Although trypsin remains a dominant protease in proteomics studies, digesting proteins with diverse proteases is becoming popular 1. New fragmentation technologies have emerged and high-precision mass spectrometers like Orbitrap have become widely available. Mass spectrometry (MS) instruments and experimental protocols have greatly advanced over the last decade. We emphasize that although MS-GF+ is not specifically designed for any particular experimental set-up, it improves on the performance of tools specifically designed for these applications (for example, specialized tools for phosphoproteomics). For all these data sets, MS-GF+ significantly increases the number of identified peptides compared with commonly used methods for peptide identifications. We benchmark MS-GF+ using diverse spectral data sets: (i) spectra of varying fragmentation methods (ii) spectra of multiple enzyme digests (iii) spectra of phosphorylated peptides and (iv) spectra of peptides with unusual fragmentation propensities produced by a novel alpha-lytic protease. We present a database search tool MS-GF+ that is sensitive (it identifies more peptides than most other database search tools) and universal (it works well for diverse types of spectra, different configurations of MS instruments and different experimental protocols). Do you recommend using the CLI as I did now without a template or to modify the template from the tutorial? I am primarily working on the command line.Mass spectrometry (MS) instruments and experimental protocols are rapidly advancing, but the software tools to analyse tandem mass spectra are lagging behind. par provided in the tutorial (same basic settings). The difference in total id's and confident assignments between the CLI and SearchGUI,are very slightly different. par as before) and it looks good (but not 100% the same as tutorial): I have tested it with the IdentificationParametersCLI using the new versions (only commandline options but without using the template. par file from the tutorial and modify it with the parametersCLI on the server, but I am unable to have luck with just SearchGUI or the CLI alone. My current workaround on the server is to load in the working. I will really appreciate feedback on this, as I hope to use these tools heavily for future work, especially the commandline interface. The original files are too big to upload easily, but if needed I will upload them using Google Drive. par files is simply so github will let me paste them here). I am using SearchGUI-2.8.4, PeptideShaker-1.10.1 Paramaters produced using PeptideShaker IdentificationParametersCLI on Linux server, jdk1.8.0_31: Parameters produced using SearchGUI as per the tutorial (using Mac, java build 1.8.0_65-b17): par file from Tutorial 1.4 (Analysed using Mac, java build 1.8.0_65-b17): par files, they all have show the same settings in the GUI but seem to give very different results. ![]() par file as well, but am experiencing the same thing. I tried using the IdentificationParametersCLI to produce the correct. The only difference I believe is the parameter file as I can produce the expected results when I use the. par I produced using SearchGUI, I get no MS2 Quant values, and the percentage coverage for the protein Q15149 I get (0.26% and only one PSM) is very different from that described in the tutorial. ![]() When using the data provided in Tutorial 1.3 but the. I can't figure out why this is, as I assume they should be the same. par provided in the resources of Tutorial 1.4. I am getting very different results when I analyze the mgf file with paremeters generated with SearchGUI (as per the tutorial) then when using the. ![]() ![]() Hi Guys, I hope you can help me, I am new to PeptideShaker and am using the Bionformatics for Proteomics tutorial (April 2016) and resources you provided there to develop and and validate a command-line pipeline for use on a linux cluster.
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