Goodlett Lab
Goodlett Lab

Education

MSBM Summer
SchoolMSBM logo

  • The Summer School on Mass Spectrometry in Biotechnology and Medicine (MSBM) is a professional-level course in the fundamentals and most common applications of mass spectrometry, held each summer in Dubrovnik, Croatia. An international faculty teaches advanced graduate students, postdocs and scientists from universities and industry.

    The first three days cover the fundamentals, from sample preparation and separations to ionization, mass analyzers and data processing; the rest of the week applies them to proteomics, lipidomics, metabolomics, imaging and biologics.

    The first school was held in 2001. Dave has been a member of its organizing committee since 2007.

    Dubrovnik, Croatia · every summer

    msbm.org

UPPCON III

  • The Goodlett Laboratory hosted UPPCON III, the Third International UPPSALA Conference on Electron Capture and Transfer Dissociation in Mass Spectrometry. It was the third meeting on electron capture dissociation and the first to take in electron transfer dissociation and related ways of fragmenting ions with electrons, with lectures on the fundamental chemistry and on applications in proteomics and glycomics.

    6–9 December 2005 · Salish Lodge, near Seattle

    Full details

xComb

  • xComb is a program that computes all possible cross-links between proteins of interest (up to 30), for further interrogation with a standard search engine such as Phenyx, Mascot, Sequest, OMSSA or X!Tandem.

    It runs as two Perl scripts, so Perl must be installed first; it is free from perl.org. The first script, protein2digest.pl, takes your FASTA files and produces a directory of .digest files.

    Usage of protein2digest.pl
    protein2digest.pl (version 1.3)

FUNCTION:
Transforms DAT or FASTA protein files into DIGEST format for further use with compatible softwares.

USAGE:
protein2digest.pl -in=[value] -ez=[value] -mc=[value] [file_name]

  -in=[value]: Specify input format

    0= UniProt DAT
    1= UniProt FASTA
    2= Any FASTA

  -ez=[value]: Specify enzyme

    0= Trypsin
    1= Lys-C
    2= Arg-C
    3= Glu-C (E)
    4= Glu-C (DE)
    5= Asp-N
    6= Trypsin, no P rule
    7= ARG-C, no P rule
    8= Chymotrypsin, no P rule

  -mc=[value]: Specify nb of missed cleavage allowed (max. = 3)

  [file_name]: Specify file to be converted

Ex: protein2digest.pl -in=1 -ez=0 -mc=2 filename

    The resulting directory is then used by digest2cxdb.pl to create the cross-linked database.

    Usage of digest2cxdb.pl
    digest2cxdb.pl (version 1.2)

FUNCTION:
Creates inter & intra cross-linking databases for search with standard algorithm such as Sequest, Mascot or Phenyx. Uses pre-digested protein sequences in DIGEST format. If a single digest is present, performs only intra database. The maximum protein sequences allowed per directory in digest format is 50!!!

USAGE:
digest2cxdb.pl -i=[value] -x=[value] -mc=[value] -pl=[value] -f=[value] -t=[value] [digest_dir]

  -i=[value]: Inter/Intra type mode

    0= Both intra and inter crosslinks are generated
    1= Only inter crosslinks are generated
    2= Only intra crosslinks are generated

  -x=[value]: Specify type of cross-linker

    0= Amine/Amine (e.g. BS2, DST, DFDNB)
    1= Sulfhydryl/Sulfhydryl (e.g. BMOE, BMDB or S-S bridge)
    2= Amine/carboxyl (e.g. EDC)
    3= Amine/Non-selective (e.g. SDA)
    4= Amine/Sulfhydryl (e.g. AMAS, SPDP)
    5= Tyrosine/Tyrosine (e.g. dityrosine)
    6= Lysine/Lysine

  -mc=[value]: Specify whether amine cross-linking needs 1 trypsin missed cleavage at least. on=1 / off=0

  -pl=[value]: Specify the minimum peptide length for building a permutation [1-6]

  -f=[value]: Phenyx FASTA formatted output. on=1 / off=0

  -t=[value]: Test mode which adds "|" between the two peptides for easier reading. on=1 / off=0

  [digest_dir]: Specifies directory containing files in DIGEST format

Ex: digest2cxdb.pl -i=1 -x=1 -mc=1 -pl=4 -f=0 -t=0 digest_dir

    xComb was created at the University of Washington, which licenses it: at no charge to users at academic and non-profit research institutions, and commercially on request.

    Version 1.3 · Panchaud et al., J Proteome Res 2010

    20302351