CID Filename: Name of the CID data file. A full or partial
pathname can be specified.
CID Quality: If you would like the program to give you it's opinion
on the quality of the CID data, type "Y" or "N". I gave up on this and no longer use it, so
the default is “N”.
Peptide MW: Give the peptide molecular weight (NOT MH+!!)
including any number of decimal places, depending on the mass accuracy of the
instrument. For Sequest ".dta" files, a zero can be entered here, in
which case the peptide molecular weight is obtained from the file header.
Charge-state: This is the charge state of the precursor ion. Any
integer number can be used, although the program works best on CID spectra
obtained from singly or doubly charged ions. Triply-charged ion precursors in a
triple quad do not often yield complete sets of fragmentation ions sufficient
to delineate a full-length sequence. For Sequest ".dta" files, a zero
can be entered here, in which case the precursor charge is obtained from the
MaxEnt3: Were the data subjected to a Max Ent 3 type of
processing; ie, were the multiply charged fragment ions converted to their
singly-charged counterparts and were the C13 isotope peaks removed? Answer
"Y" or "N".
Peptide Error (u): This is the error in the peptide mass measurement in
Daltons or fractions of a Dalton. This tolerance can be set as tight as you
think your data warrants - 1 or 2 Daltons for low mass accuracy is suitable, or
you can use a few hundredths of a Dalton for very accurate mass measurements.
It is up to you. For LCQ data, the
software will try to “re-adjust” the peptide MW based on y/b ion pairs, so I
generally choose 0.65 u as the peptide MW error for ion traps. I use 0.45 for Qtof’s.
Fragment Error (u): This is the error in measurement of the m/z values
of the fragment ions. For high quality triple quad data with unit resolution in
Q3, I use a value of 0.5; for low resolution triple quad data I go with 0.75 or
1.0. For ion trap data, I typically use a value of 0.65. For poorly calibrated
Qtof data, I use a value of 0.15 to 0.25, but for very well-calibrated data
this tolerance can be reduced to 0.02 to 0.05 u.
Final Fragment Err (u): This value only applies to Qtof data. The idea is
that temperature dependent expansion and contraction of the flight tube will
change the calibration; however, the errors that result are linear. Lutefisk
operates by finding a list of candidate sequences, and then it scores these
candidates based on how well the predicted fragments match up with the observed
fragments. In the final evaluation of sequence candidates derived from Qtof
data, the calculated b- and y-type ions of each sequence are used to adjust the
calibration of the data. Once the data has been recalibrated, then this Final
Fragment Err is applied. Typically, I use a value of 0.02. If a value of zero
is entered, then this recalibration feature is disabled and not applied.
Lately, for Qtof data, I use a Peptide Error
of 0.45, a Fragment Error of 0.25, and a Final Fragment Err of 0.02. For
nanospray ion trap data (collected in profile mode so that monoisotopic peaks
can be identified), I use a Peptide Error of 0.45, a Fragment Error of 0.45,
and a Final Fragment Err of zero (no effect). Larger peptide and fragment
tolerances of 0.65 u are used for LC/MS/MS data from ion traps -- the
centroided ions are not monoisotopic, hence the greater error.
Max. Final Sequences: This is the maximum number of completed sequences
(sequences that equal the specified peptide mass plus/minus the peptide mass
tolerance) that can be stored before discarding low scoring sequences. This
value is dependent on the RAM available to the program (see below); I generally
use a value of 20000.
Max Subsequences: This is the maximum number of subsequences (partial
sequences that get extended amino acid by amino acid) that can be stored before
discarding low scoring subsequences. I usually allow 5000 subsequences to be
processed, but this is also dependent on the amount of RAM that is available
for Lutefisk. In one test case (Mac G3), I found that 12288 K was sufficient to
allow for 20000 final sequences (above) and 5000 subsequences; 4096 was
sufficient to allow for 10000 final sequences (above) and 2500 subsequences. I
would recommend giving Lutefisk a bit more than the bare minimum, since I won't
guarantee that in all cases your computer won't crash when short on RAM. In
addition, the number of subsequences allowed is also dependent on the processor
speed; I find that 5000 subsequences can take my G3 a few seconds to a minute
to process data from a 1500 u peptide.
Mass Scrambles for Statistics: To help determine if the output is correct or nearly
correct, Lutefisk compares the output to other sequences that are close
matches, but known to be wrong. Typically, a value of six is used for this
parameter, in which case, it derives the six best candidate sequences assuming
six different incorrect peptide molecular weights. The incorrect molecular
weights are 14 u, 28 u, and 42 u less than and greater than the correct peptide
mass. The results are known to be wrong, and the scores for these wrong
sequences are compared to the results derived by using the correct peptide
mass. If you don't want to make a comparison to wrong sequences, then enter a
zero for this parameter. Lately, I have
decided that this feature is not all that useful, so I use a value of zero.
CID File Type: Enter "F" if the CID data file is derived
from the Finnigan "List" program, "T" if it is a
tab-delineated ASCII file, "L" if it is a text file from the LCQ file
converter program, or "D" if it is a ".dta" file.
Profile/Centroid: Profile data is subjected to a 5-point digital
smooth; this is the only difference in processing. By entering a 'D' here, the
program automatically differentiates between profile and centroid data. When
using this default feature, I found that for some Sequest ".dta"
files the program would mistakenly decide that it was profile data, so data
files ending w/ ".dta" are automatically assumed to be centroided.
Peak Width (u): This value is used in the peak detection part of the
program, and is dependent on the resolution of the mass analyzer. For unit
resolved peaks, the program tries to identify and discard adjacent C13 peaks.
For unit resolved spectra I usually use a value of 1.5; for lower resolution
MS/MS data on a triple quad I use a value of 3. The auto-peakwidth seems to
work quite well for triple quad data. Put a zero here ("0") to use
auto-peakwidth when using profile data obtained from triple quads. For ion trap
data, use 1 and for Qtof data use a value of 0.75.
Ion Threshold: Data with an intensity greater than the average intensity
times this threshold is used for identifying peaks. I use a fairly low value of
Mass Offset (u): For data where the CID fragment ion m/z values are
consistently off by a known value, this value can be entered here. For example,
if the data is always low by 0.2 Da then 0.2 can be entered here. If it is
always high by 0.2, then the value of -0.2 is entered. This situation arises if
you acquire data at a different resolution setting than what the third
quadrupole was calibrated for.
Ions Per Window: The program steps from ion to ion and counts the
number of ions between it and a mass 120 Da higher (120 Da is close to the
weight averaged amino acid residue mass). If there are too many ions within
this moving window, then only those with the greatest intensity are retained.
For regions of a CID spectrum that could contain multiply charged fragment
ions, this window is narrowed accordingly (e.g., 60 Daltons for regions that
could possibly contain doubly-charged fragment ions). I usually use a value of
6 ions per window for unprocessed profile data. If your CID data contains
centroided or peak top data that you have already processed by hand, i.e.,
you've eliminated superfluous ions and you wish to use all of the ions in the
interpretation, try using a larger number here (like 20).
Ions Per Residue: This sets an overall limit to the number of ions to
be considered. Since an average residue is of mass 120 Da, then a peptide of
mass 1218 would be expected to have around 10 residues. I usually use a value of
2.7 here, so in this example, the number of ions used for sequencing would be
limited to 27.
Transition Mass (u): This is the mass where the fragment mass values are in
transition from monoisotopic to average mass values. Below this cutoff, peptide
molecular weights and fragment ion m/z values are assumed to be monoisotopic
masses. Above this cutoff average masses are assumed. For triple quadrupole
data, I usually use a value of 1800. The cutoff is not abrupt; rather the
switch occurs linear over a 400 Da range below the cutoff mass (ie, if 1800 is
selected, the masses below 1400 are assumed to be monoisotopic, and those
between 1400 and 1800 are in between). Since LCQ and Qtof data routinely give
at least unit resolved MSMS data, I tend to set the cutoff very high (5000) for
the trap data. This ensures that the program never has to deal with average
Fragmentation Pattern: The idea here was to allow for different types of
fragmentation patterns to be recognized by the algorithm, thereby increasing
the probability that the correct sequence will be amongst the candidate
sequence list. Currently, there are only three types available - low energy CID
of tryptic peptides on a triple quad, low energy CID of tryptic peptides on a
Qtof, and low energy CID of tryptic peptides on an ion trap. So this means that
for now you must enter 'T' (for triple quad), 'Q' (for Qtof), or 'L' (for ion
Max. Gaps: A gap is a dipeptide of unknown sequence, but of
known mass. Usually I allow the presence of only one gap per sequence. However,
since the two N-terminal amino acids are so frequently unsequenceable, this
"gap" is not counted in this limit. A value of "-1" is typically
used, which is a signal to use a default number of gaps per sequence that
depends on the peptide mass -- larger peptides are allowed more dipeptide gaps
than smaller ones.
Extension Threshold: For a given subsequence there may be several
possible amino acid extensions. The extension with the best score determines a
threshold that the other extensions must exceed - highest score times this
threshold equals the limit. I've been using a value of 0.15.
Max. Exentensions: In addition to the threshold described above, it is
possible to set a limit on the number of extensions allowed for each
subsequence. Only those extensions with the highest score are used and the low
scoring extensions are ignored. I use a value of 6 here.
Cysteine Mass: This variable is necessary to account for the
various ways of alkylating cysteine residues. The easiest way to deal with the
many possibilities is to have the user enter the residue mass of cysteine -
160.03 for carbamidomethylated cysteine, 161.01 for carboxymethylated cysteine,
208.07 for pyridylethylated cysteine, or any other value you want.
Proteolysis: This is different from the "fragmentation
pattern" described above. If tryptic proteolysis ("T") is
selected then both Arg and Lys are forced into the C-terminal position
regardless of whether there is any fragmentation data to support their
presence. This does not eliminate other possible C-terminal amino acids; it
only insures that Lys and Arg are included as possibilities. Likewise,
selecting Lys-C ("K") insures that Lys is at the C-terminus, and
selecting Glu-C or V8 ("E") insures that Asp and Glu are considered
as C-terminal amino acids. By selecting Asp-N ("D") the program makes
sure that D is considered for the N-terminal amino acid even if there is no
data supporting it is presence.
Modified N-terminus: You must specify the mass of the N-terminus. For example, use 1.0078 for an unmodified
peptide, 43.0184 if the peptide has been acetylated, or 44.0136 for
Modified C-terminus: You must specify the mass of the C-terminus. This is typically 17.0027 for unmodified
Present Amino Acids: If a complete sequence lacks one of these amino
acids then it is discarded. Use single letter code without spaces. Use '*' to
Absent Amino Acids: These amino acids are not even considered when
generating sequences. Use single letter code without spaces. Use '*' to denote
Auto Tag: Auto-tag looks at the most intense ions at m/z
values greater than the precursor. It then tries to find short stretches of
sequences called "sequence-tags", which are used to limit the number
of sequences that are generated. I recommend using it for triple quad and Qtof
data obtained for tryptic peptides with doubly-charged precursor ions. Specific
sequence tags can still be entered as described below. Since ion trap data can
have both b and y ions in the m/z region greater than the precursor ion, I find
that it is best to not use the Auto-tag when sequencing with trap data.
Tag Low Mass y Ion: A sequence tag is a short stretch of sequence,
usually interpreted by hand, that is surrounded by regions of unknown sequence
but of known mass. Typically, these sequence tags are determined from y-type
ions at m/z values greater than the precursor ion. If you have a sequence tag,
then for this parameter, enter the m/z value of the lowest mass y ion in the
series of y ions that delineates the sequence tag. If you do not wish to enter
a sequence tag, then this value should be zero.
Sequence Tag: If you have a sequence tag, use the single letter
code without spaces ordered from the low mass y ion to the high mass y ion. If
you do not have a sequence tag, enter an asterisk ("*").
Tag High Mass y Ion: If you have a sequence tag, then the m/z value of
the highest mass y ion in the y ion series that delineates the sequence tag is
entered here. If you do not wish to enter a sequence tag, then this value
should be zero.
Edman Data File: The program used to use Edman sequencing data, but
this is no longer supported.
DB Sequence File: If you have any sequences or a sequence that you
might think is correct (derived from, say, a database search), this information
is put into this file. Give the path and filename, and if this is left blank,
then no database-derived sequences are checked.
Shoe size (US): Enter your shoe size here. If no entry, then a
default value of 15 will be assumed.
Number of sequences: Number of sequences to list in the .lut output
file. This number is the upper limit,
and in many cases there will be less.
Score threshold: The lower Pr
score (probability of having half of the sequence correct) limit. Typically, a lower threshold score of 0.2 is
fine. To maximize the number of
sequences in the output, make this value 0.01 and give a high number to “Number
of sequences” (e.g., 50).