Peptide Companion - User's Manual
Copyright © 1994-2004 CSPS Pharmaceuticals All Rights Reserved.
Contents
Chapter 1 What to expect of Peptide Companion
This program enables one to evaluate elemental and amino acid composition of a peptide, to predict its MS fragmentation and to analyze problems when the molecular weight of your product does not match the theoretical value, and/or to estimate its HPLC behavior on a reversed phase (using eight different algorithms). You can add molecules of acids, salts or water to your peptide and/or try to fit the values found in the elemental analysis to the theoretical value by adding molecules of water and acetic acid (which are usually present in freeze-dried samples). You may very quickly find the amino acid sequence of any of hundreds peptides (hormones, inhibitors, protein fragments, etc.) from the database and use these structures in calculations or HPLC predictions. You can also modify any peptide bond by any known replacement. The program analyzes peptide/protein sequences for conformational profiles according to the Chou-Fasman algorithm and evaluates protein profiles and amphipathic profiles. Ten different scales are available (hydrophilicity, hydrophobicity, acrophilicity, accessibility, antigenicity, and hydropathy). You can calculate the mass distribution of the library synthesized by randomizing an unlimited number of any building blocks in up to 30 positions. You can predict amino acid composition of a peptide based on found molecular weight. Peptides or proteins can be submitted to simulated enzymatical or chemical digestion and fragments generated in this way can be analyzed in other parts of the program. Any other type of molecule composed of repeating units, such as RNA, DNA, polysaccharides, can be analyzed using this program. However, the building blocks have to be defined and, understandably, the parts of this program dedicated to peptide and protein analyses will not be available or will provide unreliable results. Chapter 2 Hardware requirements To run Peptide Companion you need the following: The faster the computer, the better. Evaluation of large proteins, libraries, or amino acid compositions may take considerable time on slow machines. The program needs at least 910KB of space on the hard disk.
Chapter 4 Nomenclature requirements Chapter 4.1 Using amino acid and protecting group abbreviations In order to get satisfactory results you have to adhere to several rules of entering data into the computer. The nomenclature generally follows the published recommendations (e.g. Eur.J.Biochem. 138, 9-37 (1984)). Abbreviations used by the computer are defined below, but you may teach it new abbreviations (up to four letters long). In the definition of new abbreviations you may use the following elements: C, H, N, O, S, F, Cl, Br, I, P, Li, Na, K, Cs, Si. Both three letter and one letter codes can be used for peptide formula entries. Formulas used in the conformation and protein profile evaluation must be in one letter code. However, the program will make the translation for you.
Chapter 4.1.2 Defining new abbreviations
A more direct way to enter a new abbreviation is to press the "New Abbreviation" button. A very similar "Abbreviation Editor" (See Figure 3) window is displayed in which the abbreviation can then be defined. The same editor is displayed after selection of an abbreviation from the list and pressing "Edit Abbreviation" button. If you try to define an abbreviation which already exists, the computer will ask whether it should overwrite the old definition with the new one. Note that some "critical" (such as H, OH, NH2) abbreviations cannot be edited.
At the end of the session (when quitting Peptide Companion) you will be given a chance to save all of the abbreviation changes to the disk. You will have to enter your password (which you have defined during the installation). Any changes must be accompanied by the correct password. You can change the password by clicking at "File" item in the menu line and continuing by clicking at "Change Password". The window "Change Password" will appear and after correctly entering the assigned password, you will be able to define the password of your choice. Chapter 4.1.3 Trifunctional amino acids In the case of trifunctional amino acids it is better to define the molecular composition without the side chain H or OH, and then to specify the functionality of the side chain which will be added automatically, when there is no protecting group on the side chain. The program will ask you which default group you want to add in these cases (H, OH or nothing). Sulfur (SH) containing amino acids (Cys, Pen, Hcy, Mpa, Cpp, Pmp, Dmp, Dep) written in the "-Cys-" form indicates the oxidized state (cyclic) peptide. If you want to specify free cysteine, you have to write "-Cys(H)-". Chapter 4.1.4 Side chain substitution of amino acids If you want to substitute the side chain of a normally unsubstituted amino acid, you must compensate for the loss of hydrogen in the side chain. The best solution is to define a new abbreviation for the modified amino acid. For example, "-Phe(Cl)-" will give you a summary formula one hydrogen too big. The correct result can be obtained by using "-PhCl-" as a new abbreviation and entering C9H8NOCl as the molecular formula of PhCl. (If there is no editing window displayed after using the new abbreviation, then this abbreviation already exists in memory, but it can be defined for something else. In this case check the result carefully or check the composition of this abbreviation!)
You must always think what is going on when you substitute the side chain - if you are replacing H (or OH, NH2, etc.) by any substituent (Cl, Br, I, NO2,...), or if you are just adding atoms (e.g. Met - Met(O) - Met(O2)). (Using the wrong nomenclature will produce the wrong result. As the program cannot guess what you want, it will do only what you ask it to do.)
Chapter 4.2 List of defined abbreviations
Chapter 4.3 Entering the peptide formula Chapter 4.3.1 Entering linear, cyclic and branched peptides The peptide formula is written in the usual way using the above given abbreviations and a dash ("-") to represent a peptide bond. The amino acid or peptide chain must have specified N and C-terminal functionality. Any peptide without N-terminal H and C-terminal OH is interpreted as a cyclic structure. Additional cyclization (side chain to side chain) may be realized by subtraction of water (addition of -1 H2O) from the structure of a linear peptide, or adding empty parentheses to amino acids engaged in cyclization. Another possibility is to add parentheses containing underline ("_") to amino acid side chains forming the additional cycle. For the rules of disulfide cyclic structure representation see 4.1.3. Repetition of a structural motif can be expressed by square brackets ("[...]n"). Everything inside of these brackets is counted n-times. This is a useful tool for writing the formulae of polymers, repeating sequences of amino acids, or the formulae of MAPs (in this case, do not forget that in repeating Lys, you must show that the side chain is substituted - add parentheses with an underline "(_)", or empty parentheses "()"). Chapter 4.3.2 Entering peptides with modified peptide bonds You can modify the peptide bond by replacing the "-" sign in the
peptide formula by "<...>" and writing either an abbreviation or a
summary formula of the peptide bond replacement within these
brackets (e.g. ...Tyr
Chapter 4.3.3 Examples of peptide formula representation acceptable to Peptide Companion
Chapter 5 Functions of Peptide Companion
After you start the program, the
"Main" (See Figure
5) window ("Peptide
Companion") is displayed. It contains the following buttons: "List
Peptides", "Write from Scratch", "Three Letter Code", "EA, AAA,
M.W.", "HPLC Prediction", "MS Fragmentation", "Difficult
Sequences", "Conformation / Profile", "Library", "Digest", "AA
Composition from M.W." and "Exit".
Chapter 5.1 Use or modify peptide formulae (Database
of sequences, "List Peptides"
(See Figure 6) button)
You can select all peptides from the given database fulfilling the
selection criteria.
Click on "List Specifications"
(See Figure 8) and a window which
allows you to define a character string which will be sought in the
peptide formulae or in peptide names.
Clicking on a
peptide name (See Figure
9) selected by the use of selection criteria
will display its structure in the lower field. If a structural element (partial
sequence) was used as the selection criteria, the first occurrence of
the defined sequence will be highlighted in the selected peptide
formula. If no peptide meets the selection criteria, the original
database will be displayed.
Chapter 5.2 Input formula (
"Write from Scratch" (See
Figure 10) button)
Chapter 5.3 Translation of codes ("Three Letter Code" button)
You can enter a peptide formula either in the one-letter code or in the
three-letter code. One-letter code can be entered in both the upper
(bigger) and lower (smaller) windows. Three-letter code typed in the
upper window is being translated into one-letter code in the lower
window automatically. If the formula is being typed in a one-letter code
(in any window), the button "Three Letter Code" must be clicked
before any calculation is attempted. The code is then translated into
the three letter code in the upper window. You will be warned to check
the termini of the peptide since the program is automatically assuming
that you want to calculate for an unprotected linear peptide.
Chapter 5.4 Calculation of elemental analysis, amino
acid composition and molecular weight ("EA, AAA, M.W."
(See Figure 11) button)
The results of the calculations are shown on the screen and can also
be sent to the printer (see section 6).
The information on the screen
shows the name of the compound, its formula, summary formula,
molecular weight, molecular weight for mass spectroscopy (M.W.
(monoisotopic)), elemental composition, and amino acid composition.
You can modify the formula in the formula window and recalculate the
result ("Recalculate" button). You can also save the peptide formula
("Save Formula" button). The "Other Elements" button will display
composition of all elements in the sample.
Chapter 5.4.1 The addition of various molecules
("Add AcOH ..." (See Figure
12) button) and calculation of probable composition of
the lyophilizate ("Fit to Found" button)
Clicking buttons "Add AcOH..." or "Fit to Found" transfers you to the
window allowing the addition of molecules of AcOH, H2O (also
subtraction), TFA, HCl, HBr, HF, and/or inorganic residues (% of Ash).
Clicking on the appropriate scroll bar can add molecules in 0.25 or
1.00 increments. Pulling the scroll bar button or entering the value in
the value window can enter any value.
Freeze-dried samples of peptides usually contain various amounts of
water and acetic acid (if this was the last solvent system from which
the peptide was lyophilized). You can try to fit the found values from
the result of elemental analysis to the theoretical values obtained by
the addition of molecules of water and acetic acid to the peptide
(either with or without added salts). You are prompted to input values
found by elemental analysis and a range in % under which you will
consider the result satisfactory. Elemental compositions satisfying the
condition are calculated. All satisfactory results are displayed in the
lower right hand corner with the best fitting analysis highlighted.
Chapter 5.5 Prediction of RP HPLC retention times
("HPLC Prediction" (See
Figure 13) button)
After pressing the "HPLC Prediction" button you will be able to
choose the prediction algorithm. You can use one of the following set
of parameters:
If you want to use a generic set, based on the data of Guo D., et al.
(J. Chromatogr. 359, 499 (1986)) with the correction for molecular weight
(Mant C.T., Burke T.W.L., Black J.A. and Hodges R.S.: J. Chromatogr.
458, 193 (1988)) just press the "Predict" button. This set is the most
complete since it was completed by the calculated values for various
protecting groups. If you want to use a different set of parameters,
select the desired option and press the "Predict" button again. The
new prediction will be overlayed on the trace. If you don't want to
overlay the new prediction, press "Clear Trace". The buttons "Load
Standard" and "Load Sample" will let you select the appropriate
peptide from any database of peptides available to you. Formulas are
loaded either by pressing the "OK" button or by double clicking on the
chosen name. Peptide formulas can be edited within their windows, or
they can be written from scratch. The peptide formula last edited in
the main window will be used as the sample in the transfer to the
"HPLC Prediction" window. An arbitrary peptide is used as default
standard in the prediction, unless otherwise specified.
For better comparison of calculated and experimentally determined
values, you can enter retention time of the standard peptide observed
in your experiment - - press "Set Standard Time". You will be
prompted to enter the "dead time" of your column (which depends on
the column dimensions, stationary phase, and flow rate) and retention
time of your standard (or retention times of your standard under
different conditions). Prediction will then be corrected for the values
observed experimentally. Newly entered column parameter (dead
time) will be used in all subsequent calculations during the present
session.
If you use an abbreviation, for which the retention characteristics are
not defined, you will be informed about this fact. However, the
prediction will be performed and in the case that both the standard
and your peptide contain the same unknown abbreviation, their
relative positions will be predicted correctly.
Results of predictions can be printed either as the values or also as
the traces. For the details see section 6.
Chapter 5.6 Fragmentation for Mass spectroscopy
("MS Fragmentation" (See
Figure 14) button)
Clicking on any value in the sorted list will highlight the appropriate
fragment. Double clicking on the value or fragment structure will
display its full structure and values for the appropriate possible types
of fragmentation. For more information about fragmentation of
peptides see e.g. Stults, J.T. in "Biomedical Applications of Mass
Spectrometry", Vol. 34, p. 145-201, Wiley, New York, 1990, or
Bieman, K. in "Methods in Enzymology", Vol. 193, p. 455-479,
Academic Press, New York, 1990.
To compare your results from the spectral measurement with the
theoretical data, click the button "Found". The displayed window will
prompt you to enter the value which you consider to be the molecular
peak of your compound. The program will analyze possible reasons
for a difference between your value and theory (by pressing the
"Analyze" (See Figure
15) button or
Enter). It will tell you whether you did not
completely remove a protecting group, modified the peptide during
work up, forgot to couple some amino acid, and so on. Remember
that this analysis depends on the precision with which you have
determined your experimental data (and which you can change by
editing the "Accuracy" window.
Chapter 5.7 Prediction of synthetically difficult
sequences ("Difficult Sequences"
(See Figure 16)button)
Clicking on the "Difficult Sequences" button will show graphical
representation of aggregation potential for amino acids starting from
the fifth position in the peptide chain. If it is difficult to associate the
point on the graph with the amino acid residue on the x axis, point to
the particular position with the mouse pointer, and the amino acid
label will be displayed in the lower left corner, together with the
predicted coupling difficulty. Only sequences containing natural
unprotected amino acids can be evaluated since the aggregation
parameters are not defined for unnatural building blocks. If you want
to use this program to evaluate unnatural sequences, replace
unnatural building blocks with natural amino acids having similar
coupling properties (make a qualified guess). This program also will
not suggest the optimal combination of protecting groups to overcome
formation of difficult sequences -- there is not enough experience to
write a successful algorithm. However, once the sequence is predicted
as difficult, one should consider various synthetic alternatives for the
given sequence (various protecting groups, protected asparagine and
glutamine, protected backbone, cyclic alternatives of Cys and/or Ser,
double couplings, chaotropic salts, high temperature coupling,
coupling in ultrasonic bath, etc.).
This part of the program analyzes peptide/protein sequences. The
protein analysis includes calculation of conformational profiles
according to the Chou-Fasman algorithm and evaluation of protein
profiles and amphipathic profiles. Ten different scales are available
(hydrophilicity, hydrophobicity, acrophilicity, accessibility, antigenicity,
and hydropathy). The program uses peptide/protein sequences stored
in files in standard NIH format (see below); the sequence can be also
typed from the keyboard, edited, and stored on disk. Although this
option is intended for evaluation of longer peptides and proteins,
peptide formulas typed in the main window, or retrieved from the
database of peptides can be used. However, only peptides composed
of natural amino acids and without any side chain modifications can
be evaluated. The program will recognize any unnatural parts of the
peptide and truncate the formula.
Amino acid sequences of proteins are stored in files in standard NIH
format. Each file can contain any number of comment lines; each
comment line must start with a semi-colon (;), and all of these lines
are ignored by the program. The line immediately preceding an amino
acid sequence contains the name of the protein and it will appear on
every output as the protein name. The program uses amino acid
sequences written in the standard one-letter amino acid code using
upper- or lower-case letters. Peptide/protein sequences written in the
three-letter code will be converted to one-letter code (when entered
in the main window, or when generated by Digest option).
Standard termination of a sequence is indicated by the digit 1 or 2 or
an asterisk (1, 2, or *). Any further lines are ignored. The present
version of the program can run proteins up to 3000 amino acid
residues long.
Chapter 5.8.2 Functions of the
"Predict" (See Figure
17) window
Clicking on the "Conformation / Profile" button brings you to the
"Predict" window. There are three categories of commands:
Chapter 5.8.2.1 Basic (File) commands
"Load/Save" button:
This option allows you to load (open) a file containing a protein
sequence, save the protein sequence in a file, and delete any file (not
only those containing protein sequences).
To load a protein sequence, click on the selected file in the current
path and directory that contains the amino acid sequence of the
peptide/protein, e.g. TEST.SEQ and click on "Load" button (or double
click on selected file). The name of the protein (but not the name of
the file) and its amino acid sequence appears on the screen. The
default directory is the working directory (e.g. C:\PCOM), it can be
changed by double clicking on the new path from the "Load/Save"
window.
To delete a file, click on the selected file (or type its name in the
File name window), and click on the "Delete" button. You will be asked to
confirm the operation.
"Setup" (See Figure
18) button:
This command enables one to change the length of the window in the
protein profile, the length of the amphiphilic helix, the probability limit
for beta-turn formation, and the path from which data are read. You can
use the new values temporarily ("Close and Use New Setup"
button), save them to disk ("Save Setup to Disk and Close") or
cancel the setup ("Cancel" button).
"Close" button:
This command returns you to the Peptide Companion main menu.
The currently loaded protein sequence and results of calculation will
be lost.
Editing a sequence:
The sequence residing currently in the memory can be edited. Peptide
Companion uses the standard Windows editor including features
Copy, Delete, Paste, and Undo. For details see your Windows
manual.
Chapter 5.8.2.2 Evaluate commands
Chou-Fasman parameters
("Chou-Fasman" (See Figure
19) button):
Conformational parameters are evaluated by the Chou-Fasman
algorithm, one of the most common secondary-structure prediction
methods (Chou, P.Y., and Fasman, G.D. (1978) Adv.Enzymol. 47,
46-148). In this method, each amino acid has been assigned a
conformational potential for a-helix, b-sheet, and b-turn formation,
derived from the frequency of its occurrence in the particular
secondary structure. Then, the mean potential of all consecutive
tetrapeptides for all three conformational states (Ph, Ps, and Pt) is
calculated. As a measure of propensity to form a b-turn, an extra
parameter, the positional probability of b-turn occurrence, p, is
calculated by multiplying empirical constants for four consecutive
amino acids. According to Chou and Fasman, the tetrapeptide tends
to form a b-turn when p 0.75 - 1x10-4.
Protein profile ("Protein Profile" button):
Nine different protein profiles can be evaluated. Each amino acid is
assigned a numerical parameter value according to the selected
scale. The program determines the mean value of a seven-peptide
window (default value) moving along the protein sequence. The
profiles are normalized for the purpose of comparing different sets of
parameters. The mean hydrophilicity (or accessibility, etc.) over the
entire protein is calculated and a zero value is arbitrarily set at this
average. The values +1 and -1 are set for the maximum and minimum
local hydrophilicity, respectively.
The following scales are available:
You can also define your own scale. Pressing
"Edit Custom Scale" (See
Figure 20)
will let you introduce new parameters, which can be saved for later
use ("Load/Save" button). Above defined scales are stored
independently on the disk (extension *.scl) and can be loaded and
modified. However, we strongly recommend saving newly defined
scales under different names to avoid possible confusion.
Amphipathic profile ("Amphipathic" button):
This subroutine evaluates the amphipathicity of all consecutive protein
fragments of a selected length (default value 11). Using the scale
selected (ten scales available), the hydrophilicity vector is calculated
and normalized in the same way as described for the protein profiles.
The highest value of local amphipathicity indicates the most
hydropathic segment of the protein. The helical amphipathicity has
been shown to correlate with the localization of T-cell determinants
(Margalit H. et al. J.Immunol. 138, 2213 (1987)).
To inspect results obtained in the Evaluate procedure, click on the
appropriate button and profiles or parameters will appear on the
screen.
View graph: Clicking on the "Profile" (protein profile or amphipathic
profile) or "Chou-Fasman" button will show you results in a graphical
representation. You can zoom in on any portion of the protein: select
the first amino acid of the zoomed window by mouse (the aa
numbering appears in the window below the profile), click and hold the
left mouse button, move the mouse to the last amino acid of the
zoomed window, and release the mouse button. The "Zoom out"
button will show you the whole protein.
View: Click on the "Chou-Fasman" button and a table with Chou-Fasman
parameters will appear on the screen. Use the scroll bar to
see any part of the protein. Since B-cell determinants very often reside
in those parts of a protein molecule that have a high tendency to form
a b-turn, the Chou and Fasman algorithm can be used for the
prediction of potential B-cell determinants. Click on the "Turn" button
and the program output lists only tetrapeptide sequences having a
probability of b-turn occurrence greater than a preselected limit,
usually 1.5x10-4 (default value).
The "Profile" button will show you a segment of protein or
amphipathic profile in the bar graph form. This is useful if you want to
see the full profile in the same scale together with the amino acid
sequence. Use the scroll bar to move along the protein sequence.
This option can display only 1000 amino acids.
An example of an output:
(See Figure 21)
Normalized profile: each bar represents the mean value of a
heptapeptide (default value) window centered at the 4-th amino acid.
The bars extend upwards when the local hydrophilicity is greater than
average, and vice versa.
The "Helical wheel" (See
Figure 22) button will show you a standard representation
of the helix in an axial view (default length 18 can be changed
permanently by pressing the "Setup" button and saving the change
after editing the "Setup" window, or temporarily by pressing "Set
Length" button) and in an unwrapped tubular view (standard length
50 amino acid residues). Hydrophobic amino acids are in green
circles, polar ones are in red (acidic), blue (basic), and/or brown
(other) circles. Use the "Next" or "Previous" buttons to walk along
the protein. For fast changes use the horizontal scroll bar. The
"3D Wheel" (See Figure
23)
shows helical arrangement in three dimensional space. The
view can be turned by defined (editable) increments by clicking on the
arrows below the picture box.
Chapter 5.9. Library
("Library" (See Figure
24) Button)
Distribution of the masses is calculated using integer values of
building block masses and it does not take into account the isotopic
distributions. It can be used for rough evaluation of the quality of
prepared library (Andrews et al., in Techniques in Protein Chemistry,
Vol. V, p. 485, Academic Press, Orlando 1994) or for library design.
The proper selection of library building blocks can simplify mass
spectroscopic evaluation of the results.
New building blocks can be defined for library construction. Care must
be taken not to use an abbreviation already defined for protecting
groups or other structural features. If the newly defined abbreviation
should be made permanent, it has to be saved when you exit the
program.
Clicking on the "Library" button will bring up a dialog box asking you
for the length of the library you wish to randomize. The default is 5
(minimum is 2 and maximum is 30). After you click "OK", the
"Library" window will appear.
Clicking on the "Table of Mass Dist" button will show the "Table of
Mass Distribution" window. In this window all possible molecular
weights generated in the library, together with the frequency of their
occurence are displayed. In the lower part of the table the highest,
lowest and average values are compiled. You can also save the table
("Save" button) for use in other spreadsheet programs (e.g. Excel,
Quattro Pro) as a text (.TXT) file. This feature can be used for that
purpose only as the table cannot be loaded in Peptide Companion.
Use the "Save Set" button in the "Library" window instead. For
printing the table see 6.3.7.
When you press the "Graph Mass Dist"
(See Figure 25)
button, the "Graph of Mass
Distribution" window appears. In this window you can press the right
mouse button to see the coordinates of the cursor, double click on the
graph and select a mass to show its value and frequency of its
occurrence in the library (this can also be done with the "Select"
button), or drag the left mouse button over the graph to zoom (press
"Zoom Out" button to zoom out).
Chapter 5.10 Enzymatic or chemical degradation of
peptides and proteins ("Digest"
(See Figure 26) button)
Proteins or peptides can be submitted to simulated enzymatic or
chemical (or combined) degradation. Loading this window brings
selected peptides to the sequence edit field. When no peptide has
been selected, an empty field will be displayed. A new sequence can
be loaded by pressing the "Load Sequence" button. Pressing
"Enzymatic", "Chemical", "Customize", or "Edit Cleavage" will let
you select the reagent or customize the cleavage specificity. The
number of expected fragments and their list would be shown in the
fragment list.
You can switch between the edit field and the fragment list ("Switch
Boxes" button or click on the tab on the bottom of the screen). After
the fragment is selected (by clicking on it), it can be loaded into the
edit field ("Edit Fragment" button) and can be edited for further
cleavage (by different reagent) or it can be loaded into the main
window or predict window ("Update Main" or "Update Predict"
buttons) and to any application from there. The "Customize" button
allows addition of any cleavage reagent and saving it in the database.
The "Digest" window uses the following command buttons.
"Enzymatic" / "Chemical" buttons load reagents from disk. The
"Customize" button enables you to write your own reagent and save
it to the disk as enzymatic, or chemical reagent (requires your
password).
"HPLC Prediction" (See
Figure 28)
button predicts the elution order of fragments on
the reversed phase column. This prediction uses algorithm of Guo et
al. (see section 5.5)
and all limitations discussed earlier apply here as
well. You can choose HPLC with detection at different wavelengths,
using different pH of mobile phase, you can zoom into the crowded
area of the trace, or you can
select (See
Figure 29) the
information (See Figure
30)
about any peak (See
Figure 31).
Chapter 5.10.1
Cleavage specificity nomenclature (See Figure
32)
Examples:
Chapter 5.11 Prediction of amino acid composition
"AA Composition from M.W."
(See Figure 33) button
Fields with blue background signalize that recalculation using newly
defined parameters was not performed. Parameters which can be
changed are: (i) Length of peptide; (ii) Molecular weight; (iii) Defined
amino acids; (iv) Amino terminal group (default H, choices Ac and
Custom); (v) Carboxy terminal group (default OH, choices NH2, OMe,
and Custom). After selection of Custom option you are prompted to
define molecular weight of terminal group and number of
exchangeable protons in this group. (If you will not be using D
Selection, you don't have to bother defining the last value.)
Any calculated composition can be transferred in the form of
sequence (generated by pressing "3 Letter Code" button) into any
other window ("Copy" button). Calculated amino acid compositions
can be saved in the file ("Save to File" button), or printed ("Print"
button). If the number of possible compositions exceed the available
memory space (usually above 4500 compositions), only fraction of
compositions is reported. (However, we believe that information of this
size is not valuable anyway.)
Chapter 5.12 Quit ("Exit" button)
Leaves the program. Program will confirm your intention to quit and it
will ask you whether you want to save any changes to abbreviation
definitions you may have made during the session. You can save the
changes only if you know your password.
Chapter 6 Printing the results
Chapter 6.1 Two ways to print in Peptide Companion
You can switch between Consecutive and Regular printing on any
window that has the "Print" menu. There are three items in the
"Print" menu, "Consecutive Printing", "Print Memory", and "Paper
Orientation". If "Consecutive Printing" is unchecked "Regular
printing" is on and "Print Memory" will be disabled. When you
check "Consecutive Printing", Consecutive printing will be on and
"Print Memory" will be enabled. When you switch the Consecutive
printing on or off the change will be done in "Print" menus in all
windows.
Chapter 6.2 Changing the paper orientation
You can change the paper orientation by selecting the "Print" menu,
choosing "Paper Orientation" submenu and choosing the orientation.
When "Consecutive Printing" is enabled the program will print the
memory when the orientation is changed.
Chapter 6.3.1 EA, AAA, M.W. window
First select what part you want to print. There are three checkboxes in
the "Print" frame: "M.W./Summary" - this option prints molecular
weight and summary formula; "AAA" prints the amino acid analysis;
"EA" prints the elemental analysis. Then press the "Print" button.
Chapter 6.3.2 Correction of Elemental Analysis window
The printing procedure is very similar to the previous one. There are
two option buttons: "All Fits" prints all fits if you calculated the best fit;
"Selected Fit" prints just the selected fit. There is also a "Results"
checkbox; if it is checked, it will print the results obtained by
calculation. Press the "Print" button.
Chapter 6.3.3 HPLC Prediction window
When you press the "Print" button in the "HPLC Prediction" window
the computer will ask you if you want to "Print All", which means that
the values plus the graph are going to be printed (this option cannot
be printed into memory and will be printed immediately), or "Only
Values" which means that only the peptide formulas plus the values
are going to be printed.
Chapter 6.3.4 MS Fragmentation window
You can print "All Fragments" or just the "Selected Fragment" by
choosing an option in the "Print" frame. You can choose to print All
Masses by checking the "All Masses" check box; they will be printed
as the last information.
Chapter 6.3.5 Prediction of Difficult Sequence window
Refer to printing Graphs in the "Predict" window.
All graphs in the "Predict" window that have a "Print" button can be
printed; you can also print the Chou-Fasman parameters. If you zoom
the graph, it will be printed zoomed.
In the "Library" window you can print the set of building blocks by
pressing the "Print" button. In the "Table of Mass Distribution"
window you can print the table by pressing the "Print" button. In the
"Graph of Mass Distribution" window you can print the graph (as
seen on screen) also by clicking the "Print" button (this is the same
as in the "Predict" window).
You can print the fragments of the peptide by pressing the "Print"
button. The computer will ask you whether you also want to print the
whole sequence.
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In all windows Close or Cancel button will return to the previous
window. Cancel button cancels all operations on the windows closed,
Close button does not.
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