MzidToTsvConverter

Overview

Converts a mzIdentML file (.mzid) created by MS-GF+ to a tab-delimited text file.

Although MS-GF+ has this option (see MzidToTsv.html), MzidToTsvConverter.exe can convert the .mzid file faster, using less memory.

Details

MzidToTsvConverter reads in the .mzid file created by MS-GF+ and creates a tsv file with the peptide identifications. The program can also read .mzid.gz files, and it includes other options for how to handle peptides that are associated with multiple proteins.

The MzidToTsvConverter uses PSI_Interface.dll to read the .mzid file.

Syntax

MzidToTsvConverter -mzid:"mzid path" [-tsv:"tsv output path"] 
  [-unroll] [-showDecoy] [-noExtended] [-singleResult]
  [-maxSpecEValue] [-maxEValue] [-maxQValue]
  [-recurse] [-skipDupIds]
  [-geneId] [-geneIdCS]
  [-proteinList] [-delim]

Required parameters:

-mzid:path

• Path to the .mzid or .mzid.gz file. If the path has spaces, it must be in quotes.
• Alternatively, the path to a directory with .mzid or .mzid.gz files. In this case, all .mzid files in the directory will be converted to .tsv

Optional parameters:

-tsv:path

• Path to tab-separated values file to be written
  • Can be a filename, a directory path, or a file path
• If not specified, will be output to the same location as the mzid
• If mzid path is a directory, this will be treated as a directory path

-unroll or -u

• Signifies that results should be unrolled, giving one line per unique peptide/protein combination in each spectrum identification

-showDecoy or -sd

• Signifies that decoy results should be included in the output .tsv file
• Decoy results have protein names that start with XXX_

-noExtended or -ne

• Do not output the extended fields (e.g., Scan Time)
• When this flag is specified, the output will have the same columns as the MS-GF+ MzidToTsv output, and be a near match when run with the same parameters

-singleResult or -1

• Only output one result per spectrum

-maxSpecEValue or -MaxSpecE or -SpecEValue

• Filter the results, excluding those with a SpecEValue greater than this threshold

-maxEValueor -MaxE or -EValue

• Filter the results, excluding those with an EValue greater than this threshold

-maxQValue or -MaxQ or -QValue

• Filter the results, excluding those with a QValue greater than this threshold
• For example, -qvalue:0.001

-recurse or -r

• If mzid path is a directory, specifying this will cause .mzid files in subdirectories to also be converted

-skipDupIds

• If there are issues converting a file due to "duplicate ID" errors, specifying this will cause the duplicate IDs to be ignored, at the likely cost of some correctness

-geneId

• If specified, adds a 'GeneID' column to the output for non-decoy identifications
• Optionally supply a regular expression (RegEx) to extract the gene name from the protein identifier and/or the protein description
• The default expression supports the UniProt SwissProt format, extracting just the gene name and not the species
  • -geneId:"(?<=(sp|tr)\|[0-9A-Z\-]{6,}\|)([A-Z0-9]{2,})(?=_[A-Z0-9]{2,})"
  • For example, given sp|P00760|TRYP_BOVIN, the extracted gene names is TRYP

-geneIdCS

• When specified, use case-sensitive pattern matching when extracting gene names

-proteinListor -proteins or -delimitedProteins

• For each PSM, include a comma-separated list of proteins in the Protein column
• This setting takes precedence over -unroll

-delim

• Separator to use for the delimited protein names (defaults to a comma and space)

Example regular expressions for -geneId

Note that many of these examples use positive lookbehind to match text before the gene name, but not capture it

• The default RegEx uses both positive lookbehind and positive lookahead

Match sp proteins, and include organism name in the gene name

• -geneId:"(?<=sp\|[0-9A-Z\-]{6,}\|)([A-Z0-9_]{2,})"
• Example protein name: sp|P02438|KR2A_SHEEP
• Extracted gene name: KR2A_SHEEP

Match sp proteins, but do not include organism name in the gene name

• -geneId:"(?<=sp\|[0-9A-Z\-]{6,}\|)([A-Z0-9]{2,})(?=_[A-Z0-9]{2,})"
• Example protein name: sp|P02438|KR2A_SHEEP
• Extracted gene name: KR2A

Match sp or tr proteins and do not include organism name in the gene name

• -geneId:"(?<=(sp|tr)\|[0-9A-Z\-]{6,}\|)([A-Z0-9]{2,})(?=_[A-Z0-9]{2,})"
• Example protein name: tr|E9PNT2|E9PNT2_HUMAN
• Extracted gene name: E9PNT2

Match gene name in the protein description, as specified by GN=GeneName

• -geneId:"GN=[^\s|]+"
• Example protein name: GN=PNPLA8
• Extracted gene name: GN=PNPLA8

Match gene name in the protein description, but do not include GN=

• -geneId:"(?<=GN=)[^\s|]+"
• Example protein name: GN=PNPLA8
• Extracted gene name: PNPLA8

The previous RegEx can also match GN=GeneName when terms are separated by vertical bars

• -geneId:"(?<=GN=)[^\s|]+"
• Example protein name: |GN=KRTAP5-1|chr=11|
• Extracted gene name: KRTAP5-1

Output Columns

The columns in the .tsv file created by the MzidToTsvConverter are:

Column	Description	Example
#SpecFile	Spectrum file name	Dataset.mzML
SpecID	Spectrum ID	controllerType=0 controllerNumber=1 scan=16231
ScanNum	Scan number	16231
ScanTime(Min)	(Can be disable with switch -ne) Scan Start time, minutes	52.534
FragMethod	Fragmentation method for the given MS/MS spectrum. Will be CID, ETD, or HCD. However, when spectra from the same precursor are merged, fragmentation methods of merged spectra will be shown in the form "FragMethod1/FragMethod2/..." (e.g. CID/ETD, CID/HCD/ETD).	HCD
Precursor	m/z value of the precursor ion	767.04388
IsotopeError	Isotope Error, indicating which isotope in the isotopic distribution the parent ion m/z corresponds to. Typically 0, indicating the first isotope. If 1, that means the second isotope was chosen for fragmentation.	0
PrecursorError(ppm)	Mass Difference (in ppm) between the observed parent ion and the computed mass of the identified peptide. This value is automatically corrected if the second or third isotope is chosen for fragmentation.	-0.8753
Charge	Charge state of the parent ion	3
Peptide	The identified peptide, with prefix and suffix residues. Also includes a numeric representation of both static and dynamic post translational modifications.	K.VPPAPVPC+57.021PPPS+79.966PGPSAVPSSPK.S
Protein	Name of the protein this peptide comes from	BAG3_HUMAN
GeneID	(Enable with switch -geneid) Gene ID, parsed from protein description. For this example, a parameter of -geneid "^([A-Z0-9]{2,})(?=_[A-Z0=9]{2,})" would be used.	BAG3
DeNovoScore	The MSGFScore of the optimal scoring peptide. Larger scores are better.	110
MSGFScore	This is MS-GF+'s main scoring value for the identified peptide. Larger scores are better.	99
SpecEValue	This is MS-GF+'s main scoring value related to peptide confidence (spectrum level e-value) of the peptide-spectrum match. MS-GF+ assumes that the peptide with the lowest SpecEValue value (closest to 0) is correct, and all others are incorrect.	4.23E-21
EValue	Probability that a match with this SpecEValue is spurious; the lower this number (closer to 0), the better the match. This is a database level e-value, representing the probability that a random PSM has an equal or better score against a random database of the same size.	9.29E-14
QValue	If MS-GF+ searches a target/decoy database, the QValue (FDR) is computed based on the distribution of SpecEValue values for forward and reverse hits. If the target/decoy search was not used, this column will be EFDR and is an estimated FDR.	0
PepQValue	Peptide-level QValue (FDR) estimated using the target-decoy approach; only shown if a target/decoy search was used. If multiple spectra are matched to the same peptide, only the best-scoring match is retained and used to compute FDR.	0

Notes on QValue and PepQValue

• QValue is defined as the minimum false discovery rate (FDR) at which the test may be called significant
  • If the value is 0, that means that no reverse hit peptides had a SpecEValue less than or equal to the current peptide's SpecEValue
• QValue is a spectrum-level FDR and is computed using the formula ReversePeptideCount ÷ ForwardPeptideCount
  • If you filter on QValue < 0.01 you are applying a 1% FDR filter
• PepQValue is a peptide-level FDR threshold, and will always be lower than QValue

Contacts

Written by Bryson Gibbons and Matthew Monroe for the Department of Energy (PNNL, Richland, WA)
E-mail: proteomics@pnnl.gov
Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://panomics.pnnl.gov/ or https://www.pnnl.gov/integrative-omics

License

The MzidToTsvConverter is licensed under the 2-Clause BSD License; you may not use this file except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/BSD-2-Clause

Copyright 2018 Battelle Memorial Institute