Available Search Engines

Protein Database Search Engines

MS Amanda

Available MS Amanda versions, starting with the newest version:

class ursgal.wrappers.msamanda_2_0_0_9706.msamanda_2_0_0_9706(*args, **kwargs)

MSAmanda 2_0_0_9706 UNode

Import functions from msamanda_2_0_0_9695

class ursgal.wrappers.msamanda_2_0_0_9695.msamanda_2_0_0_9695(*args, **kwargs)

MSAmanda 2_0_0_9695 UNode Parameter options at http://ms.imp.ac.at/inc/pd-nodes/msamanda/Manual%20MS%20Amanda%20Standalone.pdf

Note: Please download and install MSAmanda manually from http://ms.imp.ac.at/?goto=msamanda

Reference: Dorfer V, Pichler P, Stranzl T, Stadlmann J, Taus T, Winkler S, Mechtler K. (2014) MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra.

postflight()

Convert .tsv result files to .csv

preflight()

Formatting the command line via self.params

Settings file is created in the output folder and added to self.created_tmp_files (can be deleted)

Returns:self.params(dict)
class ursgal.wrappers.msamanda_1_0_0_7504.msamanda_1_0_0_7504(*args, **kwargs)

MSAmanda 1_0_0_7504 UNode

Import functions from msamanda_1_0_0_5243

class ursgal.wrappers.msamanda_1_0_0_7503.msamanda_1_0_0_7503(*args, **kwargs)

MSAmanda 1_0_0_7503 UNode

Import functions from msamanda_1_0_0_5243

class ursgal.wrappers.msamanda_1_0_0_5243.msamanda_1_0_0_5243(*args, **kwargs)

MSAmanda 1_0_0_5243 UNode Parameter options at http://ms.imp.ac.at/inc/pd-nodes/msamanda/Manual%20MS%20Amanda%20Standalone.pdf

Reference: Dorfer V, Pichler P, Stranzl T, Stadlmann J, Taus T, Winkler S, Mechtler K. (2014) MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra.

postflight()

Convert .tsv result files to .csv

preflight()

Formatting the command line via self.params

Settings file is created in the output folder and added to self.created_tmp_files (can be deleted)

Returns:self.params(dict)
class ursgal.wrappers.msamanda_1_0_0_5242.msamanda_1_0_0_5242(*args, **kwargs)

MSAmanda 1_0_0_5242 UNode

Import functions from msamanda_1_0_0_5243

MS-GF+

Available MS-GF+ versions, starting with the newest version:

class ursgal.wrappers.msgfplus_v2017_01_27.msgfplus_v2017_01_27(*args, **kwargs)

MSGF+ UNode Parameter options at https://omics.pnl.gov/software/ms-gf

Reference:
Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. (2010) The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search.

Import node for version 2016 01 27

class ursgal.wrappers.msgfplus_v2016_09_16.msgfplus_v2016_09_16(*args, **kwargs)

MSGF+ UNode Parameter options at https://omics.pnl.gov/software/ms-gf

Reference:
Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. (2010) The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search.
preflight()

Formatting the command line via self.params

Modifications file will be created in the output folder

Returns:self.params
Return type:dict
class ursgal.wrappers.msgfplus_v9979.msgfplus_v9979(*args, **kwargs)

MSGF+ UNode Parameter options at https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355

Reference: Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. (2010) The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search.

preflight()

Formatting the command line via self.params

Modifications file will be created in the output folder

Returns:self.params
Return type:dict

MSFragger

class ursgal.wrappers.msfragger_20170103.msfragger_20170103(*args, **kwargs)

MSFragger unode

Note

Please download and install MSFragger manually from http://www.nesvilab.org/software.html

Reference: Kong, A. T., Leprevost, F. V, Avtonomov, D. M., Mellacheruvu, D., and Nesvizhskii, A. I. (2017) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat. Publ. Gr. 293

Note

Addition of user amino acids not implemented yet. Only mzML search possible at the moment. The mgf file can still be passed to the node, but the mzML has to be in the same folder as the mgf.

Warning

Still in testing phase! Metabolic labeling based 15N search may still be errorprone. Use with care!

postflight()

Reads MSFragger tsv output and write final csv output file.

Adds:
  • Raw data location, since this can not be added later
  • Converts masses in Da to m/z (could be done in unify_csv)
preflight()

Formatting the command line and writing the param input file via self.params

Returns:self.params
Return type:dict

MODa

class ursgal.wrappers.moda_v1_51.moda_v1_51(*args, **kwargs)

MODa UNode Check http://prix.hanyang.ac.kr/download/moda.jsp for download, new versions and contact information

Reference: Na S, Bandeira N, Paek E. (2012) Fast multi-blind modification search through tandem mass spectrometry.

postflight()

Rewrite ModA output .tsv into .csv so that it can be unified

preflight()

Formatting the command line via self.params

Returns:self.params
Return type:dict

MyriMatch

class ursgal.wrappers.myrimatch_2_1_138.myrimatch_2_1_138(*args, **kwargs)

Myrimatch UNode

Myrimatch options: http://forge.fenchurch.mc.vanderbilt.edu/scm/viewvc.php/checkout/trunk/doc/index.html?root=myrimatch

Reference: Tabb DL, Fernando CG, Chambers MC. (2007) MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis.

postflight()

renaming MyriMatch’s output file to our desired output file name

preflight()

Formatting the command line

write_param_file()

Writes a file containing all parameters for the search

class ursgal.wrappers.myrimatch_2_2_140.myrimatch_2_2_140(*args, **kwargs)

Myrimatch UNode

Import functions from myrimatch_2_1_138

OMSSA

class ursgal.wrappers.omssa_2_1_9.omssa_2_1_9(*args, **kwargs)

omssa_2_1_9 UNode

Parameter options at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/asn_spec/omssa.asn.html

OMSSA 2.1.9 parameters at http://proteomicsresource.washington.edu/protocols06/omssa.php

Reference: Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH (2004) Open Mass Spectrometry Search Algorithm.

postflight()

Will correct the OMSSA headers and add the column retention time to the csv file

preflight()

Formatting the command line via self.params

unimod Modifications are translated to OMSSA modifications

Returns:self.params(dict)

PIPI

class ursgal.wrappers.pipi_1_3_0.pipi_1_3_0(*args, **kwargs)

PIPI unode

Note

Please download and extract PIPI manually from http://bioinformatics.ust.hk/pipi.html

Reference: Yu, F., Li, N., Yu, W. (2016) PIPI: PTM-Invariant Peptide Identification Using Coding Method. J Prot Res 15(12)

preflight()

Formatting the command line and writing the param input file via self.params

Returns:self.params
Return type:dict

X!Tandem

Available X!Tandem versions, starting with the newest version:

class ursgal.wrappers.xtandem_alanine.xtandem_alanine(*args, **kwargs)

X!Tandem UNode Parameter options at http://www.thegpm.org/TANDEM/api/

Reference: Craig R, Beavis RC. (2004) TANDEM: matching proteins with tandem mass spectra.

class ursgal.wrappers.xtandem_vengeance.xtandem_vengeance(*args, **kwargs)

X!Tandem UNode Parameter options at http://www.thegpm.org/TANDEM/api/

Reference: Craig R, Beavis RC. (2004) TANDEM: matching proteins with tandem mass spectra.

format_templates()

Returns formatted X!Tandem input files

The formating is taken from self.params

Returns:keys are the names of the three templates (15N-masses.xml, taxonomy.xml, input.xml)
Return type:dict
preflight()

Formatting the command line via self.params

Input files from format_templates are created in the output folder and added to self.created_tmp_files (can be deleted)

Returns:self.params
Return type:dict
class ursgal.wrappers.xtandem_piledriver.xtandem_piledriver(*args, **kwargs)

X!Tandem UNode Parameter options at http://www.thegpm.org/TANDEM/api/

Reference: Craig R, Beavis RC. (2004) TANDEM: matching proteins with tandem mass spectra.

format_templates()

Returns formatted X!Tandem input files

The formating is taken from self.params

Returns:keys are the names of the three templates (15N-masses.xml, taxonomy.xml, input.xml)
Return type:dict
preflight()

Formatting the command line via self.params

Input files from format_templates are created in the output folder and added to self.created_tmp_files (can be deleted)

Returns:self.params
Return type:dict
class ursgal.wrappers.xtandem_sledgehammer.xtandem_sledgehammer(*args, **kwargs)

X!Tandem UNode Parameter options at http://www.thegpm.org/TANDEM/api/

Reference: Craig R, Beavis RC. (2004) TANDEM: matching proteins with tandem mass spectra.

format_templates()

Returns formatted X!Tandem input files

The formating is taken from self.params

Returns:keys are the names of the three templates (15N-masses.xml, taxonomy.xml, input.xml)
Return type:dict
preflight()

Formatting the command line via self.params

Input files from format_templates are created in the output folder and added to self.created_tmp_files (can be deleted)

Returns:self.params
Return type:dict
class ursgal.wrappers.xtandem_jackhammer.xtandem_jackhammer(*args, **kwargs)
class ursgal.wrappers.xtandem_cyclone_2010.xtandem_cyclone_2010(*args, **kwargs)

De Novo Search Engines

Novor

class ursgal.wrappers.novor_1_1beta.novor_1_1beta(*args, **kwargs)

Novor UNode Parameter options at http://rapidnovor.com/

Reference: Bin Ma (2015) Novor: Real-Time Peptide de Novo Sequencing Software.

postflight()

Reformats the Novor output file

preflight()

Formatting the command line via self.params

Params.txt file will be created in the output folder

Returns:self.params
Return type:dict

PepNovo

class ursgal.wrappers.pepnovo_3_1.pepnovo_3_1(*args, **kwargs)

PepNovo v3.1 UNode http://proteomics.ucsd.edu/Software/PepNovo/

Reference: Ari M. Frank, Mikhail M. Savitski, Michael L. Nielsen, Roman A. Zubarev, and Pavel A. Pevzner (2007) De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry, J. Proteome Res. 6:114-123.

postflight()

Reformats the PepNovo output file

preflight()

Formatting the command line via self.params

Returns:self.params
Return type:dict