bzhanglab/PepQuery

Issues

• Using PepQuerry for identification of protein-protein interaction

  #74 opened 13 days ago by anuC
  2

• CPTAC MS dataset files in s3 bucket are not found

  #75 opened 11 days ago by pixuenan
  7

• Multiple searches FDR

  #76 opened 9 days ago by tretyacv
  2

• PepQueryDB file not found

  #73 opened 12 days ago by tretyacv
  2

• Pepquerry run halt halfway through

  #72 opened 13 days ago by anuC
  2

• S3Interface Error when retrieving MS/MS index file!

  #71 opened 18 days ago by TaboneOlivier
  2

• Trypsin digestion and unique peptide identification

  #69 opened a month ago by anuC
  3

• Modification search in web version

  #70 opened a month ago by icheeseman
  3

• mgf doesn't exist

  #68 opened 2 months ago by anuC
  3

• Could not resolve dependencies for project Proteomics:pepquery:jar:2.0.5

  #62 opened 2 months ago by adajani
  1

• Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler

  #64 opened 2 months ago by anu80125
  6

• Interpretation of psm_rank.txt file

  #67 opened 2 months ago by anuC
  2

• Quantification of the novel peptide

  #66 opened 2 months ago by anuC
  2

• Known protein validation - No valid protein found in database

  #65 opened 2 months ago by anuC
  2

• Peptide abundance from the standalone tool

  #61 opened 5 months ago by emilyhmwong-vir
  4

• Question: finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"

  #63 opened 4 months ago by lindenb
  1

• Semi tryptic searches

  #57 opened 5 months ago by colin986
  9

• ERROR: There is no file found in this dataset

  #56 opened 5 months ago by sarinita
  3

• javax.net.ssl.SSLException

  #49 opened 5 months ago by wenbostar
  0

• SdkClientException

  #48 opened 5 months ago by wenbostar
  0

• Statistical evaluation of shuffled peptides with multiple (Iso)Leucine amino acids

  #54 opened 10 months ago by HagemeijerRug
  1

• PepQuery and DIA files? - Searching in Galaxy

  #55 opened 5 months ago by prao123
  2

• Sample info not showing up in the web application

  #60 opened 5 months ago by emilyhmwong-vir
  3

• GTEx TMT sample mapping

  #59 opened 5 months ago by helenabea
  1

• Add TMTpro 16plex to the list of accepted PTMs

  #58 opened 8 months ago by bszeitz
  1

• java.net.SocketException: Connection reset

  #53 opened a year ago by a1172260832
  2

• The input file cannot be recognized:No amino acid found for letter

  #52 opened a year ago by a1172260832
  7

• How to search multiple novel proteins?

  #51 opened a year ago by mt1022
  5

• PepQuery2 didn’t finish running after several hours, even for only one peptide

  #50 opened a year ago by JasonYJWei
  5

• results differences between peppery 1 and peppery 2

  #46 opened a year ago by rboulos
  2

• Access to the website

  #47 opened 2 years ago by mirjam514
  5

• PepQuery2 Testing- discrepancy in version 1 and 2

  #45 opened 2 years ago by subinamehta
  4

• Enzyme used for protein digestion?

  #44 opened 2 years ago by PMadupe
  2

• Are tags still supported or needed in PepQuery2

  #43 opened 2 years ago by jj-umn
  2

• Cannot find sample information in TMT data

  #42 opened 2 years ago by lizhenli8888
  4

• Methionine oxidation and Phenylalanine

  #40 opened 2 years ago by apataskar
  2

• Adding ADP-ribo PTM

  #32 opened 2 years ago by jfcalcul
  2

• Get the results different from PepQuery Online

  #39 opened 3 years ago by XiaofengxBjmu
  9

• Error when running Pepquery in immunopeptidomics mode

  #35 opened 3 years ago by Zack-Ely
  9

• analysis of CPTAC PNNL files

  #36 opened 3 years ago by GuidoLeoni
  3

• Searching large datasets

  #38 opened 3 years ago by XiaofengxBjmu
  22

• Indexing and modification

  #37 opened 3 years ago by XiaofengxBjmu
  7

• label quantification (TCGA BC)

  #34 opened 3 years ago by apataskar
  7

• Additional labeling based quantification (TMT)

  #33 opened 3 years ago by andreabc
  6

• index protein database with no cut

  #29 opened 3 years ago by ATPs
  10

• Broken links on the download page

  #30 opened 4 years ago by umutcakir
  1

• Constructing standalone database for CCLE_proteome_MSV000085836

  #31 opened 4 years ago by andreabc
  2

• Signal-to-Noise-ratio, multiple raw data search

  #27 opened 4 years ago by PhilippKaulich
  5

• General Questions about PepQuery: Small bacterial proteoms, unrestricted modification search

  #28 opened 4 years ago by PhilippKaulich
  3

• precision on PTM nomenclature

  #26 opened 4 years ago by Seb-Leb
  3