OMSSA

The Open Mass Spectrometry Search Algorithm
OMSSA was developed by Lewis Geer at NCBI/NIH. This page is my OMSSA help page resource. Given that all parameters are specified on the omssacl command line, I wanted a single page where they are all listed for easy reference. The help text for OMSSA version 2.1.9 are listed below. Actually the download unpacks a 2.1.9 directory but the version output states 2.1.8. I'll assume they forgot to update the version string in the linux binary as the other distributions also unpack to a 2.1.9 directory.
Unfortunately OMSSA is no longer being supported at NIH.
Selected OMSSA publications
"Open mass spectrometry search algorithm." Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH. J Proteome Res. 2004 Sep-Oct;3(5):958-64. link
Example OMSSA command line
```
omssacl -e 16 -i 1,4 -mf 3 -mv 1 -tem 0 -tom 0 -te 1.0 -to 0.5 -tez 1 -he 100000.0 -zcc 1 -hl 5
```
- semi-tryptic search (-e 16)
- b/y-ions (-i 1,4)
- carbamidomethyl C static mod (-mf 3)
- oxidized M variable mod (-mv 1)
- monoisotopic precursor (-tem 0)
- monoisotopic fragments (-tom 0)
- precursor tolerance 1.0 (-te 1.0)
- fragment tolerance 0.5 (-to 0.5)
- linear charge dependency of precursor charge (-tez 1)
- maximum e-value 100000.0 (-he 100000.0)
- believe precursor charge (-zcc 1)
- retain top 5 hits (-hl 5)
OMSSA help (version 2.1.9)

USAGE
  omssacl [-h] [-help] [-xmlhelp] [-pm param] [-d blastdb] [-umm] [-f infile]
    [-fx xmlinfile] [-fb dtainfile] [-fp pklinfile] [-fm pklinfile]
    [-foms omsinfile] [-fomx omxinfile] [-fbz2 bz2infile] [-fxml omxinfile]
    [-o textasnoutfile] [-ob binaryasnoutfile] [-ox xmloutfile]
    [-obz2 bz2outfile] [-op pepxmloutfile] [-oc csvfile] [-w] [-to pretol]
    [-te protol] [-tom promass] [-tem premass] [-tez prozdep] [-ti isotopes]
    [-teppm] [-ta autotol] [-tex exact] [-i ions] [-cl cutlo] [-ch cuthi]
    [-ci cutinc] [-cp precursorcull] [-v cleave] [-x taxid] [-w1 window1]
    [-w2 window2] [-h1 hit1] [-h2 hit2] [-hl hitlist] [-hc hitcount]
    [-ht tophitnum] [-hm minhit] [-hs minspectra] [-he evalcut] [-mf fixedmod]
    [-mv variablemod] [-mnm] [-mm maxmod] [-e enzyme] [-zh maxcharge]
    [-zl mincharge] [-zoh maxprodcharge] [-zt chargethresh] [-z1 plusone]
    [-zc calcplusone] [-zcc calccharge] [-zn negions] [-pc pseudocount]
    [-sb1 searchb1] [-sct searchcterm] [-sp productnum] [-scorr corrscore]
    [-scorp corrprob] [-no minno] [-nox maxno] [-is subsetthresh]
    [-ir replacethresh] [-ii iterativethresh] [-p prolineruleions] [-il] [-el]
    [-ml] [-mx modinputfile] [-mux usermodinputfile] [-nt numthreads] [-ni]
    [-ns] [-os] [-nrs] [-logfile File_Name] [-conffile File_Name] [-version]
    [-version-full] [-dryrun]

DESCRIPTION
   Search engine for identifying MS/MS peptide spectra

OPTIONAL ARGUMENTS
 -h
   Print USAGE and DESCRIPTION;  ignore other arguments
 -help
   Print USAGE, DESCRIPTION and ARGUMENTS description;  ignore other arguments
 -xmlhelp
   Print USAGE, DESCRIPTION and ARGUMENTS description in XML format;  ignore
   other arguments
 -pm <String>
   search parameter input in xml format (overrides command line)
   Default = `'
 -d <String>
   Blast sequence library to search. Do not include .p* filename suffixes.
   Default = `nr'
 -umm
   use memory mapped sequence libraries
 -f <String>
   single dta file to search
   Default = `'
 -fx <String>
   multiple xml-encapsulated dta files to search
   Default = `'
 -fb <String>
   multiple dta files separated by blank lines to search
   Default = `'
 -fp <String>
   pkl formatted file
   Default = `'
 -fm <String>
   mgf formatted file
   Default = `'
 -foms <String>
   omssa oms file
   Default = `'
 -fomx <String>
   omssa omx file
   Default = `'
 -fbz2 <String>
   omssa omx file compressed by bzip2
   Default = `'
 -fxml <String>
   omssa xml search request file
   Default = `'
 -o <String>
   filename for text asn.1 formatted search results
   Default = `'
 -ob <String>
   filename for binary asn.1 formatted search results
   Default = `'
 -ox <String>
   filename for xml formatted search results
   Default = `'
 -obz2 <String>
   filename for bzip2 compressed xml formatted search results
   Default = `'
 -op <String>
   filename for pepXML formatted search results
   Default = `'
 -oc <String>
   filename for csv formatted search summary
   Default = `'
 -w
   include spectra and search params in search results
 -to <Real>
   product ion m/z tolerance in Da
   Default = `0.8'
 -te <Real>
   precursor ion m/z tolerance in Da (or ppm if -teppm flag set)
   Default = `2.0'
 -tom <Integer>
   product ion search type (0 = mono, 1 = avg, 2 = N15, 3 = exact)
   Default = `0'
 -tem <Integer>
   precursor ion search type (0 = mono, 1 = avg, 2 = N15, 3 = exact, 4 =
   multiisotope)
   Default = `0'
 -tez <Integer>
   charge dependency of precursor mass tolerance (0 = none, 1 = linear)
   Default = `0'
 -ti <Integer>
   when doing multiisotope search, number of isotopic peaks to search.  0 =
   monoisotopic peak only
   Default = `0'
 -teppm
   search precursor masses in units of ppm
 -ta <Real>
   automatic mass tolerance adjustment fraction
   Default = `1.0'
 -tex <Real>
   threshold in Da above which the mass of neutron should be added in exact
   mass search
   Default = `1446.94'
 -i <String>
   id numbers of ions to search (comma delimited, no spaces)
   Default = `1,4'
 -cl <Real>
   low intensity cutoff as a fraction of max peak
   Default = `0.0'
 -ch <Real>
   high intensity cutoff as a fraction of max peak
   Default = `0.2'
 -ci <Real>
   intensity cutoff increment as a fraction of max peak
   Default = `0.0005'
 -cp <Integer>
   eliminate charge reduced precursors in spectra (0=no, 1=yes)
   Default = `0'
 -v <Integer>
   number of missed cleavages allowed
   Default = `1'
 -x <String>
   comma delimited list of taxids to search (0 = all)
   Default = `0'
 -w1 <Integer>
   single charge window in Da
   Default = `27'
 -w2 <Integer>
   double charge window in Da
   Default = `14'
 -h1 <Integer>
   number of peaks allowed in single charge window (0 = number of ion species)
   Default = `2'
 -h2 <Integer>
   number of peaks allowed in double charge window (0 = number of ion species)
   Default = `2'
 -hl <Integer>
   maximum number of hits retained per precursor charge state per spectrum
   during the search
   Default = `30'
 -hc <Integer>
   maximum number of hits reported per spectrum (0 = all)
   Default = `0'
 -ht <Integer>
   number of m/z values corresponding to the most intense peaks that must
   include one match to the theoretical peptide
   Default = `6'
 -hm <Integer>
   the minimum number of m/z matches a sequence library peptide must have for
   the hit to the peptide to be recorded
   Default = `2'
 -hs <Integer>
   the minimum number of m/z values a spectrum must have to be searched
   Default = `4'
 -he <Real>
   the maximum evalue allowed in the hit list
   Default = `1'
 -mf <String>
   comma delimited (no spaces) list of id numbers for fixed modifications
   Default = `'
 -mv <String>
   comma delimited (no spaces) list of id numbers for variable modifications
   Default = `'
 -mnm
   n-term methionine should not be cleaved
 -mm <Integer>
   the maximum number of mass ladders to generate per database peptide
   Default = `128'
 -e <Integer>
   id number of enzyme to use
   Default = `0'
 -zh <Integer>
   maximum precursor charge to search when not 1+
   Default = `3'
 -zl <Integer>
   minimum precursor charge to search when not 1+
   Default = `1'
 -zoh <Integer>
   maximum product charge to search
   Default = `2'
 -zt <Integer>
   minimum precursor charge to start considering multiply charged products
   Default = `3'
 -z1 <Real>
   fraction of peaks below precursor used to determine if spectrum is charge 1
   Default = `0.95'
 -zc <Integer>
   should charge plus one be determined algorithmically? (1=yes)
   Default = `1'
 -zcc <Integer>
   how should precursor charges be determined? (1=believe the input file,
   2=use a range)
   Default = `2'
 -zn <Integer>
   search using negative or positive ions (1=positive, -1=negative)
   Default = `1'
 -pc <Integer>
   minimum number of precursors that match a spectrum
   Default = `1'
 -sb1 <Integer>
   should first forward (b1) product ions be in search (1=no)
   Default = `1'
 -sct <Integer>
   should c terminus ions be searched (1=no)
   Default = `0'
 -sp <Integer>
   max number of ions in each series being searched (0=all)
   Default = `100'
 -scorr <Integer>
   turn off correlation correction to score (1=off, 0=use correlation)
   Default = `0'
 -scorp <Real>
   probability of consecutive ion (used in correlation correction)
   Default = `0.5'
 -no <Integer>
   minimum size of peptides for no-enzyme and semi-tryptic searches
   Default = `4'
 -nox <Integer>
   maximum size of peptides for no-enzyme and semi-tryptic searches (0=none)
   Default = `40'
 -is <Real>
   evalue threshold to include a sequence in the iterative search, 0 = all
   Default = `0.0'
 -ir <Real>
   evalue threshold to replace a hit, 0 = only if better
   Default = `0.0'
 -ii <Real>
   evalue threshold to iteratively search a spectrum again, 0 = always
   Default = `0.01'
 -p <String>
   id numbers of ion series to apply no product ions at proline rule at (comma
   delimited, no spaces)
   Default = `'
 -il
   print a list of ions and their corresponding id number
 -el
   print a list of enzymes and their corresponding id number
 -ml
   print a list of modifications and their corresponding id number
 -mx <String>
   file containing modification data
   Default = `mods.xml'
 -mux <String>
   file containing user modification data
   Default = `usermods.xml'
 -nt <Integer>
   number of search threads to use, 0=autodetect
   Default = `0'
 -ni
   don't print informational messages
 -ns
   depreciated flag
 -os
   use omssa 1.0 scoring
 -nrs
   turn off rank score
 -logfile <File_Out>
   File to which the program log should be redirected
 -conffile <File_In>
   Program's configuration (registry) data file
 -version
   Print version number;  ignore other arguments
 -version-full
   Print extended version data;  ignore other arguments
 -dryrun
   Dry run the application: do nothing, only test all preconditions


-i options:
0: a
1: b
2: c
3: x
4: y
5: zdot
10: adot
11: x-CO2
12: adot-CO2


-e enzyme options:
0: Trypsin
1: Arg-C
2: CNBr
3: Chymotrypsin (FYWL)
4: Formic Acid
5: Lys-C
6: Lys-C, no P rule
7: Pepsin A
8: Trypsin+CNBr
9: Trypsin+Chymotrypsin (FYWLKR)
10: Trypsin, no P rule
11: Whole protein
12: Asp-N
13: Glu-C
14: Asp-N+Glu-C
15: Top-Down
16: Semi-Tryptic
17: No Enzyme
18: Chymotrypsin, no P rule (FYWL)
19: Asp-N (DE)
20: Glu-C (DE)
21: Lys-N (K)
22: Thermolysin, no P rule
23: Semi-Chymotrypsin (FYWL)
24: Semi-Glu-C


Modifications:
 # : Name
 23: 2-amino-3-oxo-butanoic acid T
182: Asparagine HexNAc
183: Asparagine dHexHexNAc
131: CAMthiopropanoyl K
130: ICAT heavy
129: ICAT light
  9: M cleavage from protein n-term
179: MMTS on C
119: N to D conversion
 83: NEM C
 84: NIPCAM
 87: O18 on peptide n-term
139: PNGasF in O18 water
113: SeMet
184: Serine HexNAc
185: Threonine HexNAc
 24: acetylation of K
 10: acetylation of protein n-term
 25: amidation of peptide c-term
163: arginine to ornithine
140: beta elimination of S
141: beta elimination of T
 13: beta methythiolation of D
 26: beta-methylthiolation of D
  3: carbamidomethyl C
 31: carbamylation of K
 32: carbamylation of n-term peptide
 29: carboxyamidomethylation of D
 30: carboxyamidomethylation of E
 28: carboxyamidomethylation of H
 27: carboxyamidomethylation of K
165: carboxykynurenin of W
  2: carboxymethyl C
 33: citrullination of R
  4: deamidation of N and Q
164: dehydro of S and T
 88: di-O18 on peptide n-term
 35: di-iodination of Y
 36: di-methylation of K
 37: di-methylation of R
 38: di-methylation of peptide n-term
 42: farnesylation of C
 46: fluorophenylalanine
 43: formylation of K
 44: formylation of peptide n-term
 82: formylation of protein n-term
 47: gamma-carboxylation of D
 48: gamma-carboxylation of E
 49: geranyl-geranyl
 50: glucuronylation of protein n-term
 51: glutathione disulfide
 53: guanidination of K
136: heavy arginine-13C6
137: heavy arginine-13C6-15N4
181: heavy lysine - 13C6 15N2
180: heavy lysine - 2H4
138: heavy lysine-13C6
 56: homoserine
 57: homoserine lactone
 64: hydroxylation of  Y
 59: hydroxylation of D
 63: hydroxylation of F
 60: hydroxylation of K
 61: hydroxylation of N
 62: hydroxylation of P
168: iTRAQ114 on K
169: iTRAQ114 on Y
167: iTRAQ114 on nterm
171: iTRAQ115 on K
172: iTRAQ115 on Y
170: iTRAQ115 on nterm
174: iTRAQ116 on K
175: iTRAQ116 on Y
173: iTRAQ116 on nterm
177: iTRAQ117 on K
178: iTRAQ117 on Y
176: iTRAQ117 on nterm
 65: iodination of Y
 67: lipoyl K
 73: methyl C
 74: methyl H
 75: methyl N
 77: methyl R
 69: methyl ester of D
 70: methyl ester of E
 71: methyl ester of S
 72: methyl ester of Y
 68: methyl ester of peptide c-term
 16: methylation of D
 17: methylation of E
  0: methylation of K
 14: methylation of Q
 18: methylation of peptide c-term
 76: methylation of peptide n-term
 11: methylation of protein n-term
 78: myristoleylation of G
 79: myristoyl-4H of G
 81: myristoylation of K
 80: myristoylation of peptide n-term G
118: n-acyl diglyceride cysteine
 22: n-formyl met addition
 34: oxidation of C to cysteic acid
162: oxidation of C to sulfinic acid
 39: oxidation of F to dihydroxyphenylalanine
 89: oxidation of H
 55: oxidation of H to D
 54: oxidation of H to N
  1: oxidation of M
111: oxidation of P to pyroglutamic acid
 90: oxidation of W
 45: oxidation of W to formylkynurenin
 58: oxidation of W to hydroxykynurenin
 66: oxidation of W to kynurenin
 85: oxidation of W to nitro
 86: oxidation of Y to nitro
 92: palmitoylation of C
 93: palmitoylation of K
 94: palmitoylation of S
 95: palmitoylation of T
 91: phosphopantetheine S
  6: phosphorylation of S
134: phosphorylation of S with ETD loss
 96: phosphorylation of S with prompt loss
  7: phosphorylation of T
135: phosphorylation of T with ETD loss
 97: phosphorylation of T with prompt loss
  8: phosphorylation of Y
 99: phosphorylation with neutral loss on C
100: phosphorylation with neutral loss on D
101: phosphorylation with neutral loss on H
132: phosphorylation with neutral loss on S
133: phosphorylation with neutral loss on T
 98: phosphorylation with prompt loss on Y
  5: propionamide C
104: propionyl heavy K
105: propionyl heavy peptide n-term
102: propionyl light K
103: propionyl light on peptide n-term
106: pyridyl K
107: pyridyl peptide n-term
108: pyro-cmC
109: pyro-glu from n-term E
110: pyro-glu from n-term Q
112: s-pyridylethylation of C
114: sulfation of Y
115: sulphone of M
166: sumoylation of K
 40: thioacylation of K
 41: thioacylation of peptide n-term
 19: tri-deuteromethylation of D
 20: tri-deuteromethylation of E
 21: tri-deuteromethylation of peptide c-term
116: tri-iodination of Y
 15: tri-methylation of K
117: tri-methylation of R
 12: tri-methylation of protein n-term
 52: ubiquitinylation residue