Run OMSSA

Description

This script runs OMSSA on a given set of spectral files and databases.

Input files

• at least 1 spectra file (.dta | .mgf | .mzdata | .mzdata.bz2 | .mzdata.gz | .mzdata.zip | .mzml | .mzml.bz2 | .mzml.gz | .mzml.zip | .mzxml | .mzxml.bz2 | .mzxml.gz | .mzxml.zip | .xml | .xml.bz2 | .xml.gz | .xml.zip)
• at least 1 database file (.fa | .faa | .fas | .fasta | .phr | .pin | .psq)

Output files

• OMSSA results (omssa-results.csv)

Context

Synopsis

This script runs OMSSA, the Open Mass Spectrometry Search Algorithm. OMSSA produces peptide/spectral matches (PSM) from a set of input MS/MS spectra and an amino acid sequence database.

References

• Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH. 2004. Open mass spectrometry search algorithm. J. proteome res 3:958-964. [PubMed]

Masses and tolerance

Precursor ion m/z tolerance

Default: 2.0 Da

Product ion m/z tolerance

Default: 0.8 Da

Precursor ion search type

Choices: monoisotopic (default), average, N15, exact

Product ion search type

Choices: monoisotopic (default), average, N15, exact

Precursor charge dependency

Charge dependency of precursor mass tolerance

Choices: none (default), linear

Neutron mass add threshold

Threshold above which the mass of neutron should be added in exact mass search

Default: 1446.94 Da

Preprocessing

Low intensity cutoff

Low intensity cutoff as a fraction of max peak

Default: 0.0

Single charge window

Default: 20 Da

Double charge window

Default: 14 Da

Min peaks in single charge window

Default: 2

Min peaks in double charge window

Default: 2

Eliminate charge reduced precursors

Eliminate charge reduced precursors in spectra

Choices: no (default), yes

Min peak count (spectrum)

The minimum number of m/z values a spectrum must have to be searched

Default: 4

Min precursor spectrum match count

Minimum number of precursors that match a spectrum

Default: 1

Proline exception

Id numbers of ion series to apply no product ions at proline rule at

Choices: a, b, c, x, y, z

Charge handling

Min precursor ion charge

Minimum precursor ion charge to search when not +1

Default: 1

Max precursor ion charge

Maximum precursor ion charge to search when not +1

Default: 3

Min charge for considering multi

Minimum precursor charge to start considering multiply charged products

Default: 3

Peaks fraction below precursor for +1

Fraction of peaks below precursor used to determine if spectrum is charge +1

Default: 0.95

Determine charge +1

Should charge +1 be determined algorithmically?

Choices: no, yes (default)

Precursor charge determination

Choices: believe the input file, use a range (default)

Max product ion charge

Maximum product ion charge to search

Default: 2

Enzyme specification

Missed cleavages allowed

Number of missed cleavages allowed.

Default: 1

Enzyme

Choices: Trypsin, Arg-C, CNBr, Chymotrypsin, Formic Acid, Lys-C, Lys-C, no P rule, Pepsin A, Trypsin+CNBr, Trypsin+Chymotrypsin, Trypsin, no P rule, Whole protein, Asp-N, Glu-C, Asp-N+Glu-C, Top-Down, Semi-Tryptic, No Enzyme, Chymotrypsin, no P rule, Asp-N (DE), Glu-C (DE)

Min peptide length for NE and ST searches

Minimum length of peptides for no-enzyme and semi-tryptic searches

Default: 4

Max peptide length for NE and ST searches

Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)

Default: 40

Ions to search

Ions to search

Ions to search

Choices: a, b, c, x, y, z

Search c-term ions

Should c terminus ions be searched?

Choices: yes (default), no

Max ions to search per series

Max number of ions in each series being searched (0: all)

Default: 100

Search first forward b1 product ions

Should first forward (b1) product ions be in search?

Choices: yes, no (default)

Sequence library

Taxonomy IDs to search

comma delimited list of taxids to search (0 = all)

Default: 0

Cleave n-term methionine

Choices: yes (default), no

Fixed modifications

Choices: 2-amino-3-oxo-butanoic acid T, Asparagine HexNAc, Asparagine dHexHexNAc, CAMthiopropanoyl K, ICAT heavy, ICAT light, M cleavage from protein n-term, MMTS on C, NEM C, NIPCAM, O18 on peptide n-term, PNGasF in O18 water, SeMet, Serine HexNAc, Threonine HexNAc, acetylation of K, acetylation of protein n-term, amidation of peptide c-term, arginine to ornithine, beta elimination of S, beta elimination of T, beta methythiolation of D, beta-methylthiolation of D, carbamidomethyl C, carbamylation of K, carbamylation of n-term peptide, carboxyamidomethylation of D, carboxyamidomethylation of E, carboxyamidomethylation of H, carboxyamidomethylation of K, carboxykynurenin of W, carboxymethyl C, citrullination of R, deamidation of N and Q, dehydro of S and T, di-O18 on peptide n-term, di-iodination of Y, di-methylation of K, di-methylation of R, di-methylation of peptide n-term, farnesylation of C, fluorophenylalanine, formylation of K, formylation of peptide n-term, formylation of protein n-term, gamma-carboxylation of D, gamma-carboxylation of E, geranyl-geranyl, glucuronylation of protein n-term, glutathione disulfide, guanidination of K, heavy arginine-13C6, heavy arginine-13C6-15N4, heavy lysine – 13C6 15N2, heavy lysine – 2H4, heavy lysine-13C6, homoserine, homoserine lactone, hydroxylation of Y, hydroxylation of D, hydroxylation of F, hydroxylation of K, hydroxylation of N, hydroxylation of P, iTRAQ114 on K, iTRAQ114 on Y, iTRAQ114 on nterm, iTRAQ115 on K, iTRAQ115 on Y, iTRAQ115 on nterm, iTRAQ116 on K, iTRAQ116 on Y, iTRAQ116 on nterm, iTRAQ117 on K, iTRAQ117 on Y, iTRAQ117 on nterm, iodination of Y, lipoyl K, methyl C, methyl H, methyl N, methyl R, methyl ester of D, methyl ester of E, methyl ester of S, methyl ester of Y, methyl ester of peptide c-term, methylation of D, methylation of E, methylation of K, methylation of Q, methylation of peptide c-term, methylation of peptide n-term, methylation of protein n-term, myristoleylation of G, myristoyl-4H of G, myristoylation of K, myristoylation of peptide n-term G, n-acyl diglyceride cysteine, n-formyl met addition, oxidation of C to cysteic acid, oxidation of C to sulfinic acid, oxidation of F to dihydroxyphenylalanine, oxidation of H, oxidation of H to D, oxidation of H to N, oxidation of M, oxidation of P to pyroglutamic acid, oxidation of W, oxidation of W to formylkynurenin, oxidation of W to hydroxykynurenin, oxidation of W to kynurenin, oxidation of W to nitro, oxidation of Y to nitro, palmitoylation of C, palmitoylation of K, palmitoylation of S, palmitoylation of T, phosphopantetheine S, phosphorylation of S, phosphorylation of S with ETD loss, phosphorylation of S with prompt loss, phosphorylation of T, phosphorylation of T with ETD loss, phosphorylation of T with prompt loss, phosphorylation of Y, phosphorylation with neutral loss on C, phosphorylation with neutral loss on D, phosphorylation with neutral loss on H, phosphorylation with neutral loss on S, phosphorylation with neutral loss on T, phosphorylation with prompt loss on Y, propionamide C, propionyl heavy K, propionyl heavy peptide n-term, propionyl light K, propionyl light on peptide n-term, pyridyl K, pyridyl peptide n-term, pyro-cmC, pyro-glu from n-term E, pyro-glu from n-term Q, s-pyridylethylation of C, sulfation of Y, sulphone of M, sumoylation of K, thioacylation of K, thioacylation of peptide n-term, tri-deuteromethylation of D, tri-deuteromethylation of E, tri-deuteromethylation of peptide c-term, tri-iodination of Y, tri-methylation of K, tri-methylation of R, tri-methylation of protein n-term, ubiquitinylation residue

Variable modifications

Choices: 2-amino-3-oxo-butanoic acid T, Asparagine HexNAc, Asparagine dHexHexNAc, CAMthiopropanoyl K, ICAT heavy, ICAT light, M cleavage from protein n-term, MMTS on C, NEM C, NIPCAM, O18 on peptide n-term, PNGasF in O18 water, SeMet, Serine HexNAc, Threonine HexNAc, acetylation of K, acetylation of protein n-term, amidation of peptide c-term, arginine to ornithine, beta elimination of S, beta elimination of T, beta methythiolation of D, beta-methylthiolation of D, carbamidomethyl C, carbamylation of K, carbamylation of n-term peptide, carboxyamidomethylation of D, carboxyamidomethylation of E, carboxyamidomethylation of H, carboxyamidomethylation of K, carboxykynurenin of W, carboxymethyl C, citrullination of R, deamidation of N and Q, dehydro of S and T, di-O18 on peptide n-term, di-iodination of Y, di-methylation of K, di-methylation of R, di-methylation of peptide n-term, farnesylation of C, fluorophenylalanine, formylation of K, formylation of peptide n-term, formylation of protein n-term, gamma-carboxylation of D, gamma-carboxylation of E, geranyl-geranyl, glucuronylation of protein n-term, glutathione disulfide, guanidination of K, heavy arginine-13C6, heavy arginine-13C6-15N4, heavy lysine – 13C6 15N2, heavy lysine – 2H4, heavy lysine-13C6, homoserine, homoserine lactone, hydroxylation of Y, hydroxylation of D, hydroxylation of F, hydroxylation of K, hydroxylation of N, hydroxylation of P, iTRAQ114 on K, iTRAQ114 on Y, iTRAQ114 on nterm, iTRAQ115 on K, iTRAQ115 on Y, iTRAQ115 on nterm, iTRAQ116 on K, iTRAQ116 on Y, iTRAQ116 on nterm, iTRAQ117 on K, iTRAQ117 on Y, iTRAQ117 on nterm, iodination of Y, lipoyl K, methyl C, methyl H, methyl N, methyl R, methyl ester of D, methyl ester of E, methyl ester of S, methyl ester of Y, methyl ester of peptide c-term, methylation of D, methylation of E, methylation of K, methylation of Q, methylation of peptide c-term, methylation of peptide n-term, methylation of protein n-term, myristoleylation of G, myristoyl-4H of G, myristoylation of K, myristoylation of peptide n-term G, n-acyl diglyceride cysteine, n-formyl met addition, oxidation of C to cysteic acid, oxidation of C to sulfinic acid, oxidation of F to dihydroxyphenylalanine, oxidation of H, oxidation of H to D, oxidation of H to N, oxidation of M, oxidation of P to pyroglutamic acid, oxidation of W, oxidation of W to formylkynurenin, oxidation of W to hydroxykynurenin, oxidation of W to kynurenin, oxidation of W to nitro, oxidation of Y to nitro, palmitoylation of C, palmitoylation of K, palmitoylation of S, palmitoylation of T, phosphopantetheine S, phosphorylation of S, phosphorylation of S with ETD loss, phosphorylation of S with prompt loss, phosphorylation of T, phosphorylation of T with ETD loss, phosphorylation of T with prompt loss, phosphorylation of Y, phosphorylation with neutral loss on C, phosphorylation with neutral loss on D, phosphorylation with neutral loss on H, phosphorylation with neutral loss on S, phosphorylation with neutral loss on T, phosphorylation with prompt loss on Y, propionamide C, propionyl heavy K, propionyl heavy peptide n-term, propionyl light K, propionyl light on peptide n-term, pyridyl K, pyridyl peptide n-term, pyro-cmC, pyro-glu from n-term E, pyro-glu from n-term Q, s-pyridylethylation of C, sulfation of Y, sulphone of M, sumoylation of K, thioacylation of K, thioacylation of peptide n-term, tri-deuteromethylation of D, tri-deuteromethylation of E, tri-deuteromethylation of peptide c-term, tri-iodination of Y, tri-methylation of K, tri-methylation of R, tri-methylation of protein n-term, ubiquitinylation residue

Tweaks

Min matching peaks (database)

The minimum number of m/z matches a sequence library peptide must have for the hit to the peptide to be recorded

Default: 2

Min matching peaks (spectrum)

Number of m/z values corresponding to the most intense peaks that must include one match to the theoretical peptide

Default: 6

Use memory mapped sequence libraries

Choices: no (default), yes

Maximum hit list size

Default: 30

Mass ladders per database peptide

The maximum number of mass ladders to generate per database peptide

Default: 128

Use correlation correction

Choices: yes, no

Auto mass tolerance adjustment

Automatic mass tolerance adjustment fraction

Default: 1.0

Consecutive ion probability

Probability of consecutive ion (used in correlation correction)

Default: 0.5

Result handling

e value cutoff

The maximum evalue allowed in the hit list

Default: 1.0

Report spectra and search parameters

Include spectra and search parameters in search results

Choices: no (default), yes

Tweaks

Spectrum batch size

Default: 2000

Search threads

Number of search threads to use. 0 means autodetect.

Default: 0

Source code

run-omssa.rb, run-omssa.yaml (GitHub)