Supplementary data files used to construct data sets -*- mode:org; -*-

* From Foster et al 2006 

Supplemental data file from http://www.cell.com/supplemental/S0092-8674(06)00369-2

** Table S1 -- PIIS0092867406003692.mmc2.xls
All proteins identified in this study, including the IPI and UniProt accession numbers (hyperlinked to the UniProt Knowledgebase) and a description of the protein. Following these entries are the sequence coverage (as percent) and the number of unique peptides observed for each protein, as well as the sequences of those unique peptides.

xls2csv PIIS0092867406003692.mmc2.xls > PIIS0092867406003692.mmc2.csv

** Table S2 -- PIIS0092867406003692.mmc3.xls
All peptides identified in this study, including their sequences in the single letter IUPAC nomenclature, the best relative mass error measured for each (in parts per million), the highest Mascot IonsScore recorded for each and the number of amino acids in each.

xls2csv PIIS0092867406003692.mmc3.xls  > PIIS0092867406003692.mmc3.csv

** Table S3 -- PIIS0092867406003692.mmc4.xls
Protein correlation profiles for each measured protein from three different sets of experiments: high and low-density sucrose gradients, and cytoplasm versus nucleus. In each worksheet the IPI and UniProt codes, as well as protein names and measured abundances (expressed as  log10[ion intensity]), are listed before the normalized abundances of each protein in each 2 fraction. The high-density page contains ion intensities for only the first eight fractions (Fr01-08) while the low-density page contains information for fractions 09 through 30 (Fr25-29 were not included as they are equivalent to Fr30).

Each worksheet has been opened in gnumeric and saved as a csv file.
Sheet 1 (PCP-High density): PIIS0092867406003692.mmc4-highDensity.csv
Sheet 2 (PCP-Low density):  PIIS0092867406003692.mmc4-lowDensity.csv
Sheet 3 (Cytoplasm or Nucleus): not used here

** Table S4 -- PIIS0092867406003692.mmc5.xls
Peptide correlation profiles for each measured peptide from three different sets of experiments: high and low-density sucrose gradients, and cytoplasm versus nucleus (three separate worksheets). In each worksheet the charge state, molecular weight and amino acid sequence  of each peptide precede the measured ion volumes (in Da·s). The high-density page contains ion intensities for only the first eight fractions (Fr01-08) while the low-density page contains information for fractions 09 through 30 (Fr25-29 were not included as they are equivalent to Fr30).

Each worksheet has been opened in gnumeric and saved as a csv file.
Sheet 1 (PCP-High density): PIIS0092867406003692.mmc5-highDensity.csv
Sheet 2 (PCP-Low density):  PIIS0092867406003692.mmc5-lowDensity.csv
Sheet 3 (Cytoplasm or Nucleus): not used here

** Table S5 -- PIIS0092867406003692.mmc6.xls
Localizations for all proteins measured in this study. IPI and UniProt accession codes, protein descriptions, abundances and the number of peptides upon which the localization was based are listed in the first five columns of each sheet. In the Localizations Sheet the subsequent columns contain the χ2 values for that protein’s PCP versus the marker for the given organelle where the protein met the assignment criteria (see Experimental Procedures). Where the assignment criteria were not met (e.g., where the χ2 value was higher than the cutoff) no value is shown. The fold enrichments for proteins in the nucleus are indicated in the Cytoplasm/Nucleus column (only those proteins enriched more than two-fold). In the Refined Locations Sheet the result of evaluating our measured localizations versus the published literature is shown (see Experimental Procedures). 'Yes' was assigned where annotation indicated the protein was in the organelle but also in the case where secreted proteins were identified in the secretory pathway (ER, ERGDV, Golgi). 'No' was assigned where the measured location was not among the annotated locations for a protein. 'Probably' was assigned in several instances: 1) where no location was otherwise annotated, 2) where a protein annotated as cytosolic was measured in an organelle since it would encounter than organelle and could be specifically associated with it, 3) where a protein annotated as nuclear was found in the cytosol since most proteins are not completely excluded by the nuclear pore, 4) where a non-proteasomal protein was found in the proteasome since most proteins are degraded by this machinery at some point, 5) where cytoskeletal proteins were measured in an organelle. 'Co-migrating' was assigned for ribosomal proteins that peaked in fractions 17 and/or 19.

Each worksheet has been opened in gnumeric and saved as a csv file.
Sheet 1 (Localizations): PIIS0092867406003692.mmc6-localizations.csv
Sheet 2 (Refined localizations):PIIS0092867406003692.mmc6-refinedLoc.csv

Marker proteins have been extracted from the paper, second paragraph on page 188:

To determine the PCP of well-studied organelles, we
examined the profiles of several well-characterized
marker proteins, including 130 kDa Golgi phosphoprotein
(GPP130, Golgi), AP-2 assembly subunit AP17 (plasma
membrane [PM]), early endosome antigen 1 (EEA1, early
endosomes [EE]), transferrin receptor 2 (TfR2, recycling
endosome [RE]), calnexin (ER), p115 (ER/Golgi-derived
vesicles [ERGDV]), and F1-F0 ATP synthase b subunit (mi-
tochondria). Each of these markers peaked in different
gradient fractions and had distinct profiles; thus at least
these seven organelles could be distinguished with confi-
dence (Figure 2B). Markers of other compartments were
also observed, but their profiles matched closely to one
of the seven mentioned above. In particular, ERGIC-53,
a marker for the ER-Golgi intermediate compartment,
overlapped very closely with the ER, as has been reported
previously (Breuza et al., 2004). Likewise, the profiles of
cation-independent mannose 6-phosphate receptor and
adaptor-related protein 1b, markers of the late endosome
and trans-Golgi network, respectively, largely overlapped
with TfR2 (Tables S3 and S4). This suggests that these
compartments migrate similarly in rate-zonal centrifuga-
tion and is in agreement with the specialized conditions re-
quired for even partial segregation reported by others
(Tulp et al., 1998; Hashiramoto and James, 2000).

Organelle marker had a chi2 scores of 0 for the expected organelle, except where otherwise noted:
- Golgi: 130 kDa Golgi phosphoprotein (GPP130) - IPI00269029 
- PM: AP-2 assembly subunit AP17 (AP-2 assembly subunit AP17) - IPI00118022 
- EE (early endosome): early endosome antigen 1 - IPI00453776 [a]
- TGN/RE (recycling endosome): Transferrin receptor protein 2 - IPI00223651
- ER: Calnexin precursor - IPI00119618
- ERGDV (ER/Golgi-derived vesicles): Vesicle docking protein - IPI00128071 [b]
- Mito: ATP synthase beta chain, mitochondrial precursor - IPI00113801
- Proteasome: Proteasome subunit beta type 1 - IPI00113845  [c]
              Proteasome subunit alpha type 6 - IPI00131845 [d]
              Proteasome subunit alpha type 7 - IPI00131406 [e]

[a] Also chi2 of 0.048 for ERGDV
[b] General vesicular transport factor p115 in UniProt, 
    also chi2 value of 0.027 for Golgi.
[c] chi2 value of 0.0018 for proteasome
[d] chi2 value of 0.0055 for proteasome 
[e] chi2 value of 0.0057 for proteasome


* From Dunkley et al 2006 

Supporting Information from http://www.pnas.org/content/103/17/6518/suppl/DC1

** Supporting Table 2 -- 06958Table2.xls
Table 2. Spreadsheet of protein found in both comparison A and B in terms of protein identification data, predicted subcellular location, and GFP fusion data.
This table contains the 6 possible ratios for each iTRAQ 4-plex run. Not used here

** Supporting Table 3 -- 06958Table3.xls
Table 3. Spreadsheet containing normalized reported ion intensities.
This table has been converted to Dunkley2006.csv for easy input into R.


* From Tan et al 2009

Supporting Information from http://pubs.acs.org/doi/suppl/10.1021/pr800866n

File [[http://pubs.acs.org/doi/suppl/10.1021/pr800866n][pr800866n_si_004.xls]] contains relative quantitation data for the 3 replicates in separate sheets, that have been saved to 3 csv files 
pr800866n_si_004-rep1.csv
pr800866n_si_004-rep2.csv
pr800866n_si_004-rep3.csv

File [[http://pubs.acs.org/doi/suppl/10.1021/pr800866n/suppl_file/pr800866n_si_007.xls][pr800866n_si_007.xls]] (available as csv file) contains the original markers.

The two following csv files contain Uniprot ID and Entry Names for the the proteins that appear in the above 3 datasets. This information has been downloaded from www.flymine.org using the 'list analysis' tool using the protein CG numbers as input. 
TanFlyMineFiltered.csv 
TanFlyMineUnfiltered.csv 
The filtered dataset contains only Uniprot IDs that have been reviewed i.e. that come from Swiss-Prot. Some CG numbers give rise to more than one reviewed Uniprot ID. The unfiltered dataset contains all Uniprot IDs per CG number which includes corresponding IDs from both Swiss-Prot (reveiwed) and TrEMBl (unreviewed), again some CG numbers have multiple IDs. Four columns have been added to the Tan MSnSet instances to include this information which are called ProteinAccession, EntryName, ProteinAccessionAll and EntryNameAll. ProteinAccession contains a single Uniprot accession ID per protein, for proteins with multiple Uniprot IDs the ID which is reveiwed appears here, if none are reviewed (or multiple are reviewed) the ID that appears first in the csv file for that protein is used. The column ProteinAccessionAll contains all UniprotIDs per protein (both reviewed and unreviewed). Similarly the columns EntryName and EntryNameAll conatin the Uniprot entry names for each protein with EntryName containing only one name and EntryNameAll containing all names per protein. 


* From Ferro et al 2010

The file AT_CHLORO_table_120906.xls was email by Myriam Ferro to be included in the pRolocdata package. The first sheet (README) ws used to prepare feature annotation. The second sheet was converted to AT_CHLORO_table_120906.csv and used to generate the at_chloro MSnSet.



* From Nikolovski 2012
Reformated manually and fixed column names
 - S1: Summary of the 1385 proteins observed at least twice in any of the 4 LOPIT experiments with normalized reporter ion intensities
 - S2: Functional annotations, classification results, and fractionation profiles of the 1385 proteins studied
 - S3: List of the 12 novel putative GT families with their members

* From Hall 2009
** S1 - Complete protein-level iTRAQ quantitation values. Spreadshhet manually simplified and exported to csv.
See supplementary file 1 for details about the design. The number below represebt fractions.
AC = membrane protein-enriched pellet and soluble/preripheral proteins from fractions 1, 4, 13+14 and 21
BD = membrane protein-enriched pellet and soluble/preripheral proteins from fractions 1, 9+10, 16 and 18

|-------+----------------------------------+------+------------------------------+------|
|       | membrane protein-enriched pellet |      | soluble/preripheral proteins |      |
|-------+----------------------------------+------+------------------------------+------|
| iTRAQ |                                A |    B |                            C |    D |
|-------+----------------------------------+------+------------------------------+------|
|   114 |                                1 |    1 |                            1 |    1 |
|   115 |                                4 | 9+10 |                            4 | 9+10 |
|   116 |                            13+14 |   16 |                        13+14 |   16 |
|   117 |                               21 |   18 |                           21 |   18 |
|-------+----------------------------------+------+------------------------------+------|


** S3 - iTRAQ ratios (21 ?) - not considered.
** S4 - markers, converted from xls to csv with xls2csv
** S5 - PLS-DA assignments, converted from xls to csv with xls2csv


