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emowse |
Given a one-per-line file of molecular weights cut by enzymes/reagents, emowse will search a protein database for matches with the mass spectrometry data.
One of eight cutting enzymes/reagents can be specified and an optional whole sequence molecular weight.
Determination of molecular weight has always been an important aspect of the characterization of biological molecules. Protein molecular weight data, historically obtained by SDS gel electrophoresis or gel permeation chromatography, has been used establish purity, detect post-translational modification (such as phosphorylation or glycosylation) and aid identification. Until just over a decade ago, mass spectrometric techniques were typically limited to relatively small biomolecules, as proteins and nucleic acids were too large and fragile to withstand the harsh physical processes required to induce ionization. This began to change with the development of 'soft' ionization methods such as fast atom bombardment (FAB)[1], electrospray ionisation (ESI) [2,3] and matrix-assisted laser desorption ionisation (MALDI)[4], which can effect the efficient transition of large macromolecules from solution or solid crystalline state into intact, naked molecular ions in the gas phase. As an added bonus to the protein chemist, sample handling requirements are minimal and the amounts required for MS analysis are in the same range, or less, than existing analytical methods.
As well as providing accurate mass information for intact proteins, such techniques have been routinely used to produce accurate peptide molecular weight 'fingerprint' maps following digestion of known proteins with specific proteases. Such maps have been used to confirm protein sequences (allowing the detection of errors of translation, mutation or insertion), characterise post-translational modifications or processing events and assign disulphide bonds [5,6].
Less well appreciated, however, is the extent to which such peptide mass information can provide a 'fingerprint' signature sufficiently discriminating to allow for the unique and rapid identification of unknown sample proteins, independent of other analytical methods such as protein sequence analysis.
Practical experience has shown that sample proteins can be uniquely identified using as few as 3- 4 experimentally determined peptide masses when screened against a fragment database derived from over 50,000 proteins. Experimental errors of a few Daltons are tolerated by the scoring algorithms, permitting the use of inexpensive time-of-flight mass spectrometers. As with other types of physical data, such as amino acid composition or linear sequence, peptide masses can clearly provide a set of determinants sufficiently unique to identify or match unknown sample proteins. Peptide mass fingerprints can prove as discriminating as linear peptide sequence, but can be obtained in a fraction of the time using less material. In many cases, this allows for a rapid identification of a sample protein before committing to protein sequence analysis. Fragment masses also provide structural information, at the protein level, fully complementary to large-scale DNA sequencing or mapping projects [7,8,9].
For each entry in the specified set of sequences to search, emowse derives both whole sequence molecular weight and calculated peptide molecular weights for complete digests using the range of cleavage reagents and rules detailed in Table 1. Cleavage is disallowed if the target residue is followed by proline (except for CNBr or Asp N). Glu C (S. aureus V8 protease) cleavages are also inhibited if the adjacent residue is glutamic acid. Peptide mass calculations are based entirely on the linear sequence and use the average isotopic masses of amide-bonded amino acid residues (IUPAC 1987 relative atomic masses). To allow for N-terminal hydrogen and C-terminal hydroxyl the final calculated molecular weight of a peptide of N residues is given by the equation:
N __ \ / Residue mass + 18.0153 -- n=1Molecular weights are rounded to the nearest integer value before being used. Cysteine residues are calculated as the free thiol, anticipating that samples are reduced prior to mass analysis. CNBr fragments are calculated as the homoserine lactone form. Information relating to post- translational modification (phosphorylation, glycosylation etc.) is not incorporated into calculation of peptide masses.
Reagent no. Reagent Cleavage rule 1 Trypsin C-term to K/R 2 Lys-C C-term to K 3 Arg-C C-term to R 4 Asp-N N-term to D 5 V8-bicarb C-term to E 6 V8-phosph C-term to E/D 7 Chymotrypsin C-term to F/W/Y/L/M 8 CNBr C-term to M
Current versions of emowse also incorporate calculated peptide Mw's resulting from incomplete or partial cleavages. At present, this is achieved by computing all nearest-neighbour pairs for each enzyme or reagent detailed in table 1.
Computing all possible nearest-neighbour partial fragments adds significantly to the number of peptides entered in the database (by a factor of two). The major effect of this is to increase the background score by increasing the number of random Mw matches, which can significantly reduce discrimination. The use of a low '-partials' factor (eg 0.1 - 0.3) is a useful way of limiting this effect - partial peptide matches will add a little to the cumulative frequency score, but without compromising discrimination.
More experienced users can utilise the '-partials' factor to optimize searches where the peptide Mw data contain a significant proportion of partial cleavage fragments (eg > 30%). In such cases, setting the '-partials' factor within the range 0.4 - 0.6 can help to improve discrimination. Conversely, if the digestion is perfect, with no partial fragments present, the lowest '-partials' factor of 0.1 will give maximum discrimination.
For each peptide Mw entry in the data file, emowse matches individual fragment molecular weights (FMWs) with database entry molecular weights (DBMWs). A 'hit' is scored when the following criterion is met:
DBMW-tolerance-1 < FMW < DBMW+tolerance+1
If an intact protein Mw is specified (SMW) then the program prompts for a molecular weight filter percentage (MWFP). emowse then restricts the search to those entries which match the following criteria:
R = SMW x MWFP / 100 0 < SMW-R < emowse entry Mol.wt. < SMW+R
Default search parameters are a tolerance of +/- 2 Daltons, intact Mw specified and the MWFP set to 25.
Cell value = Old value / Fmax
to yield floating point numbers between 0 and 1. These distribution frequency values, calculated for each cleavage reagent, were then built into the emowse search program. For every database entry scanned, all matching fragments contribute to the final score. In the current implementation, non-matching fragments are ignored (neutral). For each matching peptide Mw a score is assigned by looking up the appropriate normalised distribution frequency value. In the case of multiple 'hits' in any one target protein (i.e. more than one matching peptide Mw), the distribution frequency scores are multiplied. The final product score is inverted and then normalised to an 'average' protein Mw of 50 kDaltons to reduce the influence of random score accumulation in large proteins (>200 kDaltons). The final score is thus calculated as:
Score = 50/(Pn x H)
Where Pn is the product of n distribution scores and H the 'hit' protein molecular weight in kD.
Important consequences of this type of scoring scheme are that matches with peptides of higher Mw carry more scoring weight, and that the non-random distribution of fragment molecular weights in proteins of different sizes is compensated for.
This distribution was somewhat dependent on protein size, as smaller proteins generally yield fewer peptide fragments. Thus, all proteins of 30 kD and over were identified using 13% or less of possible fragments (1 in 8), with all proteins of 40 kD and above requiring less than 10% (1 in 10). In this latter group, therefore, more than 90% of the potential information (all possible peptides) was redundant. For the simulation a 'unique' identification required matching not only of protein type (e.g. globin) but correct discrimination of type, species, and isoform or isozyme. Discrimination could be further improved by reducing the error tolerance to only +/- 1 Dalton (mean=2.7 peptides). Such accuracies are easily bettered using more sophisticated ESI/quadrupole or high-field FAB spectrometers, but the default search value (+/- 2 Daltons) compensates for the reduced accuracy obtainable from the smaller time-of-flight (TOF) instruments. Mass accuracies better than +/- 1 Dalton were not essential, and in fact the error tolerance could be relaxed to +/- 5 Daltons in many cases with little degradation in performance. The simulation thus clearly demonstrated the high degree of discrimination afforded by relatively few peptide masses, even with generous allowance for error.
% emowse Protein identification by mass spectrometry Input sequence(s): sw:* Input file: test.mowse Whole sequence molwt [0]: Output file [100k_rat.emowse]:
Mandatory qualifiers: [-sequences] seqall Sequence database USA [-infile] infile Name of molecular weight data file -weight integer Whole sequence molwt -outfile outfile Output file name Optional qualifiers: (none) Advanced qualifiers: -enzyme menu Enzyme or reagent -aadata string Molecular weight data for amino acids -pcrange integer Allowed whole sequence weight variability -frequencies string Frequencies file -tolerance float (no help text) float value -partials float Partials factor General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
[-sequences] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required | ||||||||||||||||
[-infile] (Parameter 2) |
Name of molecular weight data file | Input file | Required | ||||||||||||||||
-weight | Whole sequence molwt | Any integer value | 0 | ||||||||||||||||
-outfile | Output file name | Output file | <sequence>.emowse | ||||||||||||||||
Optional qualifiers | Allowed values | Default | |||||||||||||||||
(none) | |||||||||||||||||||
Advanced qualifiers | Allowed values | Default | |||||||||||||||||
-enzyme | Enzyme or reagent |
|
1 | ||||||||||||||||
-aadata | Molecular weight data for amino acids | Any string is accepted | Eamino.dat | ||||||||||||||||
-pcrange | Allowed whole sequence weight variability | Integer from 0 to 75 | 25 | ||||||||||||||||
-frequencies | Frequencies file | Any string is accepted | Efreqs.dat | ||||||||||||||||
-tolerance | (no help text) float value | Number from 0.100 to 1.000 | 0.1 | ||||||||||||||||
-partials | Partials factor | Number from 0.100 to 1.000 | 0.4 |
6082.8 5423.0 3086.3 2930.3 2424.7 2030.2 1399.6 1086.2
Each molecular weight must be on a line of its own. Masses (M not M[H+]) are accepted in any order (ascending,descending or mixed). Peptide masses can be entered as integers or floating-point values, the latter being rounded to the nearest integer value for the search.
It is suggested that peptide masses should be selected from the range 700-4000 Daltons. This range balances the fact that very small peptides give little discrimination and minimizes the frequency of partially-cleaved peptides.
As a general rule, users are advised to identify and remove peptide masses resulting from autodigestion of the cleavage enzyme (e.g tryptic fragments of trypsin), best obtained by MS analysis of control digests containing only the enzyme.
Further information on the partial sequence and/or composition of the peptides can be given after the weight with a 'seq()' or 'comp()' specification. This should be formatted like:
mw seq(...) comp(...)
where mw is the molecular mass of the fragment, seq(...) is sequence information and comp(...) is composition information. A line may contain more than one sequence information qualifiers. For example:
7176 seq(b-t[pqt]ln) 1744 1490 1433 comp(3[ed]1[p]) seq(gmde)
Sequence information
The sequence information should be given in standard One-character code. It should be preceded by a prefix as outlined in the table below, to indicate what type of sequence it is.
Prefix | Meaning | Example |
---|---|---|
b- | N->C sequence | seq(b-DEFG) |
y- | C->N sequence | seq(y-GFED) |
*- | Orientation unknown | seq(*-DEFG) seq(*-GFED) |
n- | N terminal sequence | seq(n-ACDE) |
c- | C terminal sequence | seq(c-FGHI) |
The examples are all correct data for a
peptide with a sequence ACDEFGHI. Note that *-DEFG will search for both DEFG and GFED |
Both lower and upper case characters may be used for amino-acids. An unknown amino acid may be indicated by an 'X'. More than one amino acid may be specified for a position by putting them between square brackets. A line may contain several sequence information qualifiers. An example for a peptide with the actual sequence ACDEFGHI might look like:
12345 seq(n-AC[DE]) seq(c-HI)
comp(2[H]0[M]3[DE]*[K])indicates a peptide which contains 2 histidines, no methionines, 3 acidic residues (glutamic or aspartic acid) and at least 1 lysine.
Matching peptides marked with a '*' denote partially-cleaved fragments.
This is the output from search all of the SwissProt database with the input file above:
Using data fragments of: 1086.2 1399.6 2030.2 2424.7 2930.3 3086.3 5423.0 6082.8 1 100K_RAT 100 KDA PROTEIN (EC 6.3.2.-). 2 POLG_MCFA GENOME POLYPROTEIN [CONTAINS: CAPSID PROTEIN C (CORE PROTEIN); 3 PGCV_HUMAN VERSICAN CORE PROTEIN PRECURSOR (LARGE FIBROBLAST PROTEOGLYCAN 4 POL1_BAYMJ GENOME POLYPROTEIN 1 [CONTAINS: CYTOPLASMIC INCLUSION PROTEIN 5 RRPB_CVMJH RNA-DIRECTED RNA POLYMERASE (EC 2.7.7.48) (ORF1B). 6 DMD_HUMAN DYSTROPHIN. 7 STRH_STRPN BETA-N-ACETYLHEXOSAMINIDASE PRECURSOR (EC 3.2.1.52). 8 NGCA_CHICK NEURONAL-GLIAL CELL ADHESION MOLECULE PRECURSOR (NG-CAM). 9 RIR1_ASFB7 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE CHAIN (EC 1.17.4.1) 10 YMW6_YEAST HYPOTHETICAL 147.0 KDA PROTEIN IN ABF2-CHL12 INTERGENIC REGION 11 UBR1_YEAST N-END-RECOGNIZING PROTEIN (UBIQUITIN-PROTEIN LIGASE E3 COMPONE 12 MCR_RAT MINERALOCORTICOID RECEPTOR (MR). 13 CD8A_FELCA T-CELL SURFACE GLYCOPROTEIN CD8 ALPHA CHAIN PRECURSOR. 14 YM27_MYCTU HYPOTHETICAL 26.6 KDA PROTEIN RV2227. 15 CD52_MACFA CAMPATH-1 ANTIGEN PRECURSOR (CD52 ANTIGEN) (CDW52) (CAMBRIDGE 16 POL1_BAYMG GENOME POLYPROTEIN 1 [CONTAINS: CYTOPLASMIC INCLUSION PROTEIN 17 CP7B_RAT CYTOCHROME P450 7B1 (OXYSTEROL 7-ALPHA-HYDROXYLASE) (EC 1.14.1 18 CCAE_RAT VOLTAGE-DEPENDENT R-TYPE CALCIUM CHANNEL ALPHA-1E SUBUNIT (CAL 19 CCAE_MOUSE VOLTAGE-DEPENDENT R-TYPE CALCIUM CHANNEL ALPHA-1E SUBUNIT (CAL 20 GCST_MYCTU PROBABLE AMINOMETHYLTRANSFERASE (EC 2.1.2.10) (GLYCINE CLEAVAG 21 LYST_HUMAN LYSOSOMAL TRAFFICKING REGULATOR (BEIGE HOMOLOG). 22 FIXI_BRAJA NITROGEN FIXATION PROTEIN FIXI (E1-E2 TYPE CATION ATPASE FIXI) 23 MAP4_MOUSE MICROTUBULE-ASSOCIATED PROTEIN 4. 24 RAD3_SCHPO DNA REPAIR PROTEIN RAD3. 25 MTHR_SCHPO PROBABLE METHYLENETETRAHYDROFOLATE REDUCTASE 1 (EC 1.5.1.20). 26 BCA1_RAT CRK-ASSOCIATED SUBSTRATE (P130CAS) (BREAST CANCER ANTI-ESTROGE 27 G6PE_RABIT GDH/6PGL ENDOPLASMIC BIFUNCTIONAL PROTEIN [INCLUDES: GLUCOSE 1 28 MRP3_RAT CANALICULAR MULTISPECIFIC ORGANIC ANION TRANSPORTER 2 (MULTIDR 29 PTVB_ECOLI PTS SYSTEM, FRUCTOSE-LIKE-1 IIBC COMPONENT (PHOSPHOTRANSFERASE 30 YMHA_CAEEL HYPOTHETICAL 83.2 KDA PROTEIN F58A4.11 IN CHROMOSOME III. 31 DAB_DROME DISABLED PROTEIN. 32 EGLN_HUMAN ENDOGLIN PRECURSOR (CD105 ANTIGEN). 33 DPOZ_YEAST DNA POLYMERASE ZETA CATALYTIC SUBUNIT (EC 2.7.7.7). 34 C166_BRARE CD166 ANTIGEN HOMOLOG PRECURSOR (NEUROLIN) (DM-GRASP HOMOLOG). 35 YAHB_ECOLI HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN BETT-PRPR INTERGENIC 36 ACSB_ACEXY CELLULOSE SYNTHASE 93 KDA SUBUNIT PRECURSOR (CELLULOSE SYNTHAS 37 CIN5_RAT SODIUM CHANNEL PROTEIN, CARDIAC MUSCLE ALPHA-SUBUNIT. 38 SUIS_SUNMU SUCRASE-ISOMALTASE, INTESTINAL [CONTAINS: SUCRASE (EC 3.2.1.48 39 TEGP_HSVEA PROBABLE TEGUMENT PHOSPHOPROTEIN (ORF5) (FRAGMENT). 40 YDT2_SCHPO HYPOTHETICAL 217.4 KDA PROTEIN C6B12.02C IN CHROMOSOME I. 41 YHFC_ECOLI HYPOTHETICAL 43.2 KDA PROTEIN IN PPIA-NIRB INTERGENIC REGION ( 42 TBX5_HUMAN TBX5 PROTEIN (T-BOX PROTEIN 5). 43 YEX0_YEAST HYPOTHETICAL 64.8 KDA PROTEIN IN GDI1-COX15 INTERGENIC REGION. 44 Y323_MYCPN HYPOTHETICAL PROTEIN MG323 HOMOLOG. 45 VP42_ROTS1 OUTER CAPSID PROTEIN VP4 (HEMAGGLUTININ) (OUTER LAYER PROTEIN 46 NOEC_AZOCA NODULATION PROTEIN NOEC. 47 BIB_DROME NEUROGENIC PROTEIN BIG BRAIN. 48 NB35_YEAST NBP35 PROTEIN. 49 HSCA_RICPR CHAPERONE PROTEIN HSCA HOMOLOG. 50 SYL_AERPE LEUCYL-TRNA SYNTHETASE (EC 6.1.1.4) (LEUCINE--TRNA LIGASE) (LE 1 : 100K_RAT 1.277e+06 100368.6 0.750 100 KDA PROTEIN (EC 6.3.2.-). Mw Start End Seq 1086.3 358 367 CATTPMAVHR 1399.6 6 17 GDFLNYALSLMR 2424.7 290 312 VFMEDVGAEPGSILTELGGFEVK 2930.3 671 698 QLILASQSSDADAVFSAMDLAFAVDLCK 3086.3 458 485 QLSIDTRPFRPASEGNPSDDPDPLPAHR *6082.8 817 870 QDLVYFWTSSPSLPASEEGFQPMPSITIRPPDDQHLPTANTCISR... No Match 2030.2 5423.0 2 : POLG_MCFA 2.612e+05 373265.6 0.500 GENOME POLYPROTEIN [CONTAINS: CAPSID PROTEIN C (CORE PROTEIN); MATRIX PROTEIN (ENVELOPE PROTEIN M); MAJOR ENVELOPE PROTEIN E; NONSTRUCTURAL PROTEINS NS1, NS2A, NS2B, NS4A AND NS4B; HELICASE (NS3); RNA-DIRECTED RNA POLYMERASE (EC 2.7.7.48) (NS5)]. Mw Start End Seq 2423.7 3233 3251 TSWSVHQYHEWMTTDDMLR 2931.2 951 977 EYTPDTLSDPSDQALFIPPAWGGPISR *3088.7 2174 2200 SYMDSDLVKWVILGSCLICGVLAWEMR 6084.9 1327 1382 AHQPTVAAVLAFTMVVLFLYMEQTNVSMELEFISAGETPEGVSTE... No Match 1086.2 1399.6 2030.2 5423.0 3 : PGCV_HUMAN 2.202e+05 372819.0 0.625 VERSICAN CORE PROTEIN PRECURSOR (LARGE FIBROBLAST PROTEOGLYCAN) (CHONDROITIN SULFATE PROTEOGLYCAN CORE PROTEIN 2) (GLIAL HYALURONATE- BINDING PROTEIN) (GHAP). Mw Start End Seq 1398.5 651 662 TEIELFPYSGDK *2029.2 1334 1352 TGRMSDLSVIGHPIDSESK 2426.6 842 863 DIPSFTEDGADEFTLIPDSTQK *2928.3 1190 1216 ATELIEFSTIKVTVPSDITTAFSSVDR 6081.6 3037 3092 ILDSNDQATVNPVEFNTEVATPPFSLLETSNETDFLIGINEESVE... No Match 1086.2 3086.3 5423.0 4 : POL1_BAYMJ 5.410e+04 270769.3 0.500 GENOME POLYPROTEIN 1 [CONTAINS: CYTOPLASMIC INCLUSION PROTEIN (CI); RNA-DIRECTED RNA POLYMERASE (EC 2.7.7.48); COAT PROTEIN (CP)]. Mw Start End Seq *2031.3 368 385 ISRLSSYLLDDHQGIASR *2423.7 1531 1551 RNEFQPFTQEVVDFINGPGTK 5422.0 1970 2016 FAISPQFDEEFGHDFSPELVELGLTYEFDDITSDICENPYMSLTM... 6077.8 1552 1606 IPYCPWVFDRPACGYASHTALFEKPTTLTDIIHMQASDGLHNINN... No Match 1086.2 1399.6 2930.3 3086.3 5 : RRPB_CVMJH 4.449e+04 308836.3 0.625 RNA-DIRECTED RNA POLYMERASE (EC 2.7.7.48) (ORF1B). Mw Start End Seq *1085.4 639 648 IVSSLVLARK 2030.2 172 187 DWYDFVENPDIINVYK 2422.7 414 433 FQTVKPGNFNQDFYEFILSK *2932.2 2162 2187 YTDLQCIESLNVLFDGRDNGALEAFK 6077.9 662 721 LANECAQVLGEIVMCGGCYYVKPGGTSSGDATTAFANSVFNICQA... No Match 1399.6 3086.3 5423.0 6 : DMD_HUMAN 3.824e+04 426675.4 0.625 DYSTROPHIN. Mw Start End Seq *1399.6 436 447 VASMEKQSNLHR 2031.3 2478 2494 AWTELTDWLSLLDQVIK 2426.6 1165 1183 DLSEMHEWMTQAEEEYLER *3083.4 1159 1183 TVSLQKDLSEMHEWMTQAEEEYLER 5428.2 1979 2026 EETMMVMTEDMPLEISYVPSTYLTEITHVSQALLEVEQLLNAPDL... No Match 1086.2 2930.3 6082.8 7 : STRH_STRPN 2.144e+04 144521.5 0.625 BETA-N-ACETYLHEXOSAMINIDASE PRECURSOR (EC 3.2.1.52). Mw Start End Seq 1400.6 827 839 FAEYANTLAAMAK 2029.2 655 673 ASELGYSDVHLLLGNDGLR 2423.9 729 751 DIGLIPAINSPGHMDAMLVAMEK *2930.4 1280 1308 LPETGTHDSAGLVVAGLMSTLAAYGLTKR 3089.2 255 281 GTNDYYNDPNGNHLTESQMTDLINYAK No Match 1086.2 5423.0 6082.8 8 : NGCA_CHICK 1.849e+04 136570.2 0.375 NEURONAL-GLIAL CELL ADHESION MOLECULE PRECURSOR (NG-CAM). Mw Start End Seq 2930.1 1036 1062 GGFHGAAVEFGAAQEDDVEFEVQFMNK *3087.4 110 138 CFATNALGTAVSPEANVIAENTPQWPKEK 6077.2 1 57 MALPMVGLLLLLLLGGPGAAITIPPEYGAHDFLQPPELTEEPPEQ... No Match 1086.2 1399.6 2030.2 2424.7 5423.0 9 : RIR1_ASFB7 1.768e+04 87491.8 0.375 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE CHAIN (EC 1.17.4.1) (RIBONUCLEOTIDE REDUCTASE). Mw Start End Seq *2423.6 568 589 CGDLSSSWEERVAQTTQGVLTR 2931.3 407 433 SNLSHVGTITNSNLCIEVTIPCWEGDK 5422.1 243 289 SNGIQNYIMLQNASQCYANQGGLRPGAYAVYLELWHQDIFTFLQM... No Match 1086.2 1399.6 2030.2 3086.3 6082.8 10 : YMW6_YEAST 1.760e+04 147040.9 0.375 HYPOTHETICAL 147.0 KDA PROTEIN IN ABF2-CHL12 INTERGENIC REGION. Mw Start End Seq 2028.4 977 993 FLPLVFFTAYEPDVELK 3086.6 135 161 SIVLLADLPSSNNLLIELFHIFYDPNK 5423.0 441 485 EIWEIIDTIPSTLYNLYYINDLNINEQVDSVIFEYLLPFEPDNDK No Match 1086.2 1399.6 2424.7 2930.3 6082.8 11 : UBR1_YEAST 1.661e+04 224837.6 0.375 N-END-RECOGNIZING PROTEIN (UBIQUITIN-PROTEIN LIGASE E3 COMPONENT) (N- RECOGNIN). Mw Start End Seq *1400.6 258 268 EMTQQGKMYER 3089.3 939 965 SVPDYLTEDTTEFDEALEEVSVFVEPK 5421.5 1830 1881 IPPTDEDDEDMEEGEDGFFTEGNDEMDVDDETGQAANLFGVGAEG... No Match 1086.2 2030.2 2424.7 2930.3 6082.8 12 : MCR_RAT 1.463e+04 106736.9 0.375 MINERALOCORTICOID RECEPTOR (MR). Mw Start End Seq *2031.2 19 36 WSQVSQTLERSSLGPAER 3088.4 466 495 DYYSLSGILGPPVPGFDGSCEDSAFPVGIK 5423.0 191 244 SSSVSSPLNMASSVCSPVGINSMSSSTTSFGSFPVHSPITQGTSL... No Match 1086.2 1399.6 2424.7 2930.3 6082.8 13 : CD8A_FELCA 1.074e+04 26120.3 0.250 T-CELL SURFACE GLYCOPROTEIN CD8 ALPHA CHAIN PRECURSOR. Mw Start End Seq 2422.8 42 63 VELQCEVLLSSAAPGCTWLFQK 5421.2 112 160 EEEGYYFCSVVSNSVLYFSAFVPVFLPVKPTTTPAPRPPTQAPIT... No Match 1086.2 1399.6 2030.2 2930.3 3086.3 6082.8 14 : YM27_MYCTU 1.054e+04 26614.4 0.250 HYPOTHETICAL 26.6 KDA PROTEIN RV2227. Mw Start End Seq 2426.6 99 120 EAPWPDSLDDWLASCHAAGQTR 5424.0 128 174 YGTNDWNALHQDLYGELVFPLQVVINLSDPETDYTGGEFLLVEQR... No Match 1086.2 1399.6 2030.2 2930.3 3086.3 6082.8 15 : CD52_MACFA 1.038e+04 6502.6 0.125 CAMPATH-1 ANTIGEN PRECURSOR (CD52 ANTIGEN) (CDW52) (CAMBRIDGE PATHOLOGY 1 ANTIGEN). Mw Start End Seq 6087.0 4 60 FLFLLLTISLLVMVQIQTGVTSQNATSQSSPSASSNLSGGGFLFF... No Match 1086.2 1399.6 2030.2 2424.7 2930.3 3086.3 5423.0 16 : POL1_BAYMG 9.354e+03 270875.5 0.625 GENOME POLYPROTEIN 1 [CONTAINS: CYTOPLASMIC INCLUSION PROTEIN (CI); RNA-DIRECTED RNA POLYMERASE (EC 2.7.7.48); COAT PROTEIN (CP)]. Mw Start End Seq *1398.5 899 909 DEIPHELRYAR *2031.2 1308 1325 MEISQHDPDFLKQNGSGK *2423.8 910 931 VPFSVTTLSKFDWPALALACEK 5422.0 1972 2018 FAISPQFDEEFGHDFSPELVELGLTYEFDDITSDICENPYMSLTM... *6082.9 550 603 MGDHCIQVMTYGSALQCHAMDPSFISTFDAIFLDEAHDVKEHSLV... No Match 1086.2 2930.3 3086.3 17 : CP7B_RAT 9.319e+03 48226.8 0.375 CYTOCHROME P450 7B1 (OXYSTEROL 7-ALPHA-HYDROXYLASE) (EC 1.14.13.-) (HCT-1) (FRAGMENT). Mw Start End Seq 2030.4 249 266 EQLDSLVCLESAILEVLR *2928.4 85 110 VFDFCSSLVFEITFTTIYGKILAANK 5421.2 179 224 YYGHEEFEIGAHHLGLLWASLANTIPAMFWAMYYLLQHPEAMEVL... No Match 1086.2 1399.6 2424.7 3086.3 6082.8 18 : CCAE_RAT 9.273e+03 252115.4 0.375 VOLTAGE-DEPENDENT R-TYPE CALCIUM CHANNEL ALPHA-1E SUBUNIT (CALCIUM CHANNEL, L TYPE, ALPHA-1 POLYPEPTIDE, ISOFORM 6) (RBE-II) (RBE2) (BRAIN CALCIUM CHANNEL II) (BII). Mw Start End Seq 2424.9 1711 1731 IHYTEMYEMLTLMSPPLGLGK *5424.5 1349 1393 MEMSIFYVVYFVVFPFFFVNIFVALIIITFQEQGDKMMEECSLEK 6081.2 426 477 SQVFYWIVLSVVALNTACVAIVHHNQPQWLTHLLYYAEFLFLGLF... No Match 1086.2 1399.6 2030.2 2930.3 3086.3 19 : CCAE_MOUSE 9.088e+03 257235.0 0.375 VOLTAGE-DEPENDENT R-TYPE CALCIUM CHANNEL ALPHA-1E SUBUNIT (CALCIUM CHANNEL, L TYPE, ALPHA-1 POLYPEPTIDE, ISOFORM 6) (BRAIN CALCIUM CHANNEL II) (BII). Mw Start End Seq 2424.9 1762 1782 IHYTEMYEMLTLMSPPLGLGK *5424.5 1400 1444 MEMSIFYVVYFVVFPFFFVNIFVALIIITFQEQGDKMMEECSLEK 6081.2 476 527 SQVFYWIVLSVVALNTACVAIVHHNQPQWLTHLLYYAEFLFLGLF... No Match 1086.2 1399.6 2030.2 2930.3 3086.3 20 : GCST_MYCTU 8.954e+03 39628.9 0.250 PROBABLE AMINOMETHYLTRANSFERASE (EC 2.1.2.10) (GLYCINE CLEAVAGE SYSTEM T PROTEIN). Mw Start End Seq 3085.4 30 58 ELGASFAEFGGWLMPVSYAGTVSEHNATR 5422.1 307 360 GVLRPGLAVLVGDETVGVTTSGTFSPTLQVGIGLALIDSDAGIED... No Match 1086.2 1399.6 2030.2 2424.7 2930.3 6082.8 21 : LYST_HUMAN 8.339e+03 429123.8 0.625 LYSOSOMAL TRAFFICKING REGULATOR (BEIGE HOMOLOG). Mw Start End Seq 1400.6 3733 3743 LWSTWDLKPVR *2031.2 690 705 WDALKAYQNFVFEEDR *2928.2 2981 3006 SEDVVKPPLSYLFEDKTHSSFSSTVK 3086.5 3703 3732 EIICSVAFSNQPEGVSINVIAGGLENGIVR *5424.1 3106 3151 VRDDVYHNILTNNLPNLLEYGNITALTNLWYTGQITNFEYLTHLN... No Match 1086.2 2424.7 6082.8 22 : FIXI_BRAJA 7.585e+03 77338.3 0.250 NITROGEN FIXATION PROTEIN FIXI (E1-E2 TYPE CATION ATPASE FIXI) (EC 3.6.1.-). Mw Start End Seq 2932.4 244 271 FVGPDEISQVPVAAISPGDIVLLRPGER 6087.3 356 415 LYAPVVHATALITILGWVIAGASWHDAIVTGVAVLIITCPCALGL... No Match 1086.2 1399.6 2030.2 2424.7 3086.3 5423.0 23 : MAP4_MOUSE 7.184e+03 117675.3 0.250 MICROTUBULE-ASSOCIATED PROTEIN 4. Mw Start End Seq 3087.5 431 458 DVTLPLEAERPLVTDMTPSLETEMTLGK 6085.7 272 327 DIEEITKPDVILANVTQPSTESDMFLAQDMELLTGTEAAHANNII... No Match 1086.2 1399.6 2030.2 2424.7 2930.3 5423.0 24 : RAD3_SCHPO 6.503e+03 121973.3 0.250 DNA REPAIR PROTEIN RAD3. Mw Start End Seq 3085.4 860 888 LQPLYVDAATAIANTGAHSAYDCYDILSK 6087.7 713 765 VLQEIYAGIDDPDEIEAVSLNFHDYSFDQQLLLHENSGTWDSALS... No Match 1086.2 1399.6 2030.2 2424.7 2930.3 5423.0 25 : MTHR_SCHPO 6.242e+03 69012.0 0.375 PROBABLE METHYLENETETRAHYDROFOLATE REDUCTASE 1 (EC 1.5.1.20). Mw Start End Seq 1399.4 118 129 DTDWTEGESGFR *3085.5 400 426 ISSLPWSDLPISDEADLIRDQLLSMNR 6079.9 43 98 TWGRPMFVDVTWGAGGTSSELTPGIVNVIQTDFEVDTCMHLTCTN... No Match 1086.2 2030.2 2424.7 2930.3 5423.0 26 : BCA1_RAT 5.803e+03 104261.8 0.375 CRK-ASSOCIATED SUBSTRATE (P130CAS) (BREAST CANCER ANTI-ESTROGEN RESISTANCE 1 PROTEIN). Mw Start End Seq *1399.5 14 26 RAGGLEDVSWGPR 5422.9 249 299 QTPHHSFPSPATDLYQVPPGPGSPAQDIYQVPPSAGTGHDIYQVP... *6086.8 422 477 EETYDVPPAFAKPKPFDPTRHPLILAAPPPDSPPAEDVYDVPPPA... No Match 1086.2 2030.2 2424.7 2930.3 3086.3 27 : G6PE_RABIT 5.630e+03 85285.1 0.250 GDH/6PGL ENDOPLASMIC BIFUNCTIONAL PROTEIN [INCLUDES: GLUCOSE 1- DEHYDROGENASE (EC 1.1.1.47) (HEXOSE-6-PHOSPHATE DEHYDROGENASE); 6- PHOSPHOGLUCONOLACTONASE (EC 3.1.1.31) (6PGL)]. Mw Start End Seq 2929.4 453 477 ESFVPTEHLLASWVFWTPLLESLAR 5428.1 564 614 VGTFHLALSGGSSPIALFQQLASGHYGFPVPLSDPESNFQGLQAH... No Match 1086.2 1399.6 2030.2 2424.7 3086.3 6082.8 28 : MRP3_RAT 5.465e+03 168977.6 0.625 CANALICULAR MULTISPECIFIC ORGANIC ANION TRANSPORTER 2 (MULTIDRUG RESISTANCE-ASSOCIATED PROTEIN 3) (MRP-LIKE PROTEIN-2) (MLP-2). Mw Start End Seq 1086.2 279 288 IAGEDEVLLK 2426.8 1494 1517 GVVAEFDSPVNLIAAGGIFYGMAK *2930.4 1359 1384 SQLTIIPQDPILFSGTLRMNLDPFGR *3087.5 757 785 VSLARAVYSDANIFLLDDPLSAVDSHVAK *6086.0 165 217 ILDPFRFTTFYIYFALVLCAFILSCFQEKPPLFSPENLDTNPCPE... No Match 1399.6 2030.2 5423.0 29 : PTVB_ECOLI 5.278e+03 51322.6 0.250 PTS SYSTEM, FRUCTOSE-LIKE-1 IIBC COMPONENT (PHOSPHOTRANSFERASE ENZYME II, BC COMPONENT) (EC 2.7.1.69). Mw Start End Seq 3084.7 340 368 HIYDWYAIVGVVALMPPVAAGLATFIAPK 5419.7 257 306 ALQPLLGSMLIPFVTLLVFGVLTYYVIGPVMSDLMGGLLHFLNTI... No Match 1086.2 1399.6 2030.2 2424.7 2930.3 6082.8 30 : YMHA_CAEEL 5.268e+03 83221.0 0.375 HYPOTHETICAL 83.2 KDA PROTEIN F58A4.11 IN CHROMOSOME III. Mw Start End Seq *1400.6 277 288 SVFSTNLKVHLR 2030.2 559 579 GGGNVTTPPTPNSSSFPSTPK 5428.2 5 50 LFVFGSGADDPSHFNYYHCSDLILSSTFSSFSFLILIYLYIFIFY... No Match 1086.2 2424.7 2930.3 3086.3 6082.8 31 : DAB_DROME 5.168e+03 264048.0 0.500 DISABLED PROTEIN. Mw Start End Seq 2029.1 1588 1604 MNSCDEDYDYDGEFVAR *2423.5 2159 2179 FDDNVKVSQFDDAAFEDDFAK *3087.6 1018 1045 LNVPASKLSTMTLVQLTAYLSEYLSSEK 5426.0 2305 2357 CVNDTTFILPSQSLLSAAATAQPATELESPCLLQLASPAVAGASE... No Match 1086.2 1399.6 2930.3 6082.8 32 : EGLN_HUMAN 4.635e+03 70577.9 0.250 ENDOGLIN PRECURSOR (CD105 ANTIGEN). Mw Start End Seq 2930.4 305 333 MLNASIVASFVELPLASIVSLHASSCGGR 5418.3 94 143 EVLLVLSVNSSVFLHLQALGIPLHLAYNSSLVTFQEPPGVNTTEL... No Match 1086.2 1399.6 2030.2 2424.7 3086.3 6082.8 33 : DPOZ_YEAST 4.530e+03 172956.7 0.375 DNA POLYMERASE ZETA CATALYTIC SUBUNIT (EC 2.7.7.7). Mw Start End Seq 1398.7 1169 1180 VTQNNPKPIFLK 2028.4 1358 1375 LFNLIGINVGNWAQEIVK 6078.9 730 780 IQHCINEIPVMFYESEFEMFEALTDLVLLLDPDILSGFEIHNFSW... No Match 1086.2 2424.7 2930.3 3086.3 5423.0 34 : C166_BRARE 4.297e+03 61273.4 0.250 CD166 ANTIGEN HOMOLOG PRECURSOR (NEUROLIN) (DM-GRASP HOMOLOG). Mw Start End Seq 3085.5 306 334 CSLLDNDVMESTQIVTVSFLDASLTPTGK 5426.4 1 52 MHSVICLFGAFIAAALFAPGSCLPTVIGLYGETIEVPCNNGNNKP... No Match 1086.2 1399.6 2030.2 2424.7 2930.3 6082.8 35 : YAHB_ECOLI 4.268e+03 34865.9 0.250 HYPOTHETICAL TRANSCRIPTIONAL REGULATOR IN BETT-PRPR INTERGENIC REGION. Mw Start End Seq 2029.3 1 18 MNSIFTEENLLAFTTAAR 5424.0 121 171 QFPTCQITVTTEVYNGVWDAIINNQANIAIGAPDTLLDGGGIDYT... No Match 1086.2 1399.6 2424.7 2930.3 3086.3 6082.8 36 : ACSB_ACEXY 4.019e+03 85381.9 0.500 CELLULOSE SYNTHASE 93 KDA SUBUNIT PRECURSOR (CELLULOSE SYNTHASE PROTEIN B). Mw Start End Seq 1087.2 186 195 LNFSFASSSK 2424.8 541 562 MPNLAFMASAGYPFTTYADLSR *2928.4 359 385 MDVAPIDVGARVAYDAPSFIPTNRPVR 3083.5 739 764 SSPLYTVGTVPLWLEPDWYMHNHPSR No Match 1399.6 2030.2 5423.0 6082.8 37 : CIN5_RAT 3.905e+03 227366.6 0.375 SODIUM CHANNEL PROTEIN, CARDIAC MUSCLE ALPHA-SUBUNIT. Mw Start End Seq *2425.7 661 682 QRALSAVSVLTSALEELEESHR 2928.0 1096 1122 AWSQVSETTSSEAGASTSQADWQQEQK 3084.8 251 278 LADVMVLTVFCLSVFALIGLQLFMGNLR No Match 1086.2 1399.6 2030.2 5423.0 6082.8 38 : SUIS_SUNMU 3.806e+03 208173.0 0.500 SUCRASE-ISOMALTASE, INTESTINAL [CONTAINS: SUCRASE (EC 3.2.1.48); ISOMALTASE (EC 3.2.1.10)]. Mw Start End Seq *2028.3 365 381 IPFDAQVTDIDYMEDKK 2424.7 1551 1571 QDPVSWNETFASMSTDILNIR 3086.4 1226 1250 QLYEDMVSAQIPYDVQYTDIDYMER *6083.9 301 354 VIGGILDFYIFLGDTPGQVVQQYQELTGRPAMPSYWSLGFQLSRW... No Match 1086.2 1399.6 2930.3 5423.0 39 : TEGP_HSVEA 3.789e+03 7633.1 0.125 PROBABLE TEGUMENT PHOSPHOPROTEIN (ORF5) (FRAGMENT). Mw Start End Seq 5418.5 22 76 GSGMSDQEVSEEQSAGDAWVSAAMAAAEAVAAAATSTGIDNTNDY... No Match 1086.2 1399.6 2030.2 2424.7 2930.3 3086.3 6082.8 40 : YDT2_SCHPO 3.706e+03 217433.0 0.500 HYPOTHETICAL 217.4 KDA PROTEIN C6B12.02C IN CHROMOSOME I. Mw Start End Seq *1398.6 1073 1083 LQPLHSRQYTR *2422.9 1461 1482 SVHLNLLTAVFCNMAKLYADAK 5421.9 1483 1530 TNGFASSQYLQSLFIHYLSSLLSSMQHSYETNGHSSDTHSLFVIN... *6083.6 1477 1530 LYADAKTNGFASSQYLQSLFIHYLSSLLSSMQHSYETNGHSSDTH... No Match 1086.2 2030.2 2930.3 3086.3 41 : YHFC_ECOLI 3.697e+03 43166.3 0.250 HYPOTHETICAL 43.2 KDA PROTEIN IN PPIA-NIRB INTERGENIC REGION (O393). Mw Start End Seq 5418.4 273 323 ILTVLAGLAAILMYVFNTGTPAHMAWSILALGFFSSAIYTTIITL... *6083.3 329 385 LVNFVLTCGTIGTMLTFVVTGPIVEHSGPQAALLTANGLYAVVFV... No Match 1086.2 1399.6 2030.2 2424.7 2930.3 3086.3 42 : TBX5_HUMAN 3.628e+03 57438.9 0.250 TBX5 PROTEIN (T-BOX PROTEIN 5). Mw Start End Seq 2028.3 1 19 MADADEALAGAHLWSLTQK 6083.7 373 429 QACMYASSAPPSEPVPSLEDISCNTWPSMPSYSSCTVTTVQPWTG... No Match 1086.2 1399.6 2424.7 2930.3 3086.3 5423.0 43 : YEX0_YEAST 3.609e+03 64793.9 0.250 HYPOTHETICAL 64.8 KDA PROTEIN IN GDI1-COX15 INTERGENIC REGION. Mw Start End Seq 2930.5 328 355 STLSIVINILCGPMVSVVGSEVLVDWAK 5423.5 223 271 CLLVSMSLTYVTIHGYVLVYQAISLNIAVNSYSNALLTLLLSMQF... No Match 1086.2 1399.6 2030.2 2424.7 3086.3 6082.8 44 : Y323_MYCPN 3.263e+03 25772.7 0.250 HYPOTHETICAL PROTEIN MG323 HOMOLOG. Mw Start End Seq 1398.6 171 182 EHTNANLISIMR 5426.1 39 89 TNTAAQEFDHVVCCDGSNLTALAELQLEEFSAVIVGVTNIEASIM... No Match 1086.2 2030.2 2424.7 2930.3 3086.3 6082.8 45 : VP42_ROTS1 3.237e+03 86774.3 0.375 OUTER CAPSID PROTEIN VP4 (HEMAGGLUTININ) (OUTER LAYER PROTEIN VP4) [CONTAINS: OUTER CAPSID PROTEINS VP5 AND VP8] (VERSION 2). Mw Start End Seq 2030.2 648 666 STQISPNTIPDIVTEASEK 2931.2 186 210 TAHYSTTNYDSVNMTAFCDFYIIPR *6077.9 370 427 SLAANLNSVMCTGGSYNFSLPVGQWPVLTGGAVSLHSAGVTLSTQ... No Match 1086.2 1399.6 2424.7 3086.3 5423.0 46 : NOEC_AZOCA 3.086e+03 33615.6 0.250 NODULATION PROTEIN NOEC. Mw Start End Seq 1400.7 27 39 NGLLFVPVLICGR 6081.1 204 260 GYELSDHSIVALICVSAGYAAVVFLELFVQMSSVAQGPAPIFVSN... No Match 1086.2 2030.2 2424.7 2930.3 3086.3 5423.0 47 : BIB_DROME 3.070e+03 76951.0 0.375 NEUROGENIC PROTEIN BIG BRAIN. Mw Start End Seq 2425.5 570 593 GQSAQSDDSSYGSYHGSAVTPPAR 2932.4 214 241 FMGNSAASIGCAYSACCFVSMPYLNPAR *6083.5 316 375 YQQSQGTYPRGQSNGNGGGQAAGNGQHQAANMGQMPGVVANAGQG... No Match 1086.2 1399.6 2030.2 3086.3 5423.0 48 : NB35_YEAST 3.035e+03 35253.1 0.500 NBP35 PROTEIN. Mw Start End Seq *1398.7 281 293 FLGSVPLDPRIGK 2031.2 56 74 GPDPDIPLITDNLSGIEHK *2931.3 48 74 EICESLPKGPDPDIPLITDNLSGIEHK 3087.4 294 322 SCDMGESFLDNYPDSPASSAVLNVVEALR No Match 1086.2 2424.7 5423.0 6082.8 49 : HSCA_RICPR 2.923e+03 66019.3 0.375 CHAPERONE PROTEIN HSCA HOMOLOG. Mw Start End Seq *1399.6 549 560 DAVQTRDQILIK 2028.3 467 484 ISNISHNIEIKPNHGINK 5426.1 195 244 YLVYDLGGGTFDVSILNIQEGIFQVIATNGDNMLGGDDIDVVITQ... No Match 1086.2 2424.7 2930.3 3086.3 6082.8 50 : SYL_AERPE 2.902e+03 110518.7 0.500 LEUCYL-TRNA SYNTHETASE (EC 6.1.1.4) (LEUCINE--TRNA LIGASE) (LEURS). Mw Start End Seq 1085.3 476 484 MEFLPGHVR 2928.3 770 795 FIEVQTLLIAPFAPHTAEEAWEAMGR *3084.5 769 795 RFIEVQTLLIAPFAPHTAEEAWEAMGR 5419.0 214 261 DGLVYPALTYRPETVFGVTNLWVHPDATYLVAEVDGEERWIIGEQ... No Match 1399.6 2030.2 2424.7 6082.8
Program name | Description |
---|---|
backtranseq | Back translate a protein sequence |
charge | Protein charge plot |
checktrans | Reports STOP codons and ORF statistics of a protein sequence |
compseq | Counts the composition of dimer/trimer/etc words in a sequence |
freak | Residue/base frequency table or plot |
iep | Calculates the isoelectric point of a protein |
mwcontam | Shows molwts that match across a set of files |
mwfilter | Filter noisy molwts from mass spec output |
octanol | Displays protein hydropathy |
pepinfo | Plots simple amino acid properties in parallel |
pepstats | Protein statistics |
pepwindow | Displays protein hydropathy |
pepwindowall | Displays protein hydropathy of a set of sequences |