Re: [spctools-discuss] combining multiple iprophet results / Run NSP in iprophet if processing through protein prophet afterwards?

I've uploaded the files (and some notes for interpretation) to Dropbox and hopefully you will have received a link? (I used a contact email from an old paper that is hopefully still valid!). Please let me know if you're unable to access the files / if you need any further files/info Thanks

[spctools-discuss] combining multiple iprophet results / Run NSP in iprophet if processing through protein prophet afterwards?

Hi All, I have 2 questions I'd be grateful if people could help answer: 1) Is it valid to combine multiple iprophet.pep.xml files by passing through iprophet for a second time? - alternatively, is it valid to combine a single iprophet.pep.xml file with interact.pep.xml files in iprophet? I am

Re: [spctools-discuss] Re: No prot-MODELS

Hi Luis, I suspect that my problem may be due to multiple installations of TPP (from this post): https://groups.google.com/forum/#!msg/spctools-discuss/Tq-i-7SVoJE/4XZcq4EGCgAJ;context-place=forum/spctools-discuss I had originally installed 5.1 in a preferred location, but parts of TPP

Re: [spctools-discuss] Valid combination of multiple samples, fractions and digestions with different enzymes, using prophets

Please note - I've discovered a similar problem (no models html file generated) in the following thread: https://groups.google.com/forum/#!searchin/spctools-discuss/interact$20prot%7Csort:date/spctools-discuss/Yrg2yEO4otg/8u0bNKzpAAAJ Cheers Pete On Monday, 11 June 2018 14:58:53 UTC-7,

Re: [spctools-discuss] Re: No prot-MODELS

Hi Luis, I've got the same problem with my dataset (also a large dataset, combining multiple experiments). - No models html file is generated. Please can you tell me if this issue was resolved? Thanks Pete On Monday, 7 May 2018 19:01:28 UTC-7, Luis wrote: > > Hi Heeyoun, > > Does it seem

Re: [spctools-discuss] Valid combination of multiple samples, fractions and digestions with different enzymes, using prophets

Hi David, Thanks for your advice - I've had success using the experiment flag in Petunia, and have found that using an experiment label including fraction, replicate and also enzyme (used for digest) works well when processed through iProphet/protein prophet. However, my problem now is that

Re: [spctools-discuss] Valid combination of multiple samples, fractions and digestions with different enzymes, using prophets

Thanks David, I wasn't aware of the experiment label - that sounds ideal. I'll give it a try On Wednesday, 6 June 2018 00:34:47 UTC-7, David Shteynberg wrote: > > Hello Pete, > > iProphet has a sibling experiments model and uses the replicate spectra > model for replicate PSMs that are in the

Re: [spctools-discuss] Peptide prophet - use of decoy database for X! searches?

Hi David, Thanks for your reply, that's very helpful. I've now tried including an equal number of decoys (reversed) in my database, processing the same data through peptide prophet, iprophet and protein prophet. My number of identified proteins has gone down, but the PSMs are much more

[spctools-discuss] Valid combination of multiple samples, fractions and digestions with different enzymes, using prophets

Hi, I'd really appreciate advice regarding the most valid way to combine my searches with peptide / i / protein prophet. I have 3 samples, 3 fractions per sample, and each fraction was digested with multiple enzymes. Each of these digests were injected twice. The resulting data were then

[spctools-discuss] Peptide prophet - use of decoy database for X! searches?

Please can someone advise - is it recommended to include decoys in my database when using X! for searches then peptide/protein prophet in TPP? As I understand, X! recommends not including decoys in searches (when used standalone) – however when I analyse X! identified peptides using