Spectrum Mill protocols

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Spectrum Mill specifications


Unique identifier OMICS_14298
Name Spectrum Mill
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input format FASTA
Biological technology Agilent Technologies
Operating system Windows
Programming languages Java, Perl
License Commercial
Computer skills Medium
Version 05.00
Stability Stable
IIS, MSFileReader
Maintained Yes


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Spectrum Mill in pipeline

PMCID: 2323404
PMID: 18463710
DOI: 10.1371/journal.pcbi.0040012

[…] in the hupo plasma proteome project []. different expert groups used their own preferred pff software to identify proteins from the given dataset, either sequest, mascot, sequest–peptideprophet, spectrum mill, sonar, or x!tandem. the study found that, of the 608 proteins identified by at least one of the algorithms (union), 335 were identified by all of the algorithms (intersection), with 71 […]

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Spectrum Mill in publications

PMCID: 5875748
PMID: 29596499
DOI: 10.1371/journal.pone.0194164

[…] to liquid chromatography-tandem mass spectrometry (lc-ms/ms) analysis using q-tof lc/ms (agilent technologies, santa clara, ca). peptide search and protein identification were performed using the spectrum mill ms proteomic workbench (agilent technologies, santa clara, ca). trypsin-digested bovine serum albumin (bsa) was used as a quality control for ms analysis., two-color western blot […]

PMCID: 5814418
PMID: 29449592
DOI: 10.1038/s41598-018-21452-4

[…] 300 until 3000 m/z. auto ms/ms mode applied from 50 until 3000 m/z with total maximum precursor of 4 in a cycle and exception of 2 spectra for 1 minute. identification of peptides was performed by spectrum mill ms proteomics workbench (rev b.04.00.127; agilent technologies). cysteine carbamidomethylation was set as fix and variable modification. search was done online for mucorales […]

PMCID: 5813374
PMID: 29456458
DOI: 10.1186/s12953-018-0131-y

[…] using agilent masshunter data acquisition software (b.03.00)., tandem mass spectra were extracted and charge state deconvoluted by mass hunter version b.03.00 (agilent technologies, usa), while spectrum mill and x!tandem (the gpm, thegpm.org; version 2007.01.01.1) were used for protein identification. deisotoping was not performed. both spectrum mill and x!tandem were set up to search […]

PMCID: 5862596
PMID: 29568375
DOI: 10.18632/oncotarget.24418

[…] (n = 11) labelled with the itraq label 117. the itraq labelled samples were pooled and subjected to off-gel fractionation followed by lc-ms/ms. the lc-ms/ms data was analyzed independently by spectrum mill (sm). 514, 354, 569 and 581 proteins were identified with 2 or more unique peptides in set 1, set 2, set 3 and set 4 respectively, of the itraq labelled samples from sm analysis. […]

PMCID: 5794856
PMID: 29391437
DOI: 10.1038/s41598-018-20284-6

[…] labelled with 114, 116 and peptides from metaphase-i arrested cells with 115 and 117 labels. saccharomyces cerevisiae was set as taxonomy during analysis of data. data analysis was performed using spectrum mill (from agilent) as described previously., a required number of cells were taken in the fresh tube and washed twice with pbs ph 7.2. cells were resuspended in 70% ethanol for 1 min […]

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