) Delta:H(4)C(3)O(1) (C) Delta:H(4)C(3)O(1) (CHK) Delta:H(4)C(6) (K) Delta:H(6)C(3) (K) Delta:H(6)C(3) (N-term) Delta:H(6)C(6)O(1) (K) Delta:H(8)C(6)O(2) (K) Dethiomethyl (M) Dimethyl (N-term) Dimethyl (Uncleaved K) Dimethyl (Uncleaved R) Dioxidation (M) Dioxidation (W) Disuccinyl (Uncleaved K) DTT_C (C) DTT_C:2H(6) (C) DTT_ST (ST) DTT_ST:2H(6) (ST) Formyl (K) Formyl (N-term) GirardT (N) Gln->pyro-Glu (N-term Q) Glu->pyro-Glu (N-term E) GluGlnIleGlyGly (Uncleaved K) GlyGly (C) GlyGly (N-term) GlyGly (Uncleaved K) GlyTyr (N-term) Guanidinyl (K) HexNAc (ST) HexNAcHex (ST) HexNAcHexSA (ST) HNE (Uncleaved CHKPRT) HNE+Delta:H(2) (Uncleaved CHKPRT) HNE-Delta:H(2)O (Uncleaved CHKPRT) Hydroxymethyl (CRWHKNQY) ICAT-C (C) ICAT-C:13C(9) (C) ICAT-D (C) ICAT-D:2H(8) (C) IDEnT (C) iTRAQ4plex (K) iTRAQ4plex (N-term) iTRAQ4plex (Y) iTRAQ8plex (K) iTRAQ8plex (N-term) Label:13C(6) (K) Label:13C(6) (L) Label:13C(6) (R) Label:13C(6)+GlyGly (Uncleaved K) Label:13C(6)15N(1) (L) Label:13C(6)15N(2) (K) Label:13C(6)15N(2)+Carbamyl (K) Label:13C(6)15N(2)+GluGlnIleGlyGly (Uncleaved K) Label:13C(6)15N(2)+GlyGly (Uncleaved K) Label:13C(6)15N(4) (R) Label:18O(1) (C-term) Label:18O(2) (C-term) Label:2H(3) (L) LeuArgGlyGly (Uncleaved K) Met->Hsl (C-term M) Met-loss (Protein N-term M) Met-loss+Acetyl (Protein N-term M) Met-loss+Myristoyl (Protein N-term M) Methyl (C-term) Methyl (DE) Methyl (E) Methyl (H) Methyl (K) Methyl (R) Methyl:13C(1)2H(3) (C-term) Methyl:13C(1)2H(3) (DE) Methylthiol (C) Myristoyl (N-term G) Myristoyl (Uncleaved KR) Nethylmaleimide (C) NHS-LC-Biotin (Uncleaved K) Nitro (Y) Oxidation (M) Oxidation (P) Oxidation (PWY) Oxidation (W) Oxidation (Y) PEO-Iodoacetyl-LC-Biotin (C) Phospho (ST) Phospho (STY) Phospho (Y) Propionamide (C) PyridoxalPhosphate (Uncleaved K) Pyridylethyl (C) Quinone (W) SerTyr (N-term) SerTyr+iTRAQ (N-term) SerTyrLys(OAc) (N-term) SerTyrLys(OAcs) (N-term) Succinyl (Uncleaved K) Sulfo (Y) TMT (K) TMT (N-term) TMT2plex (K) TMT2plex (N-term) TMT6plex (K) TMT6plex (N-term) TriMethyl (Uncleaved K) Trioxidation (C) Trisuccinyl (Uncleaved K) Trp->Hydroxykynurenin (W) Trp->Kynurenin (W) Xlink:BSSA1 (Protein N-term) Xlink:BSSA1 (Uncleaved K) Xlink:BSSA2 (Protein N-term) Xlink:BSSA2 (Uncleaved K) Xlink:DSA1 (Uncleaved K) Xlink:DSA2 (Uncleaved K) Xlink:DSS1 (Protein N-term) Xlink:DSS1 (Uncleaved K) Xlink:DSS2 (Protein N-term) Xlink:DSS2 (Uncleaved K) Xlink:FCXL1-1 (Protein N-term) Xlink:FCXL1-1 (Uncleaved K) Xlink:FCXL1-2 (Protein N-term) Xlink:FCXL1-2 (Uncleaved K) Max Mods [-] Mass Modifications Range (Da) to Defect A C D E F G H I K L M N P Q R S T V W Y Peptide Protein N Term Peptide Protein C Term Neutral Loss Uncleaved [-] Matrix Modifications Unknown Amino Acid Single Base Change Homology	Precursor Charge 8 7 6 5 4 3 2 1 Automatic Masses are monoisotopic average Par(mi)Frag(av) Par(av)Frag(mi) Parent Tol Da % ppm mmu Sys Err Frag Tol Da % ppm mmu
[-] Instrument Ion Types Use instrument specific defaults to override ion types below AA Composition N-term C-term Satellite Sequence (side-chain loss) Neutral-loss (from ions also selected) Internal Fragment Ladder Sequencing i a b b+H2O RHK c+2 c+1 c c-1 x y Y z z+1 z+2 z+3 d v w -NH3 RKQN -H2O STED -H3PO4 STY+PO4 -SOCH4 M+Ox Internal N-term C-term
[-] Composition Ions AA Composition (based on immonium and related ions) 60 S 70 R,P 72 V 74 T 86 L,I 87 N,R 88 D 84,101,129 K,Q 102 E 104 M 110 H 120 F 126 P 136 Y 117,130,159,170 W 70,73,87,100,112,185 R AA Composition (based on loss from parent ion) -SRH,-R C (select modified Cys) -80 PO4 - S,T,Y (homology) -98 PO4 - S,T (homology) -64 Mso (homology) -17 R   Note: For ions with multiple residues (i.e. 86: means I or L). Note: Requires presence of at least one AA for each composition ion selected.
Instrument ESI-Q-TOF ESI-ION-TRAP-low-res ESI-FT-ICR-CID ESI-FT-ICR-ECD ESI-ETD-low-res MALDI-Q-TOF MALDI-TOFTOF Data Format PP M/Z Charge PP M/Z Intensity Charge mgf pkl dta Data Paste Area 1784.8375 60.0260 70.0468 84.0637 86.0800 87.0435 102.0332 112.0623 120.0685 129.0865 136.0690 157.0753 158.0879 159.0808 175.1034 185.0819 202.0876 217.1499 233.1270 234.1454 240.1426 245.1380 250.1414 258.1417 261.1298 262.1239 272.1949 278.1367 300.1896 320.1692 358.2232 365.1832 391.1774 392.1980 417.1967 434.2274 462.2164 479.2096 486.3239 543.3594 544.3416 545.3406 598.3135 599.4026 609.2665 626.2820 658.4249 859.5782 900.5853 902.5632 1013.6333 1030.6641 1084.7102 1159.7124 1306.7697 1403.8115

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