This format is the main goal of the whole program. It is designed to be the pre-step of a bulk data uploader of a database.
The file is line oriented.
Empty lines may be in the file and should be ignored.
Every other line has a character describing its purpose in column 1. A number may follow immediately. The true content follows after a blank.
Roughly, a line has this format:
cnum data...where c is a purpose code, num is the optional number and data is the content of the line.
Characters in lower case indicate a description of a line. The corresponding upper case character contains data without a description. E.g. the fictional lines
m "ID";"MESSAGE" M7 42;"This example is rather stupid."show that a line pair exists for the code M. The first like with the lower case M acts as a pattern how to parse the next line. M7 indicates that this is the 7th item of M. The counting itself is independent of data specific id numbers as shown in this case. 42 is the value of the ID entry, "This example is rather stupid." is the value of the MESSAGE entry.
Some contraints of the structure:
This line is given once directly after the pattern lines.
| name | content |
|---|---|
| PROGRAM | Name of the producer. This is "MRES2X" in all cases. |
| CODEPAGE | The used codepage while processing the input files. This value may not be of any interest, because the input data was generated in another codepage. |
| PRG_VERSION | This value is a string and represents the version of this program in our source repository. Even small changes should change tis number. |
| DATA_VERSION | This value is a number with two fractional digits. The fractional part is increased if new fields have been added to the various content lines. The integer part is increased on structural changes, e.g. new line codes or removal of fields or lines. |
| MAX_FILES | This value contains the number of input files that are about to be processed. The final number of processed files may not be the number of input files mentioned here, because mres2x does a single step processing and continues its work even when errorneous input files have been detected. The buggy file names are included in this number. |
This line is given once as the last line in the output file. A severe error can be considered if this line doesn't appear. A roleback is suggested for the last data set.
| name | content |
|---|---|
| RETURNCODE | Code that will be returned to the caller of the program. This is either 0 or 1 currently. 0 indicates full success, 1 indicates at least one error. |
| LISTED | In opposite to Code H, field MAX_FILES, this entry contains the number of actually listed input files in the output file. Note that even errorneous data sets are counted if they are shown at least partially. |
This line introduces the processing of a new input file. All following lines up to EOF (in case of en error) or a Code O-line are related to this individual file.
| name | content |
|---|---|
| TYPE | Processed data type. "MIS" indicates an MS/MS run. "PMF" indicates a peptide mass fingerprint. Other elements are not planned to be supported. |
| AVERAGE | This is the kind of processing that has been made. 0 indicates a
monoisotopic computation, 1 a computation with average mass values. See parameters:MASS |
| CLEAVAGE | This is the chemical digest used in this experiment. A typical value is
"Trypsin". See parameters:CLE |
| DB1 | This is the description of the database used. There is no list or
nomenclatura to use, so expect differences where no differences are
and vice versa. This name is hopefully comparable with other experiment's
DB1 field. An example is
"yeastsgd". See parameters:DB |
| DB2 | This is a more exactly description of the database used. There is no list
or nomenclatura to use, so expect differences where no differences are
and vice versa. An example is
"yeast_all_sgd.fasta 3018992". The used filename by
Mascot is listed, followed by the number of residues. The intention for
this field is to create a possibility to distinguish between several
experiments with the same database but with a different dataset, which
may result in incomparable values. See header:release and header:residues |
| FILENAME | This field contains the filename of the experiment. The path components
are stripped off as well as the suffix (as far as it is well known). This
is not the input file name. It is the name of the file that has
been listed in the input file. See parameters:FILE |
| PROGRAM | This field contains the program name that produced the input file.
A typical value is
"MASCOT 2.0.04". The text "MASCOT" is constant, the
number part is the version string passed in the input file. See header:version |
| ICAT | This field contains either 0 or 1. ICAT has been enabled if 1 is given.
ICAT is a dangerous field. It changes the results extremely but
is hard to detect if activated incidentally. See parameters:ICAT |
| INSTRUMENT | This field contains a string describing the used instrument. The big
differences between instruments become manifest in the following
parameter SEARCHES. Note that "Default" is a common value
and is it wrong in most cases where you don't use your microwave oven
as the instrument. See parameters:INSTRUMENT |
| SEARCHES | This field contains a list of numbers. Each number selects a different
ion series. The overall selection is done by chosing the instrument,
which is translated to this ion series list in the file
fragmentation_rules. Currently used rules (at RVZ):
|
| FRAGMENT_TOL | This field contains the fragment mass tolerance value. This is the radius
of the window around the measured points that must be hit to let a
fragment fulfill its "hit" criteria. See parameters:ITOL |
| FRAGMENT_TOLU | This field contains the fragment mass tolerance unit. This is either
"Da" or "mmu". See parameters:ITOLU |
| PEPTIDE_TOL | This field contains the peptide mass tolerance value. This is the radius
of the window around the computed peptide masses that must be hit by the
precursor mass to let a peptide fulfill its "hit" criteria. This value has an active influence on the intensity threshold(s), because the count of matching theoretical peptides in the window defines the threshold. See parameters:TOL |
| PEPTIDE_TOLU | This field contains the peptide mass tolerance unit. This is either
"Da", "mmu",
"%" or "ppm". See parameters:TOLU |
| VARIABLE_MODS | This field contains a comma-separated list of
modifications. Each modification has this form:
special=diff=description or
special=diff[neutral]=description
special is a special character selected by mres2x to be appended
to the modificated amino acid character later described. The special
character is choosen from the this list "@~#§!^°:;`'/={}[]()/"
from left to right.diff is the mass difference between the used value and the standard value (u - s). Note that Mascot uses the last amino acid in the mod_file to compute the value. Many things may go wrong if more than one mass difference has been applied to the various residues of one modification. [neutral] is given only if a neutral loss exists. neutral is a signed value describing the gain to the modification mass. E.g. @=79.978699[-97.995200]=Phospho (T) shows a modification gain of roughly 80 Da, but in case of a neutral loss you will have more or less 80-98 Da, which is an overall loss of 18 Da. description is a freely choosen text by the modifier of mod_file hopefully describing the modification enough. An empty string is possible for this variable. See masses:deltai and masses:NeutralLossi |
| FIXED_MODS | This field contains a comma-separated list of modifications. Each
modification has this form:
AA=diff
AA is a one of the characters used for amino acids, one of
the atoms
Hydrogen,
Carbon,
Nitrogen,
Oxygen, the electron mass electron or one of the
two terminus placeholders C_term or N_term.diff is the mass difference between the used value and the standard value (u - s). Default values are the weight of the molecules H and OH for the N terminus and the C terminus. An empty string is possible for this variable. See the section masses |
| PFA | This field contains either a whole number >= 0 which is the partials
factor. This is the maximum number of missed cleavages Mascot will compute with. The default value is 0 despite the documentation. See parameters:PFA |
| USER | This field contains the user name associated with the experiment. Note
that mres2x has the opportunity to
overwrite this field. An empty string is possible for this variable. See parameters:USER and the flags -u and -U |
| TIMESTAMP | This field contains the unix time stamp of the run of the analyzer
program, which is Mascot. Unix time stamps are seconds since
January, 1st 1970. See header:date |
| IDENTITY_THRES | This field contains the identity threshold shown
by Mascot. It is computed as follows for those who always want to know
how Earth spins.
Be m the average value of all qmatchi in the summary block. This value has to be divided by 20*p, but p is usually the famous p value of 0.05. Keep this in mind for the following computation: IDENTITY_THRESHOLD = 10 * log10(m) This value is shown in Mascot result presentations. See summary:qmatchi |
| QUERIES | This field contains the number of queries (series of measurement)
contained in the input file. See header:queries |
| COMMENT | This field contains the comment associated with the experiment. This
is the content of Mascot's TITLE entry. If this field isn't set or
bound to the empty string, the COM field is used. An empty string is possible for this variable. See parameters:TITLE and parameters:COM |
| CHARGE | This field contains the content of the charge search field of Mascot. This field is not the charge Mascot actually uses. In fact, Mascot ignores this field if the experiment provides a value. See here for used values during evaluation. An empty string is possible for this variable. See parameters:CHARGE |
| SEG | This field contains the content of the protein mass search field of
Mascot. This field changes all possible results significantly. Every non-empty value should be treated as a sign that this computation has been done for experimental reason. Never ever use results of this input file in a comparison of/groups with other results. An empty string is possible and expected for this variable. See parameters:SEG |
This line is given once for each occurence of the Code I input file description line. A severe error can be considered if this line doesn't appear after a Code I line or before the second occurrence of that line. A roleback is suggested for the last data set.
The number directly following the O will match the number following the I in the corresponding input file description line.
| name | content |
|---|---|
| SUCCESS | Code that indicates either success by a value of 1 or a failure in
case of a value of 0. In the later case it is advisable to
consider a roleback. Note that one failure in a containing query results in a failure of the input file. Nothing is said about other query results. They may be usable. |
This line introduces the beginning of a new query processing. At least one query usually is part of an input file. All following lines up to EOF (in case of en error) or a Code E-line are related to this individual file.
A query is characterised by a list of ions representing a peaklist with some additional informations. Most of these informations are extracted by programs out of the raw data file of the mass spectrometer.
| name | content |
|---|---|
| QUERY | This is the number of the query (1-based) in the current input file.
The number doesn't need to be consecutive. This number can be used for direct references into the source file. The numbering is identical. |
| CHARGE | This is the charge of the precursor found in the current query. See summary:qexpi's second value There exists a relation between CHARGE, MASS and PRECURSOR, see here. |
| MASS | This is the uncharged mass of the precursor molecule. See summary:qmassi There exists a relation between CHARGE, MASS and PRECURSOR, see here. |
| PRECURSOR | This is the value of the famous value of m/z of the charged
precursor ion. See summary:qexpi's first value There exists a relation between CHARGE, MASS and PRECURSOR, with H being the mass of a Hydrogen (either monoisotopic or average depending on AVERAGE!) it is: |
| MATCH | This field contains the number of matching peptides at different sites
of different proteins with their mass matching the range spanned by the
PEPTIDE_TOL around the
MASS value. See summary:qmatchi |
| IDENTITY_THRES | This field contains the identity threshold. It is
computed as follows from MATCH known as the MOWSE
score threshold (MOWSE = More Of Weird Statistical Errors).
IDENTITY_THRES = 10 * log10(MATCH) Note that this value isn't shown by Mascot usually. Mascot uses the overall value for the complete file explained here. See summary:qmatchi |
| HOMOLOGY_THRES | This field contains the homology threshold computed by Mascot.
The homology theshold is shown by Mascot in its overviews as threshold
of significant homology with p < 0.05 if this value
is less than IDENTITY_THRES. The author suggests max(IDENTITY_THRES, HOMOLOGY_THRES) currently as a good threshold of convincing results. See summary:qplugholei |
| TITLE | This field contains a string describing the title of the peak serie. An empty string is possible for this variable. See queryi:title |
| PEAKLIST | This field contains the list of peaks measured by the instrument.
Each peak is a couple of value and intensity (in this order) delimited by
a colon. The peaks itself are delimited by commas. See queryi:Ions1 |
This line is given once for each occurence of the Code B beginning of a new query processing. A severe error can be considered if this line doesn't appear after a Code B line or before the second occurrence of that line. A roleback is strongly suggested for the last data set.
The number directly following the E will match the number following the B of the beginning of the new query processing.
| name | content |
|---|---|
| SUCCESS | Code that indicates either success by a value of 1 or a failure in case of a value of 0. In the later case it is strongly suggested to do a data roleback. |
This line shows data of the summary section relating a distinct query.
Some lines in the summary section may be invalidated, which is normal, because the summary section contains protein choices of Mascot for the "best hit". This doesn't contain all different peak lists if more than one peak list is given at all. Thus, the HITNUMBER may have non-consecutive numbers if more than one query is used in an input file.
| name | content | ||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PROTEIN | This is the name of the protein Mascot assigned to a specific hit. The
kind and specification of the name is database depending. A string containing a comma is possible for this variable. The PROTEIN field with the QUERY field should be unique in one input file. See summary:hi's first element |
||||||||||||||||||||||||||||||||||||
| HITNUMBER | This is the number under which the PROTEIN is positioned
in the hit list. The smaller the number, the better the hit of the
protein. The HITNUMBER field with the QUERY field are unique in one input file. See the i in summary:hi |
||||||||||||||||||||||||||||||||||||
| TOTAL_SCORE | This is the total score of the proteine. It is the result of a complexe
formula known by Matrix Science. In general, is is the sum of each
individual peptide in the input file that matches this protein. Even
low scored peptides contribute their score to the sum, maybe partially.
One of the things not mentioned very well in the documentation is the
fact, that even different peptides generated by one peak
list will add their amount of score to the total score. |
||||||||||||||||||||||||||||||||||||
| TOTAL_MASS | This is the computed mass of the protein. See summary:hi's forth element |
||||||||||||||||||||||||||||||||||||
| MISSED_CLEAVAGE | This is the number of missed cleavages detected by Mascot for the
PEPTIDE. See summary:hi_qj's first element |
||||||||||||||||||||||||||||||||||||
| QUERY | This is the j in summary:hi_qj and is equal to the QUERY of a Code B line. | ||||||||||||||||||||||||||||||||||||
| PEPTIDE | This field contains the modified peptide
sequence. Every ambiguous amino acid code (B, X, Z) has been replaced by
a valid amino acid code. Every variable modification is annotated by
a modification code. It isn't impossible that
even the termini are modificated. Exactly in this case the modifications
of the termini is delimited by a period from the peptide's sequence. An example is "@.HMIIM~KKM" which has two modifications, one at the N-terminus, one other at the M in the middle. See summary:hi_qj's seventh element |
||||||||||||||||||||||||||||||||||||
| PEPTIDE_MASS | This is the computed mass of the peptide without charge. See summary:hi_qj's second element |
||||||||||||||||||||||||||||||||||||
| PEPTIDE_START | This is the position of the peptide in the protein (1-based). See summary:hi_qj's forth element |
||||||||||||||||||||||||||||||||||||
| PEPTIDE_SCORE | This is the score of the PEPTIDE Mascot has computed. The value is more or less useful depending on the thresholds. See summary:hi_qj's tenth element |
||||||||||||||||||||||||||||||||||||
| OCCURANCES | This is the number of occurances of the PEPTIDE's mass
in the pool of the masses of each possible peptide in the protein.
The information may be useful for PMF searches. See summary:hi_qj's eleventh element |
||||||||||||||||||||||||||||||||||||
| MATCHING_FRAGMENTS | This is number of matching ions. We still need to know which ions are counted both as "found" and which ion series are possible. See summary:hi_qj's sixth element |
||||||||||||||||||||||||||||||||||||
| MATCHING_PEAKS | This is number of matching peaks in the list of peaks for this peptide. See summary:hi_qj's eighth element |
||||||||||||||||||||||||||||||||||||
| SERIES_FOUND | This is a list of ion series found in the peak list matching the
theoretical spektrum of the peptide.
This string should have 17 characters (which is known to be different in some Mascot versions) being either 0 (not found), 1 (more than a random peak), 2 (scored peak).
See summary:hi_qj's twelveth element |
||||||||||||||||||||||||||||||||||||
| SERIES_FOUND_STR | This is a list of ion series found in the peak list matching the
theoretical spektrum of the peptide in a user readable form.
This value is the representation of SERIES_FOUND. Only
known series are displayed with at least more than random matches.
Unscored values are displayed in parentheses, scored values are displayed
directly. The entries are comma-separated. |
This line shows data of the peptides section relating a distinct query. AG Sickmann of RVZ uses this data preferable.
| name | content | ||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PROTEIN | This is the name of the protein Mascot assigned to a specific hit. The
kind and specification of the name is database depending. A string containing a comma is possible for this variable. See peptides:qi_pj's twelfth element |
||||||||||||||||||||||||||||||||||||
| PROTEIN_NUMBER | This is the running number of the various proteins in the list of
matching protein list for a particular PEPTIDE. The HITNUMBER field with the PROTEIN_NUMBER field and the QUERY field are unique in one input file. See peptides:qi_pj's twelfth element |
||||||||||||||||||||||||||||||||||||
| HITNUMBER | This is the number under which the PEPTIDE is positioned
in the hit list. The smaller the number, the better the hit of the
peptide for one particular query. The HITNUMBER field with the PROTEIN_NUMBER field and the QUERY field are unique in one input file. See the j in peptides:qi_pj |
||||||||||||||||||||||||||||||||||||
| TOTAL_MASS | This is the computed mass of the protein. This field may not be set due to Mascot#s format. The value is 0.0 in this case. The value is extracted out of the summary section or the proteins section. |
||||||||||||||||||||||||||||||||||||
| MISSED_CLEAVAGE | This is the number of missed cleavages detected by Mascot for the
PEPTIDE. See peptides:qi_pj's first element |
||||||||||||||||||||||||||||||||||||
| QUERY | The HITNUMBER field with the PROTEIN_NUMBER field and the QUERY field are unique in one input file.This is the i in peptides:qi_pj and is equal to the QUERY of a Code B line. | ||||||||||||||||||||||||||||||||||||
| PEPTIDE | This field contains the modified peptide
sequence. Every ambiguous amino acid code (B, X, Z) has been replaced by
a valid amino acid code. Every variable modification is annotated by
a modification code. It isn't impossible that
even the termini are modificated. Exactly in this case the modifications
of the termini is delimited by a period from the peptide's sequence. An example is "@.HMIIM~KKM" which has two modifications, one at the N-terminus, one other at the M in the middle. See peptides:qi_pj's fifth element |
||||||||||||||||||||||||||||||||||||
| PEPTIDE_MASS | This is the computed mass of the peptide without charge. See summary:hi_qj's second element |
||||||||||||||||||||||||||||||||||||
| PEPTIDE_START | This is the position of the peptide in the protein (1-based). See peptides:qi_pj's twelfth element |
||||||||||||||||||||||||||||||||||||
| PEPTIDE_SCORE | This is the score of the PEPTIDE Mascot has computed. The value is more or less useful depending on the thresholds. See peptides:qi_pj's eighth element |
||||||||||||||||||||||||||||||||||||
| OCCURANCES | This is the number of occurances of the PEPTIDE's mass
in the pool of the masses of each possible peptide in the protein.
The information may be useful for PMF searches. See peptides:qi_pj's twelfth element |
||||||||||||||||||||||||||||||||||||
| MATCHING_FRAGMENTS | This is number of matching ions. We still need to know which ions are counted both as "found" and which ion series are possible. See peptides:qi_pj's forth element |
||||||||||||||||||||||||||||||||||||
| MATCHING_PEAKS | This is number of matching peaks in the list of peaks for this peptide. See peptides:qi_pj's sixth element |
||||||||||||||||||||||||||||||||||||
| SERIES_FOUND | This is a list of ion series found in the peak list matching the
theoretical spektrum of the peptide.
This string should have 17 characters (which is known to be different in some Mascot versions) being either 0 (not found), 1 (more than a random peak), 2 (scored peak).
See peptides:qi_pj's nineth element |
||||||||||||||||||||||||||||||||||||
| SERIES_FOUND_STR | This is a list of ion series found in the peak list matching the
theoretical spektrum of the peptide in a user readable form.
This value is the representation of SERIES_FOUND. Only
known series are displayed with at least more than random matches.
Unscored values are displayed in parentheses, scored values are displayed
directly. The entries are comma-separated. |