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Add parameter file and FASTA file referenced by unit tests
Update unit test to use Tryp_Pig_Bov.fasta
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‎docs/ParameterFiles/MSGFPlus_Tryp_MetOx_20ppmParTol.txt‎

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# Precursor mass tolerance
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# Examples: 2.5Da or 30ppm
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# Use comma to set asymmetric values, for example "0.5Da,2.5Da" will set 0.5Da to the left (expMass<theoMass) and 2.5Da to the right (expMass>theoMass)
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PrecursorMassTolerance=20ppm
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# Max Number of Dynamic (Variable) Modifications per peptide
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# If this value is large, the search will be slow
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NumMods=3
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# Modifications (see below for examples)
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StaticMod=None
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DynamicMod=O1, M, opt, any, Oxidation # Oxidized methionine
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# Fragmentation Method
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# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra
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# 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap and Lumos with high res MS2 spectra
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# 2 means TOF
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# 3 means Q-Exactive; use InstrumentID=3 for Q Exactive and QEHFX instruments
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# 4 means UVPD
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FragmentationMethodID=0
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# Instrument ID
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# 0 means Low-res LCQ/LTQ (Default for CID and ETD); use InstrumentID=0 if analyzing a dataset with low-res CID and high-res HCD spectra
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# 1 means High-res LTQ (Default for HCD; also appropriate for high res CID); use InstrumentID=1 for Orbitrap, Lumos, and QEHFX instruments
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# 2 means TOF
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# 3 means Q-Exactive
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InstrumentID=0
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# Enzyme ID
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# 0 means unspecific cleavage (cleave after any residue)
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# 1 means Trypsin (Default); optionally use this along with NTT=0 for a no-enzyme-specificity search of a tryptically digested sample
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# 2: Chymotrypsin, 3: Lys-C, 4: Lys-N, 5: Glu-C, 6: Arg-C, 7: Asp-N, 8: alphaLP, 9: No Cleavage (for peptidomics)
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EnzymeID=1
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# Isotope error range
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# Takes into account the error introduced by not choosing the monoisotopic peak for fragmentation.
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# Useful for accurate precursor ion masses.
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# Ignored if the parent mass tolerance is > 0.5Da or 500ppm.
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# The combination of -t and -ti determines the precursor mass tolerance.
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# e.g. "-t 20ppm -ti -1,2" tests abs(observed - theoretical - n * 1.00335Da) < 20ppm for n=-1, 0, 1, 2
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IsotopeErrorRange=-1,2
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# Number of tolerable termini
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# The number of peptide termini that must have been cleaved by the enzyme (default 1)
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# For trypsin, 2 means fully tryptic only, 1 means partially tryptic, and 0 means no-enzyme search
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NTT=2
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# Control N-terminal methionine cleavage
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# 0 means to consider protein N-term Met cleavage (Default)
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# 1 means to ignore protein N-term Met cleavage
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IgnoreMetCleavage=0
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# Target/Decoy search mode
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# 0 means don't search decoy database (default)
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# 1 means search decoy database to compute FDR (source FASTA file must be forward-only proteins)
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TDA=1
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# Number of Threads (by default, uses all available cores)
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NumThreads=All
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# Minimum peptide length to consider
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MinPepLength=6
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# Maximum peptide length to consider
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MaxPepLength=50
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# Minimum precursor charge to consider (if not specified in the spectrum)
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MinCharge=2
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# Maximum precursor charge to consider (if not specified in the spectrum)
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MaxCharge=5
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# Number of matches per spectrum to be reported
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# If this value is greater than 1, the FDR values computed by MS-GF+ will be skewed by high-scoring 2nd and 3rd hits
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NumMatchesPerSpec=1
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# Mass of charge carrier
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# Default: mass of proton
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#ChargeCarrierMass=1.00727649
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# Maximum missed cleavages
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# Exclude peptides with more than this number of missed cleavages from the search, Default: -1 (no limit)
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#MaxMissedCleavages=-1
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# Minimum number of ions a spectrum must have to be examined
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#MinNumPeaksPerSpectrum=10
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# Number of isoforms to consider per peptide
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# Default: 128
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#NumIsoforms=128
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# Include additional features in the output (enable this to post-process results with Percolator)
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#AddFeatures=1
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# Amino Acid Modification Examples
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# Specify static modifications using one or more StaticMod= entries
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# Specify dynamic modifications using one or more DynamicMod= entries
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# Modification format is:
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# Mass or CompositionString, Residues, ModType, Position, Name (all five fields are required).
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# CompositionString can only contain a limited set of elements, primarily C H N O S or P
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#
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# Examples:
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# C2H3N1O1, C, fix, any, Carbamidomethyl # Fixed Carbamidomethyl C (alkylation)
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# O1, M, opt, any, Oxidation # Oxidation M
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# 15.994915, M, opt, any, Oxidation # Oxidation M (mass is used instead of CompositionString)
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# H-1N-1O1, NQ, opt, any, Deamidated # Negative numbers are allowed.
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# CH2, K, opt, any, Methyl # Methylation K
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# C2H2O1, K, opt, any, Acetyl # Acetylation K
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# HO3P, STY,opt, any, Phospho # Phosphorylation STY
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# C2H3NO, *, opt, N-term, Carbamidomethyl # Variable Carbamidomethyl N-term
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# H-2O-1, E, opt, N-term, Glu->pyro-Glu # Pyro-glu from E
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# H-3N-1, Q, opt, N-term, Gln->pyro-Glu # Pyro-glu from Q
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# C2H2O, *, opt, Prot-N-term, Acetyl # Acetylation Protein N-term

‎src/test/java/msgfplus/TestMSGFPlus.java‎

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File outputDir = new File("C:\\DMS_WorkDir1");
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File specFile = Paths.get(workDir.getPath(), "20121223_ICD_individual_33_TP_A177_Elite_30k_run2_01_excerpt.mgf").toFile();
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File dbFile = Paths.get(orgDbDir.getPath(),"CPTAC_264contams.fasta").toFile();
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File dbFile = Paths.get(orgDbDir.getPath(),"Tryp_Pig_Bov.fasta").toFile();
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File confFile = Paths.get(workDir.getPath(), "MSGFPlus_Tryp_MetOx_20ppmParTol.txt").toFile();
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String versionString = getNextVersion();
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File orgDbDir = new File("C:\\DMS_Temp_Org");
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File specFile = Paths.get(workDir.getPath(), "QC_Mam_19_01_PNNL_10_06Jan21_Arwen_WBEH-20-12-01.mzML").toFile();
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File dbFile = Paths.get(orgDbDir.getPath(),"CPTAC_264contams.fasta").toFile();
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File dbFile = Paths.get(orgDbDir.getPath(),"Tryp_Pig_Bov.fasta").toFile();
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File confFile = Paths.get(workDir.getPath(), "MSGFPlus_Tryp_MetOx_StatCysAlk_20ppmParTol.txt").toFile();
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String versionString = getNextVersion();

‎src/test/resources/Tryp_Pig_Bov.fasta‎

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>Contaminant_TRYP_PIG sp|P00761|TRYP_PIG Trypsin precursor (EC 3.4.21.4) - Sus scrofa (Pig).
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FPTDDDDKIVGGYTCAANSIPYQVSLNSGSHFCGGSLINSQWVVSAAHCYKSRIQVRLGE
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HNIDVLEGNEQFINAAKIITHPNFNGNTLDNDIMLIKLSSPATLNSRVATVSLPRSCAAA
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GTECLISGWGNTKSSGSSYPSLLQCLKAPVLSDSSCKSSYPGQITGNMICVGFLEGGKDS
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CQGDSGGPVVCNGQLQGIVSWGYGCAQKNKPGVYTKVCNYVNWIQQTIAAN
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>Contaminant_Trypa1 VATVSLPR-like Promega trypsin artifact 1 (871.1) xATVSLPR (PromTArt1)
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QATVSLPR
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>Contaminant_Trypa2 VATVSLPR-like Promega trypsin artifact 2 (899.5) xxTVSLPR (PromTArt2)
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VQTVSLPR
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>Contaminant_Trypa3 VATVSLPR-like Promega trypsin artifact 3 (824.5) xxxVSLPR (PromTArt3)
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PGVVSLPR
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>Contaminant_Trypa4 LSSPATLNSR-like Promega trypsin artifact 4 (1071.5) xxxPATLNSR (PromTArt4)
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MNTLPLLAAK
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>Contaminant_Trypa5 Promega trypsin artifact 5 K to R mods (2239.1, 2914)(1987, 2003) (PromTArt5)
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LGEHNIDVLEGNEQFINAARIITHPNFNGNTLDNDIMLIRLSSPATLNSR
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>Contaminant_Trypa6 VATVSLPR 422 ion wrongly assigned z=3 (1262.8) (llhg are dummy aa's) (TrypArt6)
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LLHGVATVSLPR
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>Contaminant_TRYP_BOVIN TRYPSINOGEN. (sp|P00760|TRYP_BOVIN, gi|136425)
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VDDDDKIVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDN
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INVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGT
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QCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQ
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GDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN
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>Contaminant_CTRA_BOVIN CHYMOTRYPSINOGEN A (EC 3.4.21.1). - BOS TAURUS (BOVINE).
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CGVPAIQPVLSGLSRIVNGEEAVPGSWPWQVSLQDKTGFHFCGGSLINENWVVTAAHCGV
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TTSDVVVAGEFDQGSSSEKIQKLKIAKVFKNSKYNSLTINNDITLLKLSTAASFSQTVSA
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VCLPSASDDFAAGTTCVTTGWGLTRYTNANTPDRLQQASLPLLSNTNCKKYWGTKIKDAM
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ICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQ
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TLAAN
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>Contaminant_CTRB_BOVIN CHYMOTRYPSINOGEN B (EC 3.4.21.1). - BOS TAURUS (BOVINE).
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CGVPAIQPVLSGLARIVNGEDAVPGSWPWQVSLQDSTGFHFCGGSLISEDWVVTAAHCGV
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TTSDVVVAGEFDQGLETEDTQVLKIGKVFKNPKFSILTVRNDITLLKLATPAQFSETVSA
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VCLPSADEDFPAGMLCATTGWGKTKYNALKTPDKLQQATLPIVSNTDCRKYWGSRVTDVM
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ICAGASGVSSCMGDSGGPLVCQKNGAWTLAGIVSWGSSTCSTSTPAVYARVTALMPWVQE
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TLAAN
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>Contaminant_ALBU_HUMAN SERUM ALBUMIN PRECURSOR. (sp|P02768|ALBU_HUMAN, gi|113576)
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MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF
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EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP
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ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
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FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV
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ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK
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ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR
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RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE
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QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV
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LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL
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SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV
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AASQAALGL
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>Contaminant_ALBU_BOVIN SERUM ALBUMIN PRECURSOR. (sp|P02769|ALBU_BOVIN, gi|113574)
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MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEQFKGLVLIAFSQYLQQCPF
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DEHVKLVNELTEFAKTCVADESHAGCEKSLHTLFGDELCKVASLRETYGDMADCCEKQEP
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ERNECFLSHKDDSPDLPKLKPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLYY
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ANKYNGVFQDCCQAEDKGACLLPKIETMREKVLASSARQRLRCASIQKFGERALKAWSVA
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RLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQDTISSKLKE
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CCDKPLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFLGSFLYEYSRR
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HPEYAVSVLLRLAKEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQNLIKQNCDQFEK
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LGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGTRCCTKPESERMPCTEDYLSLIL
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NRLCVLHEKTPVSEKVTKCCTESLVNRRPCFSALTPDETYVPKAFDEKLFTFHADICTLP
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DTEKQIKKQTALVELLKHKPKATEEQLKTVMENFVAFVDKCCAADDKEACFAVEGPKLVV
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STQTALA
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>Contaminant_K2C1_HUMAN sp|P04264 Keratin, type II cytoskeletal 1 (Cytokeratin-1) (CK-1) (Keratin-1) (K1) (67 kDa cytokeratin) (Hair alpha protein) - Homo sapiens (Human).
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SRQFSSRSGYRSGGGFSSGSAGIINYQRRTTSSSTRRSGGGGGRFSSCGGGGGSFGAGGG
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FGSRSLVNLGGSKSISISVARGGGRGSGFGGGYGGGGFGGGGFGGGGFGGGGIGGGGFGG
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FGSGGGGFGGGGFGGGGYGGGYGPVCPPGGIQEVTINQSLLQPLNVEIDPEIQKVKSRER
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EQIKSLNNQFASFIDKVRFLEQQNQVLQTKWELLQQVDTSTRTHNLEPYFESFINNLRRR
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VDQLKSDQSRLDSELKNMQDMVEDYRNKYEDEINKRTNAENEFVTIKKDVDGAYMTKVDL
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QAKLDNLQQEIDFLTALYQAELSQMQTQISETNVILSMDNNRSLDLDSIIAEVKAQNEDI
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AQKSKAEAESLYQSKYEELQITAGRHGDSVRNSKIEISELNRVIQRLRSEIDNVKKQISN
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LQQSISDAEQRGENALKDAKNKLNDLEDALQQAKEDLARLLRDYQELMNTKLALDLEIAT
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YRTLLEGEESRMSGECAPNVSVSVSTSHTTISGGGSRGGGGGGYGSGGSSYGSGGGSYGS
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GGGGGGGRGSYGSGGSSYGSGGGSYGSGGGGGGHGSYGSGSSSGGYRGGSGGGGGGSSGG
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RGSGGGSSGGSIGGRGSSSGGVKSSGGSSSVRFVSTTYSGVTR
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>Contaminant_K22E_HUMAN sp|P35908 Keratin, type II cytoskeletal 2 epidermal (Cytokeratin-2e) (K2e) (CK 2e) - Homo sapiens (Human).
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MSCQISCKSRGRGGGGGGFRGFSSGSAVVSGGSRRSTSSFSCLSRHGGGGGGFGGGGFGS
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RSLVGLGGTKSISISVAGGGGGFGAAGGFGGRGGGFGGGSGFGGGSGFGGGSGFSGGGFG
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GGGFGGGRFGGFGGPGGVGGLGGPGGFGPGGYPGGIHEVSVNQSLLQPLNVKVDPEIQNV
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KAQEREQIKTLNNKFASFIDKVRFLEQQNQVLQTKWELLQQMNVGTRPINLEPIFQGYID
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SLKRYLDGLTAERTSQNSELNNMQDLVEDYKKKYEDEINKRTAAENDFVTLKKDVDNAYM
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IKVELQSKVDLLNQEIEFLKVLYDAEISQIHQSVTDTNVILSMDNSRNLDLDSIIAEVKA
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QYEEIAQRSKEEAEALYHSKYEELQVTVGRHGDSLKEIKIEISELNRVIQRLQGEIAHVK
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KQCKNVQDAIADAEQRGEHALKDARNKLNDLEEALQQAKEDLARLLRDYQELMNVKLALD
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VEIATYRKLLEGEECRMSGDLSSNVTVSVTSSTISSNVASKAAFGGSGGRGSSSGGGYSS
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GSSSYGSGGRQSGSRGGSGGGGSISGGGYGSGGGSGGRYGSGGGSKGGSISGGGYGSGGG
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KHSSGGGSRGGSSSGGGYGSGGGGSSSVKGSSGEAFGSSVTFSFR
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>Contaminant_K1C9_HUMAN sp|P35527 Keratin, type I cytoskeletal 9 (Cytokeratin-9) (CK-9) (Keratin-9) (K9) - Homo sapiens (Human).
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MSCRQFSSSYLSRSGGGGGGGLGSGGSIRSSYSRFSSSGGRGGGGRFSSSSGYGGGSSRV
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CGRGGGGSFGYSYGGGSGGGFSASSLGGGFGGGSRGFGGASGGGYSSSGGFGGGFGGGSG
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GGFGGGYGSGFGGLGGFGGGAGGGDGGILTANEKSTMQELNSRLASYLDKVQALEEANND
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LENKIQDWYDKKGPAAIQKNYSPYYNTIDDLKDQIVDLTVGNNKTLLDIDNTRMTLDDFR
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IKFEMEQNLRQGVDADINGLRQVLDNLTMEKSDLEMQYETLQEELMALKKNHKEEMSQLT
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GQNSGDVNVEINVAPGKDLTKTLNDMRQEYEQLIAKNRKDIENQYETQITQIEHEVSSSG
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QEVQSSAKEVTQLRHGVQELEIELQSQLSKKAALEKSLEDTKNRYCGQLQMIQEQISNLE
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AQITDVRQEIECQNQEYSLLLSIKMRLEKEIETYHNLLEGGQEDFESSGAGKIGLGGRGG
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SGGSYGRGSRGGSGGSYGGGGSGGGYGGGSGSRGGSGGSYGGGSGSGGGSGGGYGGGSGG
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GHSGGSGGGHSGGSGGNYGGGSGSGGGSGGGYGGGSGSRGGSGGSHGGGSGFGGESGGSY
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GGGEEASGSGGGYGGGSGKSSHS
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>Contaminant_K1C10_HUMAN sp|P13645 Keratin, type I cytoskeletal 10 (Cytokeratin-10) (CK-10) (Keratin-10) (K10) - Homo sapiens (Human).
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MSVRYSSSKHYSSSRSGGGGGGGGCGGGGGVSSLRISSSKGSLGGGFSSGGFSGGSFSRG
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SSGGGCFGGSSGGYGGLGGFGGGSFHGSYGSSSFGGSYGGSFGGGNFGGGSFGGGSFGGG
98+
GFGGGGFGGGFGGGFGGDGGLLSGNEKVTMQNLNDRLASYLDKVRALEESNYELEGKIKE
99+
WYEKHGNSHQGEPRDYSKYYKTIDDLKNQILNLTTDNANILLQIDNARLAADDFRLKYEN
100+
EVALRQSVEADINGLRRVLDELTLTKADLEMQIESLTEELAYLKKNHEEEMKDLRNVSTG
101+
DVNVEMNAAPGVDLTQLLNNMRSQYEQLAEQNRKDAEAWFNEKSKELTTEIDNNIEQISS
102+
YKSEITELRRNVQALEIELQSQLALKQSLEASLAETEGRYCVQLSQIQAQISALEEQLQQ
103+
IRAETECQNTEYQQLLDIKIRLENEIQTYRSLLEGEGSSGGGGRGGGSFGGGYGGGSSGG
104+
GSSGGGYGGGHGGSSGGGYGGGSSGGGSSGGGYGGGSSSGGHGGGSSSGGHGGSSSGGYG
105+
GGSSGGGGGGYGGGSSGGGSSSGGGYGGGSSSGGHKSSSSGSVGESSSKGPRY

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