From a05131c94e5d5382f6dda7c5273a2f060509198c Mon Sep 17 00:00:00 2001 From: alchemistmatt Date: Thu, 28 Jun 2018 15:49:40 -0700 Subject: [PATCH] Update documentation --- README.md | 20 ++-- doc/Changelog.html | 138 +++++++++++++++------------ doc/MS-GFDB.html | 2 +- doc/MSGFDB_ModFile.html | 102 +++++++++++--------- doc/MSGFPlus.html | 196 +++++++++++++++++++++++++-------------- doc/MzidToTsv.html | 4 +- doc/ScoringParamGen.html | 2 +- doc/examples/Mods.txt | 47 +++++----- doc/index.html | 10 +- 9 files changed, 313 insertions(+), 208 deletions(-) diff --git a/README.md b/README.md index 9bbdc60b..fbd5a221 100644 --- a/README.md +++ b/README.md @@ -16,8 +16,8 @@ and Concatenated DTA files (_dta.txt). Requirements ====== -JRE 1.6 or greater\ -Memory 2GB or greater (recommended 4GB); larger FASTA files require more memory +Java Runtime v1.6 or higher (use 64-bit Java)\ +At least 2GB of memory (recommended to use 4GB); larger FASTA files require more memory Downloads / Updates ====== @@ -41,7 +41,7 @@ Place MSGFPlus.jar in any folder Usage Information ====== -Type `java -jar MSGFPlus.jar` for command line arguments +Type `java -jar MSGFPlus.jar` for command line arguments. To convert an mzid output file into a tsv file, run `java -cp MSGFPlus.jar edu.ucsd.msjava.ui.MzIDToTsv` @@ -50,7 +50,7 @@ It is a C# application that works on Windows or on Linux using mono. Download the Mzid-To-Tsv-Converter from GitHub. For detailed documentation, see the "doc" subfolder, or visit: -* [GitHub repo HTML help pages](http://htmlpreview.github.io/?https://github.com/MSGFPlus/msgfplus/blob/master/doc/index.html) +* [GitHub repo HTML help pages](https://htmlpreview.github.io/?https://github.com/MSGFPlus/msgfplus/blob/master/doc/index.html) * https://omics.pnl.gov/software/ms-gf * https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 @@ -63,13 +63,13 @@ Sangtae Kim [sangtae.kim (at) gmail.com] Publications ====== -MS-GF+: Universal Database Search Tool for Mass Spectrometry, Sangtae Kim, Pavel A. Pevzner, -Nat Commun. 2014 Oct 31;5:5277. doi: 10.1038/ncomms6277. -http://www.ncbi.nlm.nih.gov/pubmed/?term=25358478 +MS-GF+ makes progress towards a universal database search tool for proteomics, Sangtae Kim and Pavel A. Pevzner, +Nat Commun. 2014 Oct 31;5:5277. doi: 10.1038/ncomms6277.\ +https://www.ncbi.nlm.nih.gov/pubmed/?term=25358478 -Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases, Sangtae Kim, Nitin Gupta and Pavel Pevzner, -J Proteome Res. 2008 Aug;7(8):3354-63. doi: 10.1021/pr8001244. -http://www.ncbi.nlm.nih.gov/pubmed/?term=18597511 +Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases, Sangtae Kim, Nitin Gupta, and Pavel Pevzner, +J Proteome Res. 2008 Aug;7(8):3354-63. doi: 10.1021/pr8001244.\ +https://www.ncbi.nlm.nih.gov/pubmed/?term=18597511 Source ====== diff --git a/doc/Changelog.html b/doc/Changelog.html index f639495f..6121af51 100644 --- a/doc/Changelog.html +++ b/doc/Changelog.html @@ -14,7 +14,29 @@

MS-GF+ ChangeLog

- 01/30/2018 v2018.01.30 + v2018.06.28 +

+ + +

+ v2018.04.09 +

+ + +

+ v2018.01.30

- 08/23/2017 v2017.08.23 + v2017.08.23

- 07/21/2017 v2017.07.21 + v2017.07.21

- 05/18/2017 v2017.05.18 + v2017.05.18

- 01/27/2017 v2017.01.27 + v2017.01.27

- 01/10/2017 v2017.01.10 + v2017.01.10

- 12/12/2016 v2016.12.12 + v2016.12.12

- 12/08/2016 v2016.12.08 + v2016.12.08

- 12/02/2016 v2016.12.02 + v2016.12.02

- 11/29/2016 v2016.11.29 + v2016.11.29

- 10/26/2016 v2016.10.26 + v2016.10.26

- 10/24/2016 v2016.10.24 + v2016.10.24

- 10/14/2016 v2016.10.14 + v2016.10.14

- 10/10/2016 v2016.10.10 + v2016.10.10

- 09/22/2016 v2016.09.22 + v2016.09.22

- 08/31/2016 v2016.08.31 + v2016.08.31

- 07/26/2016 v2016.07.26 + v2016.07.26

- 06/29/2016 v2016.06.29 + v2016.06.29

- 06/15/2016 v2016.06.15 + v2016.06.15

- 05/25/2016 v2016.05.25 + v2016.05.25

- 02/12/2016 v2016.02.12 + v2016.02.12

- 01/29/2016 v2016.01.29 + v2016.01.29

- 01/21/2016 v2016.01.21 + v2016.01.21

- 07/16/2014 v10089 + 2014-07-16 v10089

- 06/30/2014 v10072 + 2014-06-30 v10072

- 02/10/2014 v9949 + 2014-02-10 v9949

- 08/28/2013 v9881 + 2013-08-28 v9881

- 08/28/2013 v9733 + 2013-08-28 v9733

- 04/03/2013 v9517 + 2013-04-03 v9517

- 04/03/2013 v9501 + 2013-04-03 v9501

- 04/02/2013 v9494 + 2013-04-02 v9494

- 03/25/2013 v9436 + 2013-03-25 v9436

- 03/05/2013 v9324 + 2013-03-05 v9324

- 02/27/2013 v9324 + 2013-02-27 v9324

- 02/15/2013 v9312 + 2013-02-15 v9312

- 02/15/2013 v9284 + 2013-02-15 v9284

- 02/14/2013 v9249 + 2013-02-14 v9249

- 02/04/2013 v9244 + 2013-02-04 v9244

- 01/03/2013 v9176 + 2013-01-03 v9176

- 12/19/2012 v9107 + 2012-12-19 v9107

- 12/10/2012 v9014 + 2012-12-10 v9014

- 11/30/2012 v9012 + 2012-11-30 v9012

- 11/09/2012 v8884 + 2012-11-09 v8884

- 11/09/2012 v8873 + 2012-11-09 v8873

- 10/30/2012 v8806 + 2012-10-30 v8806

- 10/29/2012 v8792 + 2012-10-29 v8792

- 10/11/2012 v8719 + 2012-10-11 v8719

- 10/04/2012 v8605 + 2012-10-04 v8605

- 10/03/2012 v8597 + 2012-10-03 v8597

- 09/26/2012 v8540 + 2012-09-26 v8540

- 09/20/2012 v8490 + 2012-09-20 v8490

- 09/18/2012 v8477 + 2012-09-18 v8477

- 09/18/2012 v8472 + 2012-09-18 v8472

- 09/17/2012 v8449 + 2012-09-17 v8449

- 09/13/2012 v8442 + 2012-09-13 v8442

- 08/30/2012 v8299 + 2012-08-30 v8299

- 08/29/2012 v8297 + 2012-08-29 v8297

- 08/27/2012 v8283 + 2012-08-27 v8283

-

If multiple MS-GF+ processes access the same database file, it is strongly recommended to index the database prior to the database search by running BuildSA (see below).

+

If multiple MS-GF+ processes access the same database file, it is strongly recommended to index the database prior to the database search by running BuildSA.

  • - -verbose 0/1 (0: report total progress only (Default), 1: report total and per-thread progress/status) + -verbose 0/1 (0: Report total progress only (Default), 1: Report total and per-thread progress/status)
  • - -tda 0/1 (0: don't search decoy database (default), 1: search decoy database to compute FDR) + -tda 0/1 (0: Don't search decoy database (default), 1: Search decoy database to compute FDR)
    • -

    If -tda 1 is specified, MS-GF+ automatically creates a combined target/reversed database file (DBFileName.revConcat.fasta). Thus, when specifying "-d" parameter, DatabaseFile must contain only target proteins.

    +

    + If -tda 1 is specified, MS-GF+ automatically creates a combined target/reversed database file (DBFileName.revConcat.fasta).
    + Thus, when specifying "-d" parameter, DatabaseFile must contain only target proteins. +

    -

    The meaning and the default value have changed as of version 8442 (Sept. 2012).

    MS-GF+ output example

    -

    Using MzIDToTsv one can convert MS-GF+ output (*.mzid) into the tsv format

    - +

    Shown below is a sample of the MS-GF+ output in table form, as extracted from a simple MzIdentML file: test.mzid

    + +

    There are two options for converting an MS-GF+ output file (.mzid) into a tab-separated file (.tsv).

    + +
      +
    1. The MzIDToTsv utility built into MSGFPlus.jar (see the MzIDToTsv page) +
        +
      • Easy to access (though syntax is a bit tricky)
        • +
      • Can be slow for large .mzid files
        • +
      +
      2. +
    2. The Mzid-To-Tsv-Converter standalone application, available on GitHub +
        +
      • Fast conversion
        • +
      • Handles large .mzid files
        • +
      • Runs natively on Windows, but requires mono to use on Linux
        • +
      +
      3. +
    @@ -400,5 +458,7 @@

    MS-GF+ output example

    + (Text file of this table: test_Unrolled.tsv) + diff --git a/doc/MzidToTsv.html b/doc/MzidToTsv.html index bcaab02e..8f0f2b9a 100644 --- a/doc/MzidToTsv.html +++ b/doc/MzidToTsv.html @@ -78,7 +78,7 @@

    MzIDToTsv Utility

    -unroll 0/1