Spectrum Mill Help Index
A B C D E
F G H I J K
L M N O P Q
R S T U V W
X Y Z
- adding
- amino acid choices for VML score
- amino acid modifications
- contaminant mass list files
- cyclic modifications
- enzymatic digest rules
- fixed modifications
- instrument types
- new taxonomy codes for IPI databases
- protein categories
- required/disallowed amino acids
- species filter
- variable modifications
- aligning sequences
- within Multiple Sequence Aligner (utility)
- within Protein/Peptide Summary
- amino acids
- adding custom modifications
- adding amino acid choices to VML score
- adding required/disallowed to Protein/Peptide
Summary
- composition ions
- filtering
- modifications
- user-specified
- archive data
- automatic validation
- automation
- see workflow automation
- averagine
- Protein/Peptide Summary
- MS Isotope
- Autovalidation
- defaults
- overview
- using form
- workflows
- batch size
- browser windows, multiple
- cautions
- categories, protein
- Choose button
- cICAT quantitation
- cleavages, missed
- charge assignment
- client PC
- configuring
- shortcut on desktop
- Clustal W
- within Multiple Sequence Aligner (utility)
- within Protein/Peptide Summary
- color-coded quantitation results
- combining two databases
- comparing two databases
- Completion Log Viewer
- configuration
- default cysteine modification
- default database location
- default instrument
- disable match filtering
- disable quality filtering
- protein categories
- configuring client PCs
- contaminant mass list files, adding
- convert spectra
- CPU count
- custom modifications
- cyclic modifications, adding
- cysteine modifications
- configuring default
- more than one
- data file placeholder script
- de novo Sequencing, using form
- de novo Summary, using form
- data directories, selecting
- Data Extractor
- defaults
- generic files
- how it works
- instruments supported
- Maximize CPUs
- *.mgf files
- MS/MS data files
- MS/MS spectral quality filtering
- peak detection
- peak list files
- precursor charge assignment
- settings in instrument.txt
- spectral extraction
- spectral features
- timeouts
- using form
- data file selection, troubleshooting
- data recalibration, PMF Search
- data review, MS/MS data
- database format, background
- database list, updating
- database search times
- database search
- reversed
- saving hits
- stopping
- timeouts
- database summary report
- databases
- combining two databases
- comparing two
- configuring default database location
- file naming for proprietary databases
- file naming for public databases
- making subset FASTA file from accession numbers
- updating via command line
- used with Spectrum Mill workbench
- defaults
- Autovalidation
- Data Extractor
- MS/MS Search
- PMF Search
- PMF Summary
- Protein/Peptide Summary
- Sherenga de novo Sequencing
- Sherenga de novo Summary
- Spectrum Summary
- deisotoping
- differential expression quantitation
- ICAT and most isotopic labels
- iTRAQ and TMT
- labels with small mass differences
- nitrogen isotopes
- SILAC
- disallowed amino acids, customizing
- discriminant scoring
- discriminant scoring coefficients
- digestion, theoretical
- directory structure for Spectrum Mill workbench
- disable match filtering
- disable quality filtering
- DNA databases, frame translation
- Easy MS/MS Search
- what happened to it?
- Edit Workflow form
- enzymatic digest rules, adding
- enzyme cleavages
- error messages
- page not found
- proteins not same length
- timeouts
- Excel
- exporting data
- to Excel
- to HTML files
- to LIMS
- to PepXML
- to PowerPoint files
- FAQs
- false discovery rate
- reporting false discovery rate (FDR) and
quality metrics
- overview
- use in Autovalidation
- FAQs
- FASTA format, background
- FASTA header format change
- FASTA file, making subset from accession numbers
- features, new in this version
- File Collector
- file naming
- proprietary databases
- public databases
- file permission scripts
- general
- msdataSM
- file placeholder script
- file system for Spectrum Mill workbench
- filtering
- amino acid
- protein molecular weight
- protein pI
- fixed modifications, adding
- folders for Spectrum Mill workbench
- fragment ion tag
- fragment ion types, MS Product
- fragment ions, for different instruments
- frame translation in DNA databases
- frequently asked questions
- generic files, Data Extractor
- Glyco Product Ions Score
- hits, maximum reported
- homology mode
- overview
- HTML links (changing)
- accession number
- elemental composition
- MS Digest index number
- peptide sequence
- HTML links (enabling) to BLAST search
- HTML links in results
- accession number
- elemental composition
- general features
- MS Digest index number
- peptide sequence
- ICAT quantitation
- icon for Spectrum Mill workbench
- IIS
- scripts to set configuration
- immonium ions
- indices
- creating for a new database
- for databases
- instrument types
- adding
- PMF Search
- instrument_charges_certain in instrument.txt
- instruments
- configuring default
- fragment ion types
- selecting Thermo Fisher Scientific models
- interactive automation
- iTRAQ
- applying correction factors
- creating/storing iTRAQ correction factors
- quantitation
- LC-ESI-TOF data extraction
- library spectra (File Collector)
- LIMS
- links (changing)
- accession number
- elemental composition
- MS Digest index number
- peptide sequence
- Links (enabling) to BLAST search
- links in results
- accession number
- elemental composition
- general features
- MS Digest index number
- peptide sequence
- Manual PMF Search, using
- marker ions
- mass tolerances
- mass type
- masses, inputing (m/z)
- match filtering, disabling
- maximize CPUs
- Data Extractor
- MS/MS Search
- *.mgf file support
- minimum scored peak intensity
- missed cleavages
- modifications
- adding
- choosing
- listing details
- types supported
- molecular weight filtering
- MRM Selector
- transferring results to MassHunter Acquisition
- using form
- MS Comp
- combination type
- double bond equivalent
- nitrogen rule
- using form
- MS Digest
- database entry retrieval method
- using form
- overview
- MS Edman
- mismatched AA's
- overview
- regular expressions
- search mode
- using form
- MS Isotope, using form
- MS Product
- fragment ion types
- using form
- MS/MS autovalidation and workflows
- MS/MS data, spectral preprocessing
- MS/MS Search
- batch size
- creating summary file
- defaults
- equivalent search modes across versions
- fragment ion types for various instruments
- homology mode
- introduction
- mass tolerances
- minimum scored peak intensity
- multiply-charged ions
- overview
- precursor mass shift
- ranking results
- results review
- results
- scoring based on marker ions
- scoring
- search modes
- timeouts
- using form
- view identification statistics
- MS/MS spectral quality filtering
- MS-only data files, Data Extractor
- multiple browser windows
- multiply-charged ions
- multiple sequence alignment tool
- aligning sequences within Multiple Sequence Aligner (utility)
- aligning sequences within Protein/Peptide Summary
- introduction
- peptide table
- report description
-
- naming
- proprietary databases
- public databases
- New Folder dialog box
-
- Open Workflow dialog box
- overview
- MS Edman
- MS Search
- MS/MS Autovalidation
- MS/MS Search
- workflow automation
- parameter files
- parameter table
- patches for software
- peak detection
- peak list files, Data Extractor
- Peptide List to Masses
- peptide mass fingerpinting
- automated
- manual
- Peptide Selector
- transferring results to MassHunter Acquisition
- troubleshooting
- using form
- peptide validation
- PepXML
- PMF Search
- data recalibration
- defaults
- instrument types
- mass tolerance
- overview
- scoring
- using
- PMF Summary
- defaults
- using
- Phospho Product Ions Score
- precursor charge assignment
- precursor mass shift
- process automation
- see workflow automation
- processes, stopping
- Process Report
- using form
- parseSMreport.r
- plotRatioDistributions.r
- normalizeReporterRatios.r
- reporter_sample_template.txt
- sample-annotation.csv
- .GCT v1.3
- Protein Databases
- command line version
- combining two databases
- comparing two databases
- creating indices for a new database
- creating or appending to a custom database
- creating subset databases (saved hits)
- creating subset databases (species and molecular weight)
- database summary report
- FASTA header format change
- introduction
- output files (the indices)
- re-indexing an updated database
- subset FASTA file from accession numbers
- updating the database list
- user database
- using browser version
- protein categories, configuring
- protein grouping
- protein molecular weight filtering
- protein pI filtering
- Protein/Peptide Summary
- color-coded quantitation results
- comparing results of individual samples from separate directories
- customizing amino acid filtering
- comparing results of individual samples from separate directories
- defaults
- overview
- peptide validation
- protein grouping
- review fields
- sequence alignment
- setting summary modes
- setting validation and sorting
- summarizing results
- summary modes
- troubleshooting
- using form
- quality filtering, disabling
- quantitation
- approximate
- ICAT and most isotopic labels
- iTRAQ
- labels with small mass differences
- nitrogen isotopes
- SILAC
- TMT
- questions, frequently asked
- recalibration, PMF Search
- Request Queue Viewer
- required amino acids, customizing
- results validation, automatic
- reversed database search
- review fields, for Protein/Peptide Summary
- review fields, for Spectrum Summary
- sample ID
- saved results file
- Save Workflow dialog box
- saving hits for later search
- scoring
- MS/MS Search and marker ions
- MS/MS Search
- PMF Search
- scripts, for server administration
- search engines, other
- search modes for MS/MS Search
- comparison
- definitions
- translator across Spectrum Mill versions
- search results, saving
- search statistics
- search times
- search, stopping
- Select button
- sequence alignment
- within Multiple Sequence Aligner (utility)
- within Protein/Peptide Summary
- sequence coverage, increasing
- server administration
- adding amino acid modifications
- adding VML score amino acid choices
- adding contaminant mass list files
- adding cyclic modifications
- adding digest rules
- adding fixed modifications
- adding instrument types
- adding new taxonomy codes for IPI databases
- adding species filter
- adding variable modifications
- changing links from accession number
- changing links from elemental composition
- changing links from MS Digest index number
- changing links from peptide sequence
- configuring default cysteine modification
- configuring default database location
- configuring default instrument
- configuring protein categories
- disable match filtering
- disable quality filtering
- enabling links to BLAST search
- guidelines for modifying files (read first)
- limiting the number of parallel workflow processes
- resolving timeout problems
- scripts
- starting and stopping SRM
- Shared Resource Manager
- starting
- stopping
- Sherenga de novo Sequencing
- defaults
- using form
- Sherenga de novo Summary
- defaults
- using form
- shortcut, PC desktop
- signal-to-noise filtering
- SILAC quantitation
- software
- defects
- patches
- updates, troubleshooting
- Software Status Bulletin
- sorting results
- species
- definitions for Spectrum Mill workbench
- species filtering
- including in subset database
- spectra
- library (File Collector)
- segregating good
- spectral extraction
- spectral features
- spectral preprocessing for MS/MS data
- spectral quality filtering
- MS/MS Search
- Spectrum Matcher
- Spectrum Summary
- Spectrum Summary
- defaults
- review fields
- setting validation and sorting
- spectral quality filtering
- summarizing results
- troubleshooting
- using form
- Spectrum Viewer
- troubleshooting
- using
- starting SRM
- stopping
- processes
- SRM
- subset databases
- creating for saved hits
- creating for species and molecular weight
- ensuring that species are represented
- summarizing results, PMF
- summary modes, Protein/Peptide Summary
- Thermo Fisher Scientific instruments
- timeouts
- tips
- TMT
- applying correction factors
- creating/storing TMT correction factors
- quantitation
- TOF data
- acquisition
- extraction
- TOF-TOF support
- Tool Belt
- applying iTRAQ correction factors
- calculating discriminant scoring coefficients
- converting spectra - mzXML files
- creating a saved results file
- creating iTRAQ correction factors
- creating MS/MS Search summary file
- exporting PepXML file
- listing modifications details
- overview
- stopping processes
- using the File Collector
- viewing a parameter table
- tools, server administration
- troubleshooting
- connection to server times out
- list of database names does not update
- warning about need for additional license
- page not found
- peptides appear twice in the summary report
- Peptide Selector seems to ignore settings
- premature "Search Done" message
- Protein/Peptide Summary
- results different between versions
- selecting data files
- software updates
- some programs do not work
- Spectrum Summary
- Spectrum Viewer
- timeouts
- unusual or blank selection values
- workflow stuck
- updating databases
- uploading data to LIMS
- user database, creating or appending
- user-specified amino acid
- utilities
- Archive Data
- MRM Selector
- MS Comp
- MS Digest
- MS Edman
- MS Isotope
- MS Product
- Multiple Sequence Aligner
- Peptide List to Masses
- Peptide Selector
- validation, automatic
- workflow automation
- Completion Log Viewer
- Edit Workflow form
- interactive automation
- introduction
- limiting the number of parallel processes
- New Folder dialog box
- Open Workflow dialog box
- parameter files
- Request Queue Viewer
- Save Workflow dialog box
- Spectrum Mill Workflow Manager Service
- troubleshooting
- Workflows form
- Workflows for autovalidation
-