compomics peptide-shaker issues

compomics / peptide-shaker

Interpretation of proteomics identification results

http://compomics.github.io/projects/peptide-shaker.html

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issues

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Peptide-shaker not importing data

#486 catamoreno4 closed 1 year ago
4
StringIndexOutOfBoundsException

#485 jcanderan opened 2 years ago
2
exportFactory.json file gets overwritten when running ReportCLI

#484 veitveit closed 2 years ago
8
question about exporting results

#483 jcanderan closed 2 years ago
0
Export MGF with annotated fragment ions?

#482 denisbeslic opened 2 years ago
1
SearchGUI is successful but PeptideShaker is failing

#481 Bin-cc opened 2 years ago
2
Bump spring-webmvc from 5.3.16 to 5.3.18

#480 dependabot[bot] closed 2 years ago
0
PeptideShaker error when loading SearchGui output

#479 kromer-m opened 2 years ago
10
PeptideShaker processing canceled

#478 Ysraa closed 9 months ago
1
ClassCastException Error

#477 umutcakir opened 2 years ago
3
Error opening previous output files - "compatible versions" required

#476 MNTNguyen closed 2 years ago
4
Question: replicates, LFQ, PTM, fractions

#475 r0620660 closed 2 years ago
4
Download link is not functional

#474 kromer-m closed 2 years ago
4
Unable to load data

#473 MNTsnowman closed 2 years ago
3
Error in follow-up analysis export

#472 indianAppl opened 2 years ago
10
Gene ontology download runs for several minutes reporting errors on each file

#471 orsburn closed 2 years ago
4
Hi, recently i encountered an error while using SearchGui for MS/MS analysis

#470 niks2021 opened 2 years ago
21
<CompomicsError>PeptideShaker processing canceled

#469 quark-spec closed 2 years ago
3
MS file exceeds memory mapped reader max buffer size.

#468 brvpuyve closed 2 months ago
4
target/decoy results not validated

#467 Proteomicslab57357 closed 2 years ago
2
Peptide shaker fails with any of the new versions. label: help wanted

#466 subinamehta closed 2 years ago
2
Allow different validation methods when creating projects

#465 umutcakir opened 3 years ago
1
Peptide shaker keeps failing with new version

#464 subinamehta closed 3 years ago
2
Xcorr score for PSMs using ReportCLI

#463 nattzy94 closed 3 years ago
7
Bump httpclient from 4.3.6 to 4.5.13

#462 dependabot[bot] closed 3 years ago
0
New peptide shaker version doesn't open the example

#461 deeptijk closed 3 years ago
23
correct mapping peptides to pdb using indexes instead of using sequence

#460 yehiafarag closed 3 years ago
0
TMTPro Overlabelling and Custom Modifications

#459 emhumphries closed 3 years ago
6
individual report

#458 fazeliniah closed 3 years ago
1
Getting PDB data stalls for hours and uses high GPU?

#457 orsburn closed 3 years ago
4
public data not found in PRIDE reshake

#456 aelezi01 closed 3 years ago
2
Fewer identifications in newer versions

#455 iquasere opened 3 years ago
0
cms file not found error

#454 bernt-matthias closed 3 years ago
6
Factorial only implemented for n <= 20. Reached the maximal capacoty of a long.

#453 CarlaCristinaUranga closed 3 years ago
17
make SG/PS deal better with non standard headers

#452 bernt-matthias closed 3 years ago
2
<CompomicsError>PeptideShaker processing failed.

#451 mndavies286 closed 3 years ago
3
An error occurred: Cannot invoke "com.compomics.util.experiment.identification.matches.SpectrumMatch.getPeptideAssumptionsMap()" because "spectrumMatch" is null

#450 Jacky11 closed 3 years ago
5
PeptideShakerCLI version 2.0.16

#449 CarlaCristinaUranga closed 3 years ago
17
exportFactory problem

#448 bernt-matthias closed 3 years ago
4
identXML export problem

#447 bernt-matthias closed 3 years ago
9
PeptideShaker Protein Grouping

#446 KunathBJ closed 3 years ago
1
paths.txt is always written where .jar is located no matter temp settings

#445 CarlosHorro opened 3 years ago
2
OX as part of taxonomy

#444 jcanderan closed 3 years ago
1
MzidCLI error Generating the mzID file

#443 KunathBJ closed 3 years ago
5
Error ocurred: null

#442 jackframar closed 3 years ago
5
Can filtered results be loaded into PeptideShaker?

#441 danielgeiszler closed 3 years ago
2
Reports: Algorithm score

#439 tivdnbos closed 3 years ago
2
Reports: adding multiple proteins to comma separated file

#440 tivdnbos opened 3 years ago
3
String index out of range issue

#438 jcanderan closed 3 years ago
2
Poor PTM localization scores reported where a clear ion ladder is present

#437 Kabir12321 closed 9 months ago
6

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