Spectrum Mill - Protein/Peptide Summary
Spectrum Mill
Process Report
MRM Selector
Spectrum Summary
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Excel
MPP Generic
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export
Export inclusion list for top
peptides/protein
Mode:
Peptide - Spectrum Match
Peptide - Distinct
Protein Summary Details
Protein - Protein Comparison
Protein - Peptide Comparison
Protein - Var Mod Site Comparison
Group columns by:
File
Directory
Rows by:
Sequence
VM site
PG Event
Filter by Proteogenomic Features:
Off
All
All variants
Spliceforms
Other
Filter to distinct peptides:
Off
Case insensitive - CI
Case sensitive - CS
Charge file CS
File CI
File CS
Charge CS
Data directories:
(None Selected)
Search result files:
*.spo
Search result files exclude:
Validation and Sorting
Filter results by:
sequence-not-validated
valid
good-spectrum-sequence-not-validated
all
Validation preset:
status
valid
reset
none
Protein grouping method:
unexpand subgroups
expand subgroups, all use shared
expand subgroups, top uses shared, SGT
expand subgroups, ignore shared, SGS
Sort proteins by:
Score
Number of Peptides
Protein MW
Total intensity
Category
Function
Filter by protein score:
>
<
Exclude accessions:
Sort peptides by:
Score
Scored peak intensity
Delta reverse score
Delta rank 2 score
Backbone Cleavages
Delta var mod score
Filename
Precursor MH+
Precursor m/z
Delta mass shift
N-term
Sequence
Sequence - CI file
Sequence - CS file
Sequence file charge
Seq file charge chi2
Seq charge file
Charge seq file
Start AA Position
Accession number
Total intensity
Peptide pI low
Peptide pI high
Retention Time
Fragmentation Mode
Prec Av Chi2
Dominant Ions
Similarity Score
Filter peptides by:
Score:
>
<
% SPI:
>
<
Required AAs:
Disallowed AAs:
Peptide pI: from
to
All
Accession #'s:
Require
peptides/protein
for protein intensity
mAb Accessions
Light:
Heavy:
Normalize by protein MW
Relative quantification
mAb amount:
ug
ISTD accession:
ISTD amount:
ug
Review Fields
Filename
Score
Fwd-Rev score
Rank 1-2 score
SPI (%)
Backbone Cleavage Score
Phospho Product Ions Score
Glyco Product Ions Score
Unmatched ions
Var mod sites
VML score
Solution charge
Start AA position
Proteogenomic features
Peptide overlap display
Run specific
% Coverage
Distinct peptides
Distinct peptide forms/mods
DEQ ratio
Reporter Ratios:
Ion
Sequence
b/y map
Rev Sequence
Rank 2
VML sequence
Prec Av Chi
2
Isol Pur
Ret time, width
Ion mobility
Precursor m/z
MH
+
Delta mass
Pep pI
# Sequences per MH+
Protein MW
Prot pI
Species
Accession #
Protein name
Precursor XIC Intensity
Mean
Total
Both
Precursor S/N
DEQ ratios
Invert
Median
Mean
Both
Reporter Ratios:
Control:
113
114
115
116
117
118
119
121
Intensities
Correction Method:
None
Static
afRICA
Modification names
N-term
C-term
Cysteines
Fragmentation mode
Max tag length
Longest tag
# b/y pairs
Category:
Protein Quantitation Options
Exclude poor isotope quality Precursor XIC's: <
Chi
2
vs. Averagine
Exclude poor Precursor Isolation Purity: <
%
Exclude outlier DEQ Ratios (> 2 std dev from mean)
Distinct Peptide Quantitation Options
Combine PSMs for Peptide Quantitation
Spectrum Grouping Options
Group missed cleavages containing VM site(s)
Show all grouped spectra
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