Spectrum Mill MS Proteomics Software

Manuals (HTML):
Spectrum Mill Basics MS/MS Search Personalized Sequence DBs Workflow Automation PMF Search Protein Databases Server Administration Tips and Tricks FAQs What's New Help Index
Installation (.PDF) Getting Started (.PDF) Custom Modifications (.PDF) Report Column Descriptions (.xlsx)
Slides (.pptx):
Spectrum Mill - Overview
Useful Tables:
Mutation Mass Shifts Dipeptide Masses
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
Mass Spectral Interpretation Tools
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
Manual PMF Search Search database with MS spectra from Peptide Mass Fingerprint data
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
Lorikeet View annotated MS/MS spectra
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
MRM Selector Build/Export MRM transition lists based on experimental data in Spectrum Mill
Multiple Sequence Aligner Run Clustal W and highlight non-identical AA's across the alignment
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
Peptide String Match Search database with a list of peptide sequences