Spectrum Mill MS Proteomics Workbench

Spectrum Mill Basics MS/MS Search Workflow Automation PMF Search Protein Databases Server Administration Tips and Tricks FAQs What's New HelpIndex
Useful Tables:
Mutation Mass Shifts Dipeptide Masses
Quick Start Guide Application Guide Familiarization Guide
Process Automation Tools
Workflows Automate data extraction, search, validation, and summary.
Request Queue View status of request queue for submitted requests, monitor results output
Completion Log View log of completed extractions, searches, validations, and summaries
Easy MS/MS Search One-step MS/MS extraction, search, validation, and summary
Mass Spectral Interpretation Tools ( disabled on this server, but UI remains visible)
Data Extractor Prepare MS/MS data files for Spectrum Mill processing
MS/MS Search Search database with MS/MS spectra
Autovalidation Autovalidate MS/MS spectra, calculate false-positive rates
Spectrum Matcher Match MS/MS spectra against other MS/MS spectra
de novo Sequencing Perform Sherenga de novo MS/MS spectral interpretation
Result Summary Tools
Protein/Peptide Summary Summarize results from MS/MS searches
Process Report Run R scripts to parse, plot distributions, and normalize reporter-ion ratios for Protein/Peptide Summary Reports
Quality Metrics & FDR Summarize metrics for quality (MS performance, MS/MS interpretation, chromatography, sample handling) and FDR (spectra, peptide, protein)
Spectrum Summary Summarize characteristics of MS/MS spectra
Tool Belt Collection of Spectrum Mill utility tools
Protein Databases Manipulate FASTA sequence databases for use with Spectrum Mill software
Archive Data Zip and Unzip dataset directories
Peptide Selector Select peptides from protein digest likely to produce high quality MS/MS spectra
Ion Assignments Generate tab-delimited files of fragment ion assignments for MS/MS search results
Multiple Sequence Aligner Run Clustal W and highlight non-identical AA's across the alignment
Peptide String Match Search database with a list of peptide sequences
MS Edman Search database with text or partial peptide sequence
Peptide List to Masses Convert a list of peptides to masses and formulas
MS Product Predict product ion masses from peptide sequence
MS Digest Predict peptide masses for enzymatic digestion of protein
MS Comp Calculate AA compositions fitting parent mass and immonium ions
MS Isotope Display isotope patterns of peptides