emowse.txt

emboss的linux版本的源代码

   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.

  Simulation studies

   In a simulation of scoring properties, 100 test proteins with masses
   between 10 kD and 100 kD were randomly selected from the OWL sequence
   database. The sets of all possible tryptic peptide masses for each
   protein were randomized and database searches performed with
   increasing numbers of fragments (default search parameters) until the
   test protein reached the top of the ranked scoring list. 99% of the
   test proteins were correctly identified using only five peptides or
   less (mean=3.6 peptides), with one example requiring six. These
   figures were surprisingly small considering that some of the proteins
   in the test sample generated more than 100 possible tryptic fragments.
   All 100 test examples were identified using 30% or less of the maximum
   number of available peptides.

   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.

Usage

   Here is a sample session with emowse


% emowse 
Protein identification by mass spectrometry
Input protein sequence(s): tsw:*
Peptide molecular weight values file: test.mowse
Whole sequence molwt [0]: 
Output file [100k_rat.emowse]: 

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Protein sequence(s) filename and optional
                                  format, or reference (input USA)
  [-infile]            infile     Peptide molecular weight values file
   -weight             integer    [0] Whole sequence molwt (Any integer value)
  [-outfile]           outfile    [*.emowse] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -aadata             datafile   [Eamino.dat] Amino acids properties and
                                  molecular weight data file
   -frequencies        datafile   [Efreqs.dat] Amino acid frequencies data
                                  file
   -enzyme             menu       [1] Enzyme or reagent (Values: 1 (Trypsin);
                                  2 (Lys-C); 3 (Arg-C); 4 (Asp-N); 5
                                  (V8-bicarb); 6 (V8-phosph); 7
                                  (Chymotrypsin); 8 (CNBr))
   -pcrange            integer    [25] Allowed whole sequence weight
                                  variability (Integer from 0 to 75)
   -tolerance          float      [0.1] Tolerance (Number from 0.100 to 1.000)
   -partials           float      [0.4] Partials factor (Number from 0.100 to
                                  1.000)

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory3        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Input file format

  Input files for usage example

   'tsw:*' is a sequence entry in the example protein database 'tsw'

  File: test.mowse

6082.8
5423.0
3086.3
2930.3
2424.7
2030.2
1399.6
1086.2

   The input file is a list of molecular weights of the peptide
   fragments. One weight is allowed per line. The example file above is a
   Trypsin digest of the protein sw:100K_rat (produced by using the
   program digest).

   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.


CAPTION: Prefixes to use with sequence information for
emowse


 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)

  Composition Information

   Composition should consist of a number, followed by the corresponding
   amino acid between square brackets. For example
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.

Output file format

  Output files for usage example

  File: 100k_rat.emowse


Using data fragments of:
          1086.2
          1399.6
          2030.2