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)

  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]

   Search engine for identifying MS/MS peptide spectra

   Print USAGE and DESCRIPTION;  ignore other arguments
   Print USAGE, DESCRIPTION and ARGUMENTS description;  ignore other arguments
   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'
   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 = `'
   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 =
   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'
   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 = `'
   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 = `'
   print a list of ions and their corresponding id number
   print a list of enzymes and their corresponding id number
   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'
   don't print informational messages
   depreciated flag
   use omssa 1.0 scoring
   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
   Print version number;  ignore other arguments
   Print extended version data;  ignore other arguments
   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

 # : 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
 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